diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..9d01039 --- /dev/null +++ b/.gitignore @@ -0,0 +1,6 @@ +.Rproj.user +.Rhistory +.RData +.Ruserdata +output/* +libs/* \ No newline at end of file diff --git a/R/extreme_scenario.Rmd b/R/extreme_scenario.Rmd new file mode 100755 index 0000000..7f17dbc --- /dev/null +++ b/R/extreme_scenario.Rmd @@ -0,0 +1,281 @@ +--- +title: "Extreme scenario (Ye et al. 2023)" +output: html_document +--- + +```{r setup, include=FALSE} +knitr::opts_chunk$set(echo = TRUE) +knitr::opts_knit$set(root.dir = here::here()) +``` + +```{r} +source("R/utils/sim_data_utils.R") +source("R/utils/sim_reporting_utils.R") +source("R/utils/sim_variance_estimators.R") +``` + +## Extreme scenario + +We consider the data generating mechanism from Ye et al. (2023) as an extreme scenario due to very large treatment effect and highly prognostic baseline covariate (odds ratio corresponding to \~150 and \~2.7, respectively). + +Specifically, we simulate trials with 200 subjects, a single covariate $X \sim N(0, 3^2)$, two arms with equal allocation and simple randomization, and outcome model + +$$ +logit[P(Y_i = 1 | A_i = a_i, X_i = x_i)] = -2 + 5I(a_i=1) + x_i +$$ + +In the following we consider a correctly specified working model + +$$ +logit[P(Y_i = 1 | A_i = a_i, X_i = x_i)] = b_0 + b_1I(a_i=1) + b_2x_i +$$ + +```{r} +# Set up the Ye et al (2023) scenario + +scenarios <- list( + list(scenario = 1, + N = 200, + covars = tibble("name"=c("x"), + "dist"=c("rnorm"), + "arg1"=c(0), + "arg2"=c(3)), + trt_assignment = 0.5, + response_func = \(df) -2 + 5*df$trt + df$x, + working_model = "y ~ trt + x" + ) + ) +``` + + +The true marginal probabilities that Y=1 are calculated below by X and treatment arm using N=10^6: + +```{r} +df <- data.frame(sim_covars(list(), scenarios[[1]], N = 1e6)) + +# for patients with X value one std dev below mean +mean(plogis(scenarios[[1]]$response_func(df |> + transform(trt = 0, + x = mean(x) - sd(x))))) + +mean(plogis(scenarios[[1]]$response_func(df |> + transform(trt = 1, + x = mean(x) - sd(x))))) + +# for patients with X value one std dev above mean +mean(plogis(scenarios[[1]]$response_func(df |> + transform(trt = 0, + x = mean(x) + sd(x))))) + +mean(plogis(scenarios[[1]]$response_func(df |> + transform(trt = 1, + x = mean(x) + sd(x))))) + +``` + +### Unconditional coverage + +We proceed to evaluate the unconditional coverage probabilities of the Ge et al. (2011) and Ye et al. (2023) methods of variance estimation. We consider the PATE estimand, effectively reproducing the simulation study performed by Ye et al. (2023), and additionally also evaluate coverage under the CPATE estimand as defined in Magirr et al (2024). + +```{r} + +## Unconditional coverage +## PATE, CPATE + +## Simulate 10,000 runs +N_runs <- 1e4 +sims <- Q(run_sim_wrapper, + scenario=rep(scenarios, each=N_runs), + n_jobs = 200) +sims <- do.call(rbind, sims) + + +var_methods = list("ye_beeca_var", + "ge_var") + +# PATE +post_sims_pate <- purrr::map(var_methods, post_sims, sims = sims %>% rename(true_diff = true_diff_pate)) +results_pate <- purrr::map_df(post_sims_pate, sum_sims) +results_pate$estimand <- "PATE" + + +# CPATE +post_sims_cpate <- purrr::map(var_methods, post_sims, sims = sims %>% rename(true_diff = true_diff_cpate)) +results_cpate <- purrr::map_df(post_sims_cpate, sum_sims) +results_cpate$estimand <- "CPATE" + +``` + +Results: Unconditional coverage for PATE estimand + +```{r} +dplyr::arrange(results_pate, scenario) +``` + +Results: Unconditional coverage for CPATE estimand + +```{r} +dplyr::arrange(results_cpate, scenario) +``` + + +### Coverage conditional on X + +We now consider conditional coverage probabilities by fixing the choice of $X$. We achieve this by selecting a specific random seed during data generation. Two random seeds were chosen to illustrate that the conditional coverage probabilities can be both above and below the nominal level depending on the specific $X$. + +```{r} + +## Conditional coverage (conditional only on X) +## PATE, CPATE + +#=============================================================================== +## simulate a base dataset that remains fixed +## we fix X, but simulate TRT and y +## (achieve this by dropping trt and y from base_data so they are re-simulated each time) + +all_res_pate <- list() +all_res_cpate <- list() +i <- 1 + +for (rseed in c(281, 44)) { + + set.seed(rseed) + + base_data <- sim_dat(scenarios[[1]]) + base_data <- base_data %>% select(-trt, -y) + + #============================================================================= + + ## Simulate 10,000 runs + N_runs <- 1e4 + sims <- Q(run_sim_wrapper, + scenario=rep(scenarios, each=N_runs), + const = list(base_data = base_data), + n_jobs = 200) + sims <- do.call(rbind, sims) + + var_methods = list("ye_beeca_var", + "ge_var") + + # PATE with conditional coverage (conditional on X) + post_sims_pate <- purrr::map(var_methods, post_sims, sims = sims %>% rename(true_diff = true_diff_pate)) + results_pate <- purrr::map_df(post_sims_pate, sum_sims) + results_pate$seed <- rseed + results_pate$estimand <- "PATE" + + + # CPATE with conditional coverage (conditional on X) + post_sims_cpate <- purrr::map(var_methods, post_sims, sims = sims %>% rename(true_diff = true_diff_cpate)) + results_cpate <- purrr::map_df(post_sims_cpate, sum_sims) + results_cpate$seed <- rseed + results_cpate$estimand <- "CPATE" + + + all_res_pate[[i]] <- results_pate + all_res_cpate[[i]] <- results_cpate + + i <- i + 1 + +} + +multi_res_pate <- do.call(rbind, all_res_pate) +multi_res_cpate <- do.call(rbind, all_res_cpate) + + +``` + +Results: Conditional coverage on X, for PATE estimand + +```{r} +multi_res_pate +``` + +Results: Conditional coverage on X, for CPATE estimand + +```{r} +multi_res_cpate +``` + + +### Coverage conditional on A, X + +We also evaluate conditional coverage probabilities by fixing both $X$ and $A$. Again, two random seeds were chosen to illustrate that the conditional coverage probabilities can be both above and below the nominal level depending on the specific $A$, $X$. + +```{r} + +## Conditional coverage (conditional on X and TRT) +## PATE, CPATE + +#=============================================================================== +## simulate a base dataset that remains fixed +## we fix X and TRT, but simulate y +## (achieve this by dropping y from base_data so it is re-simulated each time) + +all_res_pate <- list() +all_res_cpate <- list() +i <- 1 + +for (rseed in c(274, 44)) { + + set.seed(rseed) + + base_data <- sim_dat(scenarios[[1]]) + base_data <- base_data %>% select(-y) + + #============================================================================= + + ## Simulate 10,000 runs + N_runs <- 1e4 + sims <- Q(run_sim_wrapper, + scenario=rep(scenarios, each=N_runs), + const = list(base_data = base_data), + n_jobs = 200) + sims <- do.call(rbind, sims) + + + var_methods = list("ye_beeca_var", + "ge_var") + + # PATE with conditional coverage (conditional on X, TRT) + post_sims_pate <- purrr::map(var_methods, post_sims, sims = sims %>% rename(true_diff = true_diff_pate)) + results_pate <- purrr::map_df(post_sims_pate, sum_sims) + results_pate$seed <- rseed + results_pate$estimand <- "PATE" + + + # CPATE with conditional coverage (conditional on X, TRT) + post_sims_cpate <- purrr::map(var_methods, post_sims, sims = sims %>% rename(true_diff = true_diff_cpate)) + results_cpate <- purrr::map_df(post_sims_cpate, sum_sims) + results_cpate$seed <- rseed + results_cpate$estimand <- "CPATE" + + + all_res_pate[[i]] <- results_pate + all_res_cpate[[i]] <- results_cpate + + i <- i + 1 + +} + +multi_res_pate <- do.call(rbind, all_res_pate) + +multi_res_cpate <- do.call(rbind, all_res_cpate) + +``` + + +Results: Conditional coverage on A, X, for PATE estimand + +```{r} +multi_res_pate +``` + + +Results: Conditional coverage on A, X, for CPATE estimand + +```{r} +multi_res_cpate +``` + + + diff --git a/R/misspecified_scenario.Rmd b/R/misspecified_scenario.Rmd new file mode 100755 index 0000000..6b5b4ad --- /dev/null +++ b/R/misspecified_scenario.Rmd @@ -0,0 +1,262 @@ +--- +title: "Misspecified scenario" +output: html_document +--- + +```{r setup, include=FALSE} +knitr::opts_chunk$set(echo = TRUE) +knitr::opts_knit$set(root.dir = here::here()) +``` + +```{r} +source("R/utils/sim_data_utils.R") +source("R/utils/sim_reporting_utils.R") +source("R/utils/sim_variance_estimators.R") +``` + +## Misspecified scenario + +We construct a scenario to demonstrate that the Ge et al variance estimation method may under cover for the CPATE estimand when the working model is misspecified. + +As data generating mechanism, we use a simple randomization of 4000 patients using randomization ratio 1:9 to two arms. The logistic model is, +$$ +\mathrm{logit}\{P(Y_i=1 | A_i, X_i)\} = -1+ 3 X_i - 6 A_i X_i +$$ + +with a strong prognostic (and predictive) covariate $X_i$ following a Bernoulli distribution with probability $0.5$. A large sample size isolates the effect of model misspecification from any small sample size bias. Two features of this scenario expose the issue of model misspecification. Firstly, it is necessary to have unequal randomization. We use 1:9 randomization. Secondly, it is necessary to have a working model which is far from the truth. We use an extreme scenario, where the true treatment effect is a conditional odds ratio of $1$ when $X=0$ and a conditional odds ratio of $403$ when $X=1$. The working model is $\mathrm{logit}\{P(Y_i=1 | A_i, X_i)\} = \beta_0 + \beta_1 A_i + \beta_2 X_i$, which assumes a constant conditional odds ratio. + + + +```{r} +# Set up scenario + +scenarios <- list( + list(scenario = 1, + N = 4000, + + # binary covariate (x) + covars = tibble("name"=c("x"), + "dist"=c("rbinom"), + "arg1"=c(1), + "arg2"=c(0.5)), + + # 1:9 assignment + trt_assignment = 0.1, + + # outcome model + response_func = \(df) -1 - 6 * df$x * df$trt + 3 * df$x, + working_model = "y ~ trt + x" + ) +) + +``` + + +### Unconditional coverage + + +```{r} + +## Unconditional coverage +## PATE, CPATE + +## Simulate 10,000 runs +N_runs <- 1e4 +sims <- Q(run_sim_wrapper, + scenario=rep(scenarios, each=N_runs), + n_jobs = 200) +sims <- do.call(rbind, sims) + + +var_methods = list("ye_beeca_var", + "ge_hc0_var", + "ge_var") + +# PATE +post_sims_pate <- purrr::map(var_methods, post_sims, sims = sims %>% rename(true_diff = true_diff_pate)) +results_pate <- purrr::map_df(post_sims_pate, sum_sims) +results_pate$estimand <- "PATE" + + +# CPATE +post_sims_cpate <- purrr::map(var_methods, post_sims, sims = sims %>% rename(true_diff = true_diff_cpate)) +results_cpate <- purrr::map_df(post_sims_cpate, sum_sims) +results_cpate$estimand <- "CPATE" + +``` + +Results: Unconditional coverage for PATE estimand + +```{r} +dplyr::arrange(results_pate, scenario) +``` + +Results: Unconditional coverage for CPATE estimand + +```{r} +dplyr::arrange(results_cpate, scenario) +``` + + +### Coverage conditional on X + + +```{r} + +## Conditional coverage (conditional only on X) +## PATE, CPATE + +#=============================================================================== +## simulate a base dataset that remains fixed +## we fix X, but simulate TRT and y +## (achieved by dropping trt and y from base_data so they are re-simulated each time) + +all_res_pate <- list() +all_res_cpate <- list() +i <- 1 + +for (rseed in c(85, 67)) { + + set.seed(rseed) + + base_data <- sim_dat(scenarios[[1]]) + base_data <- base_data %>% select(-trt, -y) + + #============================================================================= + + ## Simulate 10,000 runs + N_runs <- 1e4 + sims <- Q(run_sim_wrapper, + scenario=rep(scenarios, each=N_runs), + const = list(base_data = base_data), + n_jobs = 200) + sims <- do.call(rbind, sims) + + var_methods = list("ye_beeca_var", + "ge_hc0_var", + "ge_var") + + # PATE with conditional coverage (conditional on X) + post_sims_pate <- purrr::map(var_methods, post_sims, sims = sims %>% rename(true_diff = true_diff_pate)) + results_pate <- purrr::map_df(post_sims_pate, sum_sims) + results_pate$seed <- rseed + results_pate$estimand <- "PATE" + + + # CPATE with conditional coverage (conditional on X) + post_sims_cpate <- purrr::map(var_methods, post_sims, sims = sims %>% rename(true_diff = true_diff_cpate)) + results_cpate <- purrr::map_df(post_sims_cpate, sum_sims) + results_cpate$seed <- rseed + results_cpate$estimand <- "CPATE" + + + all_res_pate[[i]] <- results_pate + all_res_cpate[[i]] <- results_cpate + + i <- i + 1 + +} + +multi_res_pate <- do.call(rbind, all_res_pate) +multi_res_cpate <- do.call(rbind, all_res_cpate) + + +``` + +Results: Conditional coverage on X, for PATE estimand + +```{r} +multi_res_pate +``` + +Results: Conditional coverage on X, for CPATE estimand + +```{r} +multi_res_cpate +``` + + +### Coverage conditional on A, X + + +```{r} + +## Conditional coverage (conditional on X and TRT) +## PATE, CPATE + +#=============================================================================== +## simulate a base dataset that remains fixed +## we fix X and TRT, but simulate y +## (achieved by dropping y from base_data so it is re-simulated each time) + +all_res_pate <- list() +all_res_cpate <- list() +i <- 1 + +for (rseed in c(85, 67)) { + + set.seed(rseed) + + base_data <- sim_dat(scenarios[[1]]) + base_data <- base_data %>% select(-y) + + #============================================================================= + + ## Simulate 10,000 runs + N_runs <- 1e4 + sims <- Q(run_sim_wrapper, + scenario=rep(scenarios, each=N_runs), + const = list(base_data = base_data), + n_jobs = 200) + sims <- do.call(rbind, sims) + + + var_methods = list("ye_beeca_var", + "ge_hc0_var", + "ge_var") + + # PATE with conditional coverage (conditional on X, TRT) + post_sims_pate <- purrr::map(var_methods, post_sims, sims = sims %>% rename(true_diff = true_diff_pate)) + results_pate <- purrr::map_df(post_sims_pate, sum_sims) + results_pate$seed <- rseed + results_pate$estimand <- "PATE" + + + # CPATE with conditional coverage (conditional on X, TRT) + post_sims_cpate <- purrr::map(var_methods, post_sims, sims = sims %>% rename(true_diff = true_diff_cpate)) + results_cpate <- purrr::map_df(post_sims_cpate, sum_sims) + results_cpate$seed <- rseed + results_cpate$estimand <- "CPATE" + + + all_res_pate[[i]] <- results_pate + all_res_cpate[[i]] <- results_cpate + + i <- i + 1 + +} + +multi_res_pate <- do.call(rbind, all_res_pate) + +multi_res_cpate <- do.call(rbind, all_res_cpate) + +``` + + +Results: Conditional coverage on A, X, for PATE estimand + +```{r} +multi_res_pate +``` + + +Results: Conditional coverage on A, X, for CPATE estimand + +```{r} +multi_res_cpate +``` + + + + + diff --git a/R/plot_ge_vs_ye.Rmd b/R/plot_ge_vs_ye.Rmd new file mode 100755 index 0000000..568149a --- /dev/null +++ b/R/plot_ge_vs_ye.Rmd @@ -0,0 +1,158 @@ +--- +title: "Plot Ge vs Ye for different scenarios" +output: html_document +--- + +```{r setup, include=FALSE} +knitr::opts_chunk$set(echo = TRUE) +knitr::opts_knit$set(root.dir = here::here()) +``` + + +```{r} +source("R/utils/sim_data_utils.R") +source("R/utils/sim_reporting_utils.R") +source("R/utils/sim_variance_estimators.R") + +library(ggplot2) +library(dplyr) +``` + + + +```{r} +# Set up three scenarios to compare Ye et al. vs Ge et al. + +scenarios <- list( + list(scenario = 1, + N = 200, + covars = tibble("name"=c("x"), + "dist"=c("rnorm"), + "arg1"=c(0), + "arg2"=c(3)), + trt_assignment = 0.5, + response_func = \(df) -2 + 5*df$trt + df$x, + working_model = "y ~ trt + x" + ), + + list(scenario = 2, + N = 200, + covars = tibble("name"=c("x"), + "dist"=c("rnorm"), + "arg1"=c(0), + "arg2"=c(3)), + trt_assignment = 0.5, + response_func = \(df) -2 + 0*df$trt + df$x, + working_model = "y ~ trt + x" + ), + + list(scenario = 3, + N = 200, + covars = tibble("name"=c("x1", "x2", "x3", "x4"), + "dist"=c("rnorm", "rnorm", "rnorm", "rnorm"), + "arg1"=c(0, 0, 0, 0), + "arg2"=c(3, 3, 3, 3)), + trt_assignment = 0.5, + response_func = \(df) 0 + 0*df$trt + 0*df$x1 + 0*df$x2 + 0*df$x3 + 0*df$x4, + working_model = "y ~ trt + x1 + x2 + x3 + x4" + ) +) +``` + + +```{r} + +# For each scenario, simulate $n_rseeds$ datasets, +# and calculate Ge et al and Ye et al marginal effect variance estimates + +n_rseeds <- 100 + +res <- tibble(ye_var = numeric(), + ge_var = numeric(), + sim_rseed = numeric(), + sim_name = character()) + +for (scenario in scenarios) { + + ye_var <- numeric(n_rseeds) + ge_var <- numeric(n_rseeds) + sim_rseed <- numeric(n_rseeds) + sim_name <- scenario$scenario + + for (i in 1:n_rseeds) { + + set.seed(i) + + dat <- sim_dat(scenario) + + dat$trt <- as.factor(dat$trt) + glm_formula <- as.formula(scenario$working_model) + fit <- glm(glm_formula, family="binomial", data=dat) + + ye_var[i] <- beeca_wrapper(fit, "Ye")$marginal_var + ge_var[i] <- beeca_wrapper(fit, "Ge")$marginal_var + sim_rseed[i] <- i + + } + + res <- rbind(res, data.frame(ye_var = ye_var, + ge_var = ge_var, + sim_rseed = sim_rseed, + sim_name = sim_name)) + +} + +``` + + + +```{r} + +res_plot <- res %>% + group_by(sim_name) %>% + + # order x axis by ye et al + arrange(ye_var) %>% + mutate(x_ordered = 1:n_rseeds) %>% + ungroup() %>% + + tidyr::pivot_longer(cols = c("ye_var", "ge_var")) %>% + + # make labels + mutate(name = case_match(name, + "ye_var" ~ "Ye et al.", + "ge_var" ~ "Ge et al.")) + +# rename panels in plot +facet_labeller <- c("1" = "A", + "2" = "B", + "3" = "C") + +p <- res_plot %>% + ggplot(aes(x=x_ordered, y=value, color=name, shape=name)) + + geom_point(size = 2) + + facet_wrap(vars(sim_name), scales = "free", + labeller = labeller(sim_name = facet_labeller)) + + xlab("Simulations ordered by Ye et al variance") + + ylab("Variance") + + scale_color_grey() + + scale_shape(guide = 'none') + + guides(color = guide_legend(title=element_blank()), + shape = guide_legend(title=element_blank())) + + theme_bw(base_size = 14) + + theme(legend.text=element_text(size=12)) + +p + +``` + + + +```{r} +ggsave(filename = "output/plot_three_scenarios_bw.png", + width = 11, + height = 6, + plot = p) +``` + + diff --git a/R/realistic_scenario.Rmd b/R/realistic_scenario.Rmd new file mode 100755 index 0000000..336bbd2 --- /dev/null +++ b/R/realistic_scenario.Rmd @@ -0,0 +1,349 @@ +--- +title: "Realistic scenario (Ge et al. 2011)" +output: html_document +--- + +```{r setup, include=FALSE} +knitr::opts_chunk$set(echo = TRUE) +knitr::opts_knit$set(root.dir = here::here()) +``` + +```{r} +source("R/utils/sim_data_utils.R") +source("R/utils/sim_reporting_utils.R") +source("R/utils/sim_variance_estimators.R") +``` + +## Realistic scenario + +We consider the data generating mechanism from Ge et al. (2011) as a realistic scenario. As described in the paper: + +>The simulated trials were constructed to approximately +match the conditions of the real trial described +in Section 2. +> +>Each simulated trial had 350 patients with +2:1 stratified randomization. +> +>A continuous standard normal covariate was +generated along with an independent binary +covariate with 0/1 proportions of 0.50. +> +>The continuous covariate was categorized by dividing +it at its population median to yield +2 x 2 = 4 strata levels for the design, or it was +divided at its population quartiles to yield +4 x 2 = 8 strata levels. +> +>The number of patients +in each stratum varied across the simulated trials, +but an approximate 2:1 randomization ratio +was implemented within each stratum (with +rounding to whole numbers when required). +> +>The binary response variable was simulated +based on a logistic regression model computed +using the covariate values in each simulated +data set. +The base case has coefficients b0 = -1.8, b1 = 1.6, +b2 = -0.6, and b3 = 0.0 corresponding to the +intercept (b0), treatment (b1), continuous covariate +(b2), and binary covariate (b3). + + +$$ + logit[P(Y_i = 1 | A, X)] = b_0 + b_1A + b_2X_1 + b_3X_2 +$$ + + +In this case we replicate scenario 1 (with $b_0 = -1.8$) from the paper with the 4 strata level design. We discretize the continuous covariate ('x1' in the code) at the population median (i.e., zero) to produce stratification factor 'z1'. Treatment assignment is then stratified by 'z1' and the binary covariate 'x2'. +The outcome model in this scenario corresponds to + +$$ + logit[P(Y_i = 1 | A, X)] = -1.8 + 1.6A + -0.6X_1 + 0X_2 +$$ + +Our working model is $logit[P(Y_i = 1 | A, X)] = b_0 + b_1A + b_2Z_1 + b_3X_2$ and thus our results correspond to method 'LR-Discrete-2' in Ge et al (2011). + + +```{r} +# Set up scenario + +scenarios <- list( + list(scenario = 1, + N = 350, + + # continuous (x1) and binary (x2) covariates + covars = tibble("name"=c("x1", "x2"), + "dist"=c("rnorm", "rbinom"), + "arg1"=c(0, 1), + "arg2"=c(1, 0.5)), + + # define strata variable z1 by discretizing x1 at population median + make_strata = tibble("name" = c("z1"), + "covar" = c("x1"), + "breaks" = c(0)), + + # stratified randomization according to x2 and z1 (2x2=4 strata) + stratified_randomization = T, + strata = c("x2", "z1"), + # 2:1 assignment + trt_assignment = 2/3, + + # outcome model uses discretized covariate z1 + response_func = \(df) -1.8 + 1.6*df$trt + -0.6*df$x1 + 0*df$x2, + working_model = "y ~ trt + z1 + x2" + ) +) + +``` + + +The true marginal probabilities that Y=1 are calculated below per stratum ($Z_1$) and treatment arm using $N=10^6$: + +```{r} +# True marginal probabilities that Y=1 + +df <- data.frame(sim_covars(list(), scenarios[[1]], N = 1e6)) + +# for patients in stratum Z == 0 +marginal_00 <- mean(plogis(scenarios[[1]]$response_func(df |> + transform(trt = 0) |> + filter(z1 == 0)))) +marginal_00 + +marginal_10 <- mean(plogis(scenarios[[1]]$response_func(df |> + transform(trt = 1) |> + filter(z1 == 0)))) +marginal_10 + +# marginal log-odds ratio in stratum Z == 0 +log((marginal_10/(1-marginal_10)) / (marginal_00/(1-marginal_00))) + + +# for patients in stratum Z == 1 +marginal_01 <- mean(plogis(scenarios[[1]]$response_func(df |> + transform(trt = 0) |> + filter(z1 == 1)))) +marginal_01 + +marginal_11 <- mean(plogis(scenarios[[1]]$response_func(df |> + transform(trt = 1) |> + filter(z1 == 1)))) +marginal_11 + +# marginal log-odds ratio in stratum Z == 1 +log((marginal_11/(1-marginal_11)) / (marginal_01/(1-marginal_01))) + +``` + + + +### Unconditional coverage + + +```{r} + +## Unconditional coverage +## PATE, CPATE + +## Simulate 10,000 runs +N_runs <- 1e4 +sims <- Q(run_sim_wrapper, + scenario=rep(scenarios, each=N_runs), + n_jobs = 200) +sims <- do.call(rbind, sims) + + +var_methods = list("ye_beeca_var", + "ye_beeca_strata_var", + "ge_var") + +# PATE +post_sims_pate <- purrr::map(var_methods, post_sims, sims = sims %>% rename(true_diff = true_diff_pate)) +results_pate <- purrr::map_df(post_sims_pate, sum_sims) +results_pate$estimand <- "PATE" + + +# CPATE +post_sims_cpate <- purrr::map(var_methods, post_sims, sims = sims %>% rename(true_diff = true_diff_cpate)) +results_cpate <- purrr::map_df(post_sims_cpate, sum_sims) +results_cpate$estimand <- "CPATE" + +``` + +Results: Unconditional coverage for PATE estimand + +```{r} +dplyr::arrange(results_pate, scenario) +``` + +Results: Unconditional coverage for CPATE estimand + +```{r} +dplyr::arrange(results_cpate, scenario) +``` + + +### Coverage conditional on X + + +```{r} + +## Conditional coverage (conditional only on X) +## PATE, CPATE + +#=============================================================================== +## simulate a base dataset that remains fixed +## we fix X, but simulate TRT and y +## (achieved by dropping trt and y from base_data so they are re-simulated each time) + +all_res_pate <- list() +all_res_cpate <- list() +i <- 1 + +for (rseed in c(274)) { + + set.seed(rseed) + + base_data <- sim_dat(scenarios[[1]]) + base_data <- base_data %>% select(-trt, -y) + + #============================================================================= + + ## Simulate 10,000 runs + N_runs <- 1e4 + sims <- Q(run_sim_wrapper, + scenario=rep(scenarios, each=N_runs), + const = list(base_data = base_data), + n_jobs = 200) + sims <- do.call(rbind, sims) + + var_methods = list("ye_beeca_var", + "ye_beeca_strata_var", + "ge_var") + + # PATE with conditional coverage (conditional on X) + post_sims_pate <- purrr::map(var_methods, post_sims, sims = sims %>% rename(true_diff = true_diff_pate)) + results_pate <- purrr::map_df(post_sims_pate, sum_sims) + results_pate$seed <- rseed + results_pate$estimand <- "PATE" + + + # CPATE with conditional coverage (conditional on X) + post_sims_cpate <- purrr::map(var_methods, post_sims, sims = sims %>% rename(true_diff = true_diff_cpate)) + results_cpate <- purrr::map_df(post_sims_cpate, sum_sims) + results_cpate$seed <- rseed + results_cpate$estimand <- "CPATE" + + + all_res_pate[[i]] <- results_pate + all_res_cpate[[i]] <- results_cpate + + i <- i + 1 + +} + +multi_res_pate <- do.call(rbind, all_res_pate) +multi_res_cpate <- do.call(rbind, all_res_cpate) + + +``` + +Results: Conditional coverage on X, for PATE estimand + +```{r} +multi_res_pate +``` + +Results: Conditional coverage on X, for CPATE estimand + +```{r} +multi_res_cpate +``` + + +### Coverage conditional on A, X + + +```{r} + +## Conditional coverage (conditional on X and TRT) +## PATE, CPATE + +#=============================================================================== +## simulate a base dataset that remains fixed +## we fix X and TRT, but simulate y +## (achieved by dropping y from base_data so it is re-simulated each time) + +all_res_pate <- list() +all_res_cpate <- list() +i <- 1 + +for (rseed in c(274)) { + + set.seed(rseed) + + base_data <- sim_dat(scenarios[[1]]) + base_data <- base_data %>% select(-y) + + #============================================================================= + + ## Simulate 10,000 runs + N_runs <- 1e4 + sims <- Q(run_sim_wrapper, + scenario=rep(scenarios, each=N_runs), + const = list(base_data = base_data), + n_jobs = 200) + sims <- do.call(rbind, sims) + + + var_methods = list("ye_beeca_var", + "ye_beeca_strata_var", + "ge_var") + + # PATE with conditional coverage (conditional on X, TRT) + post_sims_pate <- purrr::map(var_methods, post_sims, sims = sims %>% rename(true_diff = true_diff_pate)) + results_pate <- purrr::map_df(post_sims_pate, sum_sims) + results_pate$seed <- rseed + results_pate$estimand <- "PATE" + + + # CPATE with conditional coverage (conditional on X, TRT) + post_sims_cpate <- purrr::map(var_methods, post_sims, sims = sims %>% rename(true_diff = true_diff_cpate)) + results_cpate <- purrr::map_df(post_sims_cpate, sum_sims) + results_cpate$seed <- rseed + results_cpate$estimand <- "CPATE" + + + all_res_pate[[i]] <- results_pate + all_res_cpate[[i]] <- results_cpate + + i <- i + 1 + +} + +multi_res_pate <- do.call(rbind, all_res_pate) + +multi_res_cpate <- do.call(rbind, all_res_cpate) + +``` + + +Results: Conditional coverage on A, X, for PATE estimand + +```{r} +multi_res_pate +``` + + +Results: Conditional coverage on A, X, for CPATE estimand + +```{r} +multi_res_cpate +``` + + + + + diff --git a/R/utils/sim_data_utils.R b/R/utils/sim_data_utils.R new file mode 100755 index 0000000..fa828e4 --- /dev/null +++ b/R/utils/sim_data_utils.R @@ -0,0 +1,216 @@ + +library(dplyr) +library(clustermq) + + +## Simulate covariates and stratification variables +sim_covars <- function(df, scenario, N=NULL) { + # simulate covariates + if (is.null(N)) + N <- scenario$N + for (i in scenario$covars$name) { + this_covar <- scenario$covars[scenario$covars$name == i,] + if (this_covar$dist == "rnorm") { + rdist_func <- get(this_covar$dist) + rdist_mean <- this_covar$arg1 + rdist_sd <- this_covar$arg2 + df[[i]] <- rdist_func(N, rdist_mean, rdist_sd) + } else if (this_covar$dist == "rbinom") { + rdist_func <- get(this_covar$dist) + rdist_size <- this_covar$arg1 + rdist_prob <- this_covar$arg2 + df[[i]] <- rdist_func(N, rdist_size, rdist_prob) + } else { + stop(sprintf("unknown dist func %s", this_covar$dist)) + } + } + + # derive strata variables if needed + if (!is.null(scenario$make_strata)) { + for (i in scenario$make_strata$name) { + this_strata <- scenario$make_strata[scenario$make_strata$name == i,] + + # if creating binary strata, label as 0/1 + if (length(this_strata$breaks) == 1) { + df[[i]] <- cut(df[[this_strata$covar]], c(-Inf, this_strata$breaks, Inf), labels = F)-1 + } else { + # TODO: if > 2 strata, create additional dummy variables + stop("Attempting to create >2 strata levels. Not yet supported.") + } + + } + + } + + return(df) +} + + +## Simulate treatment assignment +sim_trt <- function(df, scenario) { + N <- scenario$N + if (is.null(scenario$stratified_randomization) || (scenario$stratified_randomization==FALSE)) { + + df[["trt"]] <- rbinom(N, 1, scenario$trt_assignment) + + } else { + + df[["trt"]] <- NA + + # define all strata if multiple strata vars + if (length(scenario$strata) > 1) { + all_strata <- apply(as.data.frame(df)[, scenario$strata], + 1, paste, collapse = "-" ) + } else { + all_strata <- df[[scenario$strata]] + } + df[["all_strata"]] <- all_strata + + for (stratum in unique(all_strata)) { + n_stratum <- sum(all_strata == stratum) + + trt_stratum <- rbinom(n_stratum, 1, scenario$trt_assignment) + + # assign stratum trt to dataframe + df[["trt"]][which(all_strata == stratum)] <- trt_stratum + } + + } + + return(df) +} + + +# Simulate complete trial dataset: covariates, treatment assignment and outcome +sim_dat <- function(scenario, base_data=NULL) { + + N <- scenario$N + + # if no base data supplied, simulate new data from scratch + if (is.null(base_data)) { + + df <- list() + + # simulate covariates + df <- sim_covars(df, scenario) + + # simulate treatment assignment + df <- sim_trt(df, scenario) + + # convert to dataframe + df <- as.data.frame(df) + + } else { + df <- base_data + } + + ## if no trt in base data, simulate treatment assignment + if (!"trt" %in% colnames(df)) { + df <- sim_trt(df, scenario) + } + + # if no outcome in base data, simulate y conditional on baseline df + if (!"y" %in% colnames(df)) { + # simulate outcome + df[["y"]] <- rbinom(N, 1, plogis(scenario$response_func(df))) + } + + # otherwise, if x, trt and y already in base_data, no new data simulated + + return(df) + +} + + +get_true_diff <- function(scenario, + estimand = c("PATE", "CPATE", "SATE"), + base_data=NULL){ + + if (estimand == "PATE") { + N <- 1e6 + + df <- list() + + # simulate population-level covariates + df <- sim_covars(df, scenario, N=N) + + df <- as.data.frame(df) + + p_1 <- mean(plogis(scenario$response_func(df %>% dplyr::mutate(trt=1)))) + p_0 <- mean(plogis(scenario$response_func(df %>% dplyr::mutate(trt=0)))) + + } else if (estimand == "CPATE") { + # use base_data x and predict counterfactuals + p_1 <- mean(plogis(scenario$response_func(base_data %>% dplyr::mutate(trt=1)))) + p_0 <- mean(plogis(scenario$response_func(base_data %>% dplyr::mutate(trt=0)))) + + } else if (estimand == "SATE") { + # TODO + stop("SATE not implemented") + } + + data.frame(scenario = scenario$scenario, + true_diff = p_1 - p_0) +} + + + +## Main simulation function. +## Simulate a single dataset based on scenario specification, +## fit working model and estimate variance with each method +one_result <- function(scenario, base_data=NULL){ + + dat <- sim_dat(scenario, base_data) + + dat$trt <- factor(dat$trt) + fit <- glm(as.formula(scenario$working_model), family = "binomial", data=dat) + + data.frame(point_estimate = beeca_wrapper(fit)$marginal_est, + + # Ye method without stratified randomization adjustment + ye_beeca_var = beeca_wrapper(fit, "Ye")$marginal_var, + + # Ye method with stratified randomization adjustment + ye_beeca_strata_var = beeca_wrapper(fit, "Ye", strata=scenario$strata)$marginal_var, + + # RobinCar implementation + #ye_robincar_var = robincar_wrapper(fit), + + # Ge method + ge_var = beeca_wrapper(fit, "Ge")$marginal_var, + + # Ye method original implementation (based on paper - deviates from RobinCar development) + ye_beeca_mod_var = beeca_wrapper(fit, "Ye", mod=T)$marginal_var, + + # Ge method with HC0 sandwich variance + ge_hc0_var = beeca_wrapper(fit, "Ge", type="HC0")$marginal_var, + + + true_diff_pate = get_true_diff(scenario, "PATE")$true_diff, + true_diff_cpate = get_true_diff(scenario, "CPATE", dat)$true_diff, + #true_diff_sate = get_true_diff(scenario, "SATE", dat)$true_diff, + + scenario = scenario[["scenario"]]) + +} + + + +## Simulation wrapper for clustermq +run_sim_wrapper <- function(scenario, base_data=NULL){ + + if(!exists('worker_setup_complete', mode='logical')) { + cat("Calling setup function:\n") + + source("R/utils/sim_variance_estimators.R") + source("R/utils/sim_data_utils.R") + + worker_setup_complete <<- TRUE + } else { + cat("Calling GC:\n") + print(gc()) + } + + one_result(scenario, base_data) + +} diff --git a/R/utils/sim_reporting_utils.R b/R/utils/sim_reporting_utils.R new file mode 100755 index 0000000..3fa93ab --- /dev/null +++ b/R/utils/sim_reporting_utils.R @@ -0,0 +1,33 @@ + + +# Calculate simulation result quantities of interest +post_sims <- function(sims_df, method){ + + post_df <- sims_df[,c("scenario", "true_diff", "point_estimate")] + post_df["var"] = sims_df[method] + post_df["lower"] <- post_df[,"point_estimate"] - qnorm(0.975) * sqrt(sims_df[method]) + post_df["upper"] <- post_df[,"point_estimate"] + qnorm(0.975) * sqrt(sims_df[method]) + post_df["cover"] <- ifelse(post_df[,"lower"] < sims_df[,"true_diff"] & post_df[,"upper"] > sims_df[,"true_diff"], 1, 0) + post_df["reject"] <- ifelse((post_df[,"lower"] > 0) | (post_df[,"upper"] < 0), 1, 0) + + return(cbind(post_df, method = method)) +} + + + + +## Summarise simulation results +sum_sims <- function(post_sims_df){ + + df_grouped <- dplyr::group_by(post_sims_df, scenario) + + df_sum <- dplyr::summarise(df_grouped, + av_se = mean(sqrt(var)), + coverage = mean(cover), + # power = mean(reject), + method = method[1]) + + return(as.data.frame(df_sum)) +} + + diff --git a/R/utils/sim_variance_estimators.R b/R/utils/sim_variance_estimators.R new file mode 100755 index 0000000..e6caa0a --- /dev/null +++ b/R/utils/sim_variance_estimators.R @@ -0,0 +1,32 @@ + +library(beeca) +library(RobinCar) + +beeca_wrapper <- function(glm_fit, method="Ge", type="model-based", mod=F, strata=NULL) { + + res <- glm_fit |> + beeca::get_marginal_effect("trt", method=method, type=type, contrast="diff", reference = "0", + mod=mod, strata=strata) + + return(list(marginal_est = res$marginal_est[[1]], + marginal_var = res$marginal_se[[1]] ^ 2)) + +} + + + +robincar_wrapper <- function(glm_fit) { + + fit_formula <- glm_fit$formula + + res <- robincar_glm(data.frame(glm_fit$data), + response_col = "y", + treat_col="trt", + formula = fit_formula, + g_family = glm_fit$family, + contrast_h = "diff", + adj_method = "homogeneous") + + return(res$contrast$varcov[[1]]) + +} \ No newline at end of file diff --git a/README.md b/README.md new file mode 100755 index 0000000..ab56b0f --- /dev/null +++ b/README.md @@ -0,0 +1,29 @@ +# Simulations supporting paper: *'Estimating the Variance of Covariate-Adjusted Estimators of Average Treatment Effects in Clinical Trials with Binary Endpoints'*, Magirr et al (2024) + +This repo contains the reproducible code for simulation results in the paper by [Magirr et al. (2024)](https://osf.io/9mp58/). +Simulations are based on variance estimators as implemented in the [{beeca}](https://github.com/openpharma/beeca) package. + + +#### Contents + +- `R/extreme_scenario.Rmd`: Results for section 4 ('Extreme scenario'). + +- `R/realistic_scenario.Rmd`: Results for section 4 ('Realistic scenario'). + +- `R/misspecified_scenario.Rmd`: Results for section 4 ('Model misspecification'). + +- `R/plot_ge_vs_ye.Rmd`: Results for section 5 ('Assessing conservativeness'). + +- **R/utils**: Helper functions for simulation machinery. + +- `sessionInfo.yaml`: snapshot of R session to aid reproducibility. + +#### References + +* Ge, Miaomiao, L Kathryn Durham, R Daniel Meyer, Wangang Xie, and Neal Thomas. 2011. "Covariate-Adjusted Difference in Proportions from Clinical Trials Using Logistic Regression and Weighted Risk Differences." *Drug Information Journal: DIJ/Drug Information Association* 45: 481--93. + +* Magirr, Dominic, Mark Baillie, Craig Wang, and Alexander Przybylski. 2024. “Estimating the Variance of Covariate-Adjusted Estimators of Average Treatment Effects in Clinical Trials with Binary Endpoints.” OSF. May 16. . + +* Przybylski A, Baillie M, Wang C, Magirr D (2024). beeca: Binary Endpoint Estimation with Covariate Adjustment. R package version 0.1.2, + +* Ye, Ting, Marlena Bannick, Yanyao Yi, and Jun Shao. 2023. "Robust Variance Estimation for Covariate-Adjusted Unconditional Treatment Effect in Randomized Clinical Trials with Binary Outcomes." *Statistical Theory and Related Fields* 7 (2): 159--63. diff --git a/beeca-simulations.Rproj b/beeca-simulations.Rproj new file mode 100644 index 0000000..8e3c2eb --- /dev/null +++ b/beeca-simulations.Rproj @@ -0,0 +1,13 @@ +Version: 1.0 + +RestoreWorkspace: Default +SaveWorkspace: Default +AlwaysSaveHistory: Default + +EnableCodeIndexing: Yes +UseSpacesForTab: Yes +NumSpacesForTab: 2 +Encoding: UTF-8 + +RnwWeave: Sweave +LaTeX: pdfLaTeX diff --git a/sessionInfo.yaml b/sessionInfo.yaml new file mode 100644 index 0000000..a0c2f24 --- /dev/null +++ b/sessionInfo.yaml @@ -0,0 +1,3461 @@ +R.version: + platform: x86_64-pc-linux-gnu + arch: x86_64 + os: linux-gnu + system: x86_64, linux-gnu + status: '' + major: '4' + minor: '3.1' + year: '2023' + month: '06' + day: '16' + svn rev: '84548' + language: R + version.string: R version 4.3.1 (2023-06-16) + nickname: Beagle Scouts +platform: x86_64-pc-linux-gnu (64-bit) +locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C +tzone: Europe/Zurich +tzcode_type: system (glibc) +running: Red Hat Enterprise Linux +RNGkind: +- Mersenne-Twister +- Inversion +- Rejection +basePkgs: +- stats +- graphics +- grDevices +- utils +- datasets +- methods +- base +otherPkgs: + ggplot2: + Package: ggplot2 + Version: 3.4.3 + Title: Create Elegant Data Visualisations Using the Grammar of Graphics + Authors@R: |- + c( + person("Hadley", "Wickham", , "hadley@posit.co", role = "aut", + comment = c(ORCID = "0000-0003-4757-117X")), + person("Winston", "Chang", role = "aut", + comment = c(ORCID = "0000-0002-1576-2126")), + person("Lionel", "Henry", role = "aut"), + person("Thomas Lin", "Pedersen", , "thomas.pedersen@posit.co", role = c("aut", "cre"), + comment = c(ORCID = "0000-0002-5147-4711")), + person("Kohske", "Takahashi", role = "aut"), + person("Claus", "Wilke", role = "aut", + comment = c(ORCID = "0000-0002-7470-9261")), + person("Kara", "Woo", role = "aut", + comment = c(ORCID = "0000-0002-5125-4188")), + person("Hiroaki", "Yutani", role = "aut", + comment = c(ORCID = "0000-0002-3385-7233")), + person("Dewey", "Dunnington", role = "aut", + comment = c(ORCID = "0000-0002-9415-4582")), + person("Posit, PBC", role = c("cph", "fnd")) + ) + Description: |- + A system for 'declaratively' creating graphics, based on "The + Grammar of Graphics". You provide the data, tell 'ggplot2' how to map + variables to aesthetics, what graphical primitives to use, and it + takes care of the details. + License: MIT + file LICENSE + URL: |- + https://ggplot2.tidyverse.org, + https://github.com/tidyverse/ggplot2 + BugReports: https://github.com/tidyverse/ggplot2/issues + Depends: R (>= 3.3) + Imports: |- + cli, glue, grDevices, grid, gtable (>= 0.1.1), isoband, + lifecycle (> 1.0.1), MASS, mgcv, rlang (>= 1.1.0), scales (>= + 1.2.0), stats, tibble, vctrs (>= 0.5.0), withr (>= 2.5.0) + Suggests: |- + covr, dplyr, ggplot2movies, hexbin, Hmisc, knitr, lattice, + mapproj, maps, maptools, multcomp, munsell, nlme, profvis, + quantreg, ragg, RColorBrewer, rgeos, rmarkdown, rpart, sf (>= + 0.7-3), svglite (>= 1.2.0.9001), testthat (>= 3.1.2), vdiffr + (>= 1.0.0), xml2 + Enhances: sp + VignetteBuilder: knitr + Config/Needs/website: ggtext, tidyr, forcats, tidyverse/tidytemplate + Config/testthat/edition: '3' + Encoding: UTF-8 + LazyData: 'true' + RoxygenNote: 7.2.3 + Collate: |- + 'ggproto.R' 'ggplot-global.R' 'aaa-.R' + 'aes-colour-fill-alpha.R' 'aes-evaluation.R' + 'aes-group-order.R' 'aes-linetype-size-shape.R' + 'aes-position.R' 'compat-plyr.R' 'utilities.R' 'aes.R' + 'utilities-checks.R' 'legend-draw.R' 'geom-.R' + 'annotation-custom.R' 'annotation-logticks.R' 'geom-polygon.R' + 'geom-map.R' 'annotation-map.R' 'geom-raster.R' + 'annotation-raster.R' 'annotation.R' 'autolayer.R' 'autoplot.R' + 'axis-secondary.R' 'backports.R' 'bench.R' 'bin.R' 'coord-.R' + 'coord-cartesian-.R' 'coord-fixed.R' 'coord-flip.R' + 'coord-map.R' 'coord-munch.R' 'coord-polar.R' + 'coord-quickmap.R' 'coord-sf.R' 'coord-transform.R' 'data.R' + 'facet-.R' 'facet-grid-.R' 'facet-null.R' 'facet-wrap.R' + 'fortify-lm.R' 'fortify-map.R' 'fortify-multcomp.R' + 'fortify-spatial.R' 'fortify.R' 'stat-.R' 'geom-abline.R' + 'geom-rect.R' 'geom-bar.R' 'geom-bin2d.R' 'geom-blank.R' + 'geom-boxplot.R' 'geom-col.R' 'geom-path.R' 'geom-contour.R' + 'geom-count.R' 'geom-crossbar.R' 'geom-segment.R' + 'geom-curve.R' 'geom-defaults.R' 'geom-ribbon.R' + 'geom-density.R' 'geom-density2d.R' 'geom-dotplot.R' + 'geom-errorbar.R' 'geom-errorbarh.R' 'geom-freqpoly.R' + 'geom-function.R' 'geom-hex.R' 'geom-histogram.R' + 'geom-hline.R' 'geom-jitter.R' 'geom-label.R' + 'geom-linerange.R' 'geom-point.R' 'geom-pointrange.R' + 'geom-quantile.R' 'geom-rug.R' 'geom-sf.R' 'geom-smooth.R' + 'geom-spoke.R' 'geom-text.R' 'geom-tile.R' 'geom-violin.R' + 'geom-vline.R' 'ggplot2-package.R' 'grob-absolute.R' + 'grob-dotstack.R' 'grob-null.R' 'grouping.R' 'guide-bins.R' + 'guide-colorbar.R' 'guide-colorsteps.R' 'guide-legend.R' + 'guides-.R' 'guides-axis.R' 'guides-grid.R' 'guides-none.R' + 'hexbin.R' 'import-standalone-obj-type.R' + 'import-standalone-types-check.R' 'labeller.R' 'labels.R' + 'layer.R' 'layer-sf.R' 'layout.R' 'limits.R' 'margins.R' + 'performance.R' 'plot-build.R' 'plot-construction.R' + 'plot-last.R' 'plot.R' 'position-.R' 'position-collide.R' + 'position-dodge.R' 'position-dodge2.R' 'position-identity.R' + 'position-jitter.R' 'position-jitterdodge.R' 'position-nudge.R' + 'position-stack.R' 'quick-plot.R' 'reshape-add-margins.R' + 'save.R' 'scale-.R' 'scale-alpha.R' 'scale-binned.R' + 'scale-brewer.R' 'scale-colour.R' 'scale-continuous.R' + 'scale-date.R' 'scale-discrete-.R' 'scale-expansion.R' + 'scale-gradient.R' 'scale-grey.R' 'scale-hue.R' + 'scale-identity.R' 'scale-linetype.R' 'scale-linewidth.R' + 'scale-manual.R' 'scale-shape.R' 'scale-size.R' 'scale-steps.R' + 'scale-type.R' 'scale-view.R' 'scale-viridis.R' 'scales-.R' + 'stat-align.R' 'stat-bin.R' 'stat-bin2d.R' 'stat-bindot.R' + 'stat-binhex.R' 'stat-boxplot.R' 'stat-contour.R' + 'stat-count.R' 'stat-density-2d.R' 'stat-density.R' + 'stat-ecdf.R' 'stat-ellipse.R' 'stat-function.R' + 'stat-identity.R' 'stat-qq-line.R' 'stat-qq.R' + 'stat-quantilemethods.R' 'stat-sf-coordinates.R' 'stat-sf.R' + 'stat-smooth-methods.R' 'stat-smooth.R' 'stat-sum.R' + 'stat-summary-2d.R' 'stat-summary-bin.R' 'stat-summary-hex.R' + 'stat-summary.R' 'stat-unique.R' 'stat-ydensity.R' + 'summarise-plot.R' 'summary.R' 'theme-elements.R' 'theme.R' + 'theme-defaults.R' 'theme-current.R' 'utilities-break.R' + 'utilities-grid.R' 'utilities-help.R' 'utilities-matrix.R' + 'utilities-resolution.R' 'utilities-table.R' + 'utilities-tidy-eval.R' 'zxx.R' 'zzz.R' + NeedsCompilation: 'no' + Packaged: 2023-08-07 18:07:11 UTC; teunv + Author: |- + Hadley Wickham [aut] (), + Winston Chang [aut] (), + Lionel Henry [aut], + Thomas Lin Pedersen [aut, cre] + (), + Kohske Takahashi [aut], + Claus Wilke [aut] (), + Kara Woo [aut] (), + Hiroaki Yutani [aut] (), + Dewey Dunnington [aut] (), + Posit, PBC [cph, fnd] + Maintainer: Thomas Lin Pedersen + Repository: RSPM + Date/Publication: 2023-08-14 11:20:02 UTC + Built: R 4.3.1; ; 2024-02-06 17:55:36 UTC; unix + RobinCar: + Package: RobinCar + Type: Package + Title: Robust Estimation and Inference in Covariate-Adaptive Randomization + Version: 0.1.0 + Author: Ting Ye, Yanyao Yi, Marlena Bannick, Faith Bian + Maintainer: Marlena Bannick + Description: Performs robust estimation and inference when using covariate adjustment + and/or covariate-adaptive randomization in randomized controlled trials. + License: MIT + file LICENSE + Encoding: UTF-8 + LazyData: 'true' + RoxygenNote: 7.1.2 + Imports: |- + dplyr, + magrittr, + tidyr, + emulator, + numDeriv, + tidyverse, + stats, + rlang, + survival, + fastDummies, + data.table, + broom, + SuperLearner, + AIPW, + MASS + Depends: R (>= 2.10) + Suggests: |- + knitr, + rmarkdown, + ranger, + forcats, + testthat (>= 3.0.0) + VignetteBuilder: knitr + Config/testthat/edition: '3' + Built: R 4.3.1; ; 2024-02-06 23:35:28 UTC; unix + beeca: + Package: beeca + Title: Binary Endpoint Estimation with Covariate Adjustment + Version: 0.1.2 + Authors@R: "\n c(person(given = \"Alex\", \n family = \"Przybylski\", + \n email = \"alexander.przybylski@novartis.com\", \n role + = c(\"cre\", \"aut\")\n ),\n person(given = \"Mark\", \n family + = \"Baillie\", \n email = \"mark.baillie@novartis.com\", \n role + = c(\"aut\"), \n comment = c(ORCID = \"0000-0002-5618-0667\")\n ),\n + \ person(given = \"Craig\", \n family = \"Wang\", \n email + = \"craig.wang@novartis.com\", \n role = c(\"aut\"),\n comment + = c(ORCID = \"0000-0003-1804-2463\")\n ),\n person(given = \"Dominic\", + \n family = \"Magirr\", \n email = \"dominic.magirr@novartis.com\", + \n role = c(\"aut\")\n ))" + Description: "A lightweight package to perform estimation of marginal treatment + \n effects for binary outcomes when using logistic regression working models + with \n covariate adjustment (see discussions in Magirr et al (2024) ). + Implements the variance estimators of \n Ge et al (2011) + and\n Ye et al (2023) . " + Maintainer: Alex Przybylski + License: LGPL (>= 3) + Encoding: UTF-8 + Roxygen: list(markdown = TRUE) + RoxygenNote: 7.2.3 + Suggests: |- + knitr, + rmarkdown, + testthat (>= 3.0.0), + tidyr, + marginaleffects, + margins, + RobinCar (== 0.3.0) + Config/testthat/edition: '3' + Depends: R (>= 2.10) + LazyData: 'true' + Imports: |- + dplyr, + lifecycle, + sandwich, + stats + VignetteBuilder: knitr + URL: https://openpharma.github.io/beeca/ + Author: |- + Alex Przybylski [cre, aut], + Mark Baillie [aut] (), + Craig Wang [aut] (), + Dominic Magirr [aut] + Built: R 4.3.1; ; 2024-06-14 12:53:20 UTC; unix + RemoteType: github + RemoteHost: api.github.com + RemoteUsername: openpharma + RemoteRepo: beeca + RemoteRef: main + RemoteSha: 6003475c6f18e363d1c16ab557d8160aaf7f6ae0 + GithubHost: api.github.com + GithubRepo: beeca + GithubUsername: openpharma + GithubRef: main + GithubSHA1: 6003475c6f18e363d1c16ab557d8160aaf7f6ae0 + clustermq: + Package: clustermq + Title: |- + Evaluate Function Calls on HPC Schedulers (LSF, SGE, SLURM, + PBS/Torque) + Version: 0.8.95.5 + Authors@R: |- + c( + person('Michael', 'Schubert', email='mschu.dev@gmail.com', + role = c('aut', 'cre'), + comment = c(ORCID='0000-0002-6862-5221')) + ) + Maintainer: Michael Schubert + Description: |- + Evaluate arbitrary function calls using workers on HPC schedulers + in single line of code. All processing is done on the network without + accessing the file system. Remote schedulers are supported via SSH. + URL: https://mschubert.github.io/clustermq/ + BugReports: https://github.com/mschubert/clustermq/issues + Depends: R (>= 3.6.2) + LinkingTo: Rcpp + SystemRequirements: ZeroMQ (libzmq) + Imports: methods, narray, progress, purrr, R6, Rcpp, utils + License: Apache License (== 2.0) | file LICENSE + Encoding: UTF-8 + Suggests: |- + callr, devtools, dplyr, foreach, iterators, knitr, parallel, + rmarkdown, roxygen2 (>= 5.0.0), testthat, tools + VignetteBuilder: knitr + RoxygenNote: 7.1.0 + NeedsCompilation: 'yes' + Packaged: 2023-02-18 23:55:01 UTC; mschu + Author: Michael Schubert [aut, cre] () + Repository: RSPM + Date/Publication: 2023-02-19 08:00:02 UTC + Built: R 4.3.1; x86_64-pc-linux-gnu; 2024-02-06 19:24:50 UTC; unix + dplyr: + Type: Package + Package: dplyr + Title: A Grammar of Data Manipulation + Version: 1.1.3 + Authors@R: |- + c( + person("Hadley", "Wickham", , "hadley@posit.co", role = c("aut", "cre"), + comment = c(ORCID = "0000-0003-4757-117X")), + person("Romain", "François", role = "aut", + comment = c(ORCID = "0000-0002-2444-4226")), + person("Lionel", "Henry", role = "aut"), + person("Kirill", "Müller", role = "aut", + comment = c(ORCID = "0000-0002-1416-3412")), + person("Davis", "Vaughan", , "davis@posit.co", role = "aut", + comment = c(ORCID = "0000-0003-4777-038X")), + person("Posit Software, PBC", role = c("cph", "fnd")) + ) + Description: |- + A fast, consistent tool for working with data frame like + objects, both in memory and out of memory. + License: MIT + file LICENSE + URL: https://dplyr.tidyverse.org, https://github.com/tidyverse/dplyr + BugReports: https://github.com/tidyverse/dplyr/issues + Depends: R (>= 3.5.0) + Imports: |- + cli (>= 3.4.0), generics, glue (>= 1.3.2), lifecycle (>= + 1.0.3), magrittr (>= 1.5), methods, pillar (>= 1.9.0), R6, + rlang (>= 1.1.0), tibble (>= 3.2.0), tidyselect (>= 1.2.0), + utils, vctrs (>= 0.6.0) + Suggests: |- + bench, broom, callr, covr, DBI, dbplyr (>= 2.2.1), ggplot2, + knitr, Lahman, lobstr, microbenchmark, nycflights13, purrr, + rmarkdown, RMySQL, RPostgreSQL, RSQLite, stringi (>= 1.7.6), + testthat (>= 3.1.5), tidyr (>= 1.3.0), withr + VignetteBuilder: knitr + Config/Needs/website: tidyverse, shiny, pkgdown, tidyverse/tidytemplate + Config/testthat/edition: '3' + Encoding: UTF-8 + LazyData: 'true' + RoxygenNote: 7.2.3 + NeedsCompilation: 'yes' + Packaged: 2023-08-25 22:28:32 UTC; hadleywickham + Author: |- + Hadley Wickham [aut, cre] (), + Romain François [aut] (), + Lionel Henry [aut], + Kirill Müller [aut] (), + Davis Vaughan [aut] (), + Posit Software, PBC [cph, fnd] + Maintainer: Hadley Wickham + Repository: CRAN + Date/Publication: 2023-09-03 16:20:02 UTC + Built: R 4.3.1; x86_64-pc-linux-gnu; 2024-02-06 17:58:10 UTC; unix +loadedOnly: + utf8: + Package: utf8 + Title: Unicode Text Processing + Version: 1.2.3 + Authors@R: |2- + + c(person(given = c("Patrick", "O."), + family = "Perry", + role = c("aut", "cph")), + person(given = "Kirill", + family = "M\u00fcller", + role = "cre", + email = "kirill@cynkra.com"), + person(given = "Unicode, Inc.", + role = c("cph", "dtc"), + comment = "Unicode Character Database")) + Description: |- + Process and print 'UTF-8' encoded international + text (Unicode). Input, validate, normalize, encode, format, and + display. + License: Apache License (== 2.0) | file LICENSE + URL: https://ptrckprry.com/r-utf8/, https://github.com/patperry/r-utf8 + BugReports: https://github.com/patperry/r-utf8/issues + Depends: R (>= 2.10) + Suggests: |- + cli, covr, knitr, rlang, rmarkdown, testthat (>= 3.0.0), + withr + VignetteBuilder: knitr, rmarkdown + Config/testthat/edition: '3' + Encoding: UTF-8 + RoxygenNote: 7.2.3 + NeedsCompilation: 'yes' + Packaged: 2023-01-31 05:28:43 UTC; kirill + Author: |- + Patrick O. Perry [aut, cph], + Kirill Müller [cre], + Unicode, Inc. [cph, dtc] (Unicode Character Database) + Maintainer: Kirill Müller + Repository: RSPM + Date/Publication: 2023-01-31 18:00:02 UTC + Built: R 4.3.1; x86_64-pc-linux-gnu; 2024-02-06 17:54:47 UTC; unix + generics: + Package: generics + Title: |- + Common S3 Generics not Provided by Base R Methods Related to + Model Fitting + Version: 0.1.3 + Authors@R: |- + c( + person("Hadley", "Wickham", , "hadley@rstudio.com", role = c("aut", "cre")), + person("Max", "Kuhn", , "max@rstudio.com", role = "aut"), + person("Davis", "Vaughan", , "davis@rstudio.com", role = "aut"), + person("RStudio", role = "cph") + ) + Description: |- + In order to reduce potential package dependencies and + conflicts, generics provides a number of commonly used S3 generics. + License: MIT + file LICENSE + URL: https://generics.r-lib.org, https://github.com/r-lib/generics + BugReports: https://github.com/r-lib/generics/issues + Depends: R (>= 3.2) + Imports: methods + Suggests: covr, pkgload, testthat (>= 3.0.0), tibble, withr + Config/Needs/website: tidyverse/tidytemplate + Config/testthat/edition: '3' + Encoding: UTF-8 + RoxygenNote: 7.2.0 + NeedsCompilation: 'no' + Packaged: 2022-07-05 14:52:13 UTC; davis + Author: |- + Hadley Wickham [aut, cre], + Max Kuhn [aut], + Davis Vaughan [aut], + RStudio [cph] + Maintainer: Hadley Wickham + Repository: RSPM + Date/Publication: 2022-07-05 19:40:02 UTC + Built: R 4.3.1; ; 2024-02-06 17:58:03 UTC; unix + tidyr: + Package: tidyr + Title: Tidy Messy Data + Version: 1.3.0 + Authors@R: |- + c( + person("Hadley", "Wickham", , "hadley@posit.co", role = c("aut", "cre")), + person("Davis", "Vaughan", , "davis@posit.co", role = "aut"), + person("Maximilian", "Girlich", role = "aut"), + person("Kevin", "Ushey", , "kevin@posit.co", role = "ctb"), + person("Posit, PBC", role = c("cph", "fnd")) + ) + Description: |- + Tools to help to create tidy data, where each column is a + variable, each row is an observation, and each cell contains a single + value. 'tidyr' contains tools for changing the shape (pivoting) and + hierarchy (nesting and 'unnesting') of a dataset, turning deeply + nested lists into rectangular data frames ('rectangling'), and + extracting values out of string columns. It also includes tools for + working with missing values (both implicit and explicit). + License: MIT + file LICENSE + URL: https://tidyr.tidyverse.org, https://github.com/tidyverse/tidyr + BugReports: https://github.com/tidyverse/tidyr/issues + Depends: R (>= 3.4.0) + Imports: |- + cli (>= 3.4.1), dplyr (>= 1.0.10), glue, lifecycle (>= 1.0.3), + magrittr, purrr (>= 1.0.1), rlang (>= 1.0.4), stringr (>= + 1.5.0), tibble (>= 2.1.1), tidyselect (>= 1.2.0), utils, vctrs + (>= 0.5.2) + Suggests: |- + covr, data.table, knitr, readr, repurrrsive (>= 1.1.0), + rmarkdown, testthat (>= 3.0.0) + LinkingTo: cpp11 (>= 0.4.0) + VignetteBuilder: knitr + Config/Needs/website: tidyverse/tidytemplate + Config/testthat/edition: '3' + Encoding: UTF-8 + LazyData: 'true' + RoxygenNote: 7.2.3 + SystemRequirements: C++11 + NeedsCompilation: 'yes' + Packaged: 2023-01-23 22:21:00 UTC; hadleywickham + Author: |- + Hadley Wickham [aut, cre], + Davis Vaughan [aut], + Maximilian Girlich [aut], + Kevin Ushey [ctb], + Posit, PBC [cph, fnd] + Maintainer: Hadley Wickham + Repository: RSPM + Date/Publication: 2023-01-24 16:00:02 UTC + Built: R 4.3.1; x86_64-pc-linux-gnu; 2024-02-06 18:03:38 UTC; unix + lattice: + Package: lattice + Version: 0.21-8 + Date: '2023-04-05' + Priority: recommended + Title: Trellis Graphics for R + Authors@R: "c(person(\"Deepayan\", \"Sarkar\", role = c(\"aut\", \"cre\"),\n\t + \ email = \"deepayan.sarkar@r-project.org\",\n\t\t comment = c(ORCID + = \"0000-0003-4107-1553\")),\n person(\"Felix\", \"Andrews\", role + = \"ctb\"),\n\t person(\"Kevin\", \"Wright\", role = \"ctb\", comment = + \"documentation\"),\n\t person(\"Neil\", \"Klepeis\", role = \"ctb\"),\n\t + \ person(\"Johan\", \"Larsson\", role = \"ctb\", comment = \"miscellaneous + improvements\"),\n person(\"Zhijian (Jason)\", \"Wen\", role = + \"cph\", comment = \"filled contour code\"),\n person(\"Paul\", + \"Murrell\", role = \"ctb\", email = \"paul@stat.auckland.ac.nz\"),\n\t person(\"Stefan\", + \"Eng\", role = \"ctb\", comment = \"violin plot improvements\"),\n\t person(\"Achim\", + \"Zeileis\", role = \"ctb\", comment = \"modern colors\")\n\t )" + Description: |- + A powerful and elegant high-level data visualization + system inspired by Trellis graphics, with an emphasis on + multivariate data. Lattice is sufficient for typical graphics needs, + and is also flexible enough to handle most nonstandard requirements. + See ?Lattice for an introduction. + Depends: R (>= 4.0.0) + Suggests: KernSmooth, MASS, latticeExtra, colorspace + Imports: grid, grDevices, graphics, stats, utils + Enhances: chron + LazyLoad: 'yes' + LazyData: 'yes' + License: GPL (>= 2) + URL: https://lattice.r-forge.r-project.org/ + BugReports: https://github.com/deepayan/lattice/issues + NeedsCompilation: 'yes' + Packaged: 2023-04-05 15:31:40 UTC; deepayan + Author: |- + Deepayan Sarkar [aut, cre] (), + Felix Andrews [ctb], + Kevin Wright [ctb] (documentation), + Neil Klepeis [ctb], + Johan Larsson [ctb] (miscellaneous improvements), + Zhijian (Jason) Wen [cph] (filled contour code), + Paul Murrell [ctb], + Stefan Eng [ctb] (violin plot improvements), + Achim Zeileis [ctb] (modern colors) + Maintainer: Deepayan Sarkar + Repository: RSPM + Date/Publication: 2023-04-05 17:43:19 UTC + Encoding: UTF-8 + Built: R 4.3.1; x86_64-pc-linux-gnu; 2024-02-06 17:45:51 UTC; unix + hms: + Package: hms + Title: Pretty Time of Day + Date: '2023-03-21' + Version: 1.1.3 + Authors@R: |- + c( + person("Kirill", "Müller", role = c("aut", "cre"), email = "kirill@cynkra.com", comment = c(ORCID = "0000-0002-1416-3412")), + person("R Consortium", role = "fnd"), + person("RStudio", role = "fnd") + ) + Description: |- + Implements an S3 class for storing and formatting time-of-day + values, based on the 'difftime' class. + Imports: |- + lifecycle, methods, pkgconfig, rlang (>= 1.0.2), vctrs (>= + 0.3.8) + Suggests: crayon, lubridate, pillar (>= 1.1.0), testthat (>= 3.0.0) + License: MIT + file LICENSE + Encoding: UTF-8 + URL: https://hms.tidyverse.org/, https://github.com/tidyverse/hms + BugReports: https://github.com/tidyverse/hms/issues + RoxygenNote: 7.2.3 + Config/testthat/edition: '3' + Config/autostyle/scope: line_breaks + Config/autostyle/strict: 'false' + Config/Needs/website: tidyverse/tidytemplate + NeedsCompilation: 'no' + Packaged: 2023-03-21 16:52:11 UTC; kirill + Author: |- + Kirill Müller [aut, cre] (), + R Consortium [fnd], + RStudio [fnd] + Maintainer: Kirill Müller + Repository: RSPM + Date/Publication: 2023-03-21 18:10:02 UTC + Built: R 4.3.1; ; 2024-02-06 18:11:21 UTC; unix + digest: + Package: digest + Author: |- + Dirk Eddelbuettel with contributions + by Antoine Lucas, Jarek Tuszynski, Henrik Bengtsson, Simon Urbanek, + Mario Frasca, Bryan Lewis, Murray Stokely, Hannes Muehleisen, + Duncan Murdoch, Jim Hester, Wush Wu, Qiang Kou, Thierry Onkelinx, + Michel Lang, Viliam Simko, Kurt Hornik, Radford Neal, Kendon Bell, + Matthew de Queljoe, Ion Suruceanu, Bill Denney, Dirk Schumacher, + Winston Chang, and Dean Attali. + Version: 0.6.33 + Date: '2023-06-28' + Maintainer: Dirk Eddelbuettel + Title: Create Compact Hash Digests of R Objects + Description: |- + Implementation of a function 'digest()' for the creation of hash + digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256', 'crc32', + 'xxhash', 'murmurhash', 'spookyhash', 'blake3' and 'crc32c' algorithms) permitting + easy comparison of R language objects, as well as functions such as'hmac()' to + create hash-based message authentication code. Please note that this package + is not meant to be deployed for cryptographic purposes for which more + comprehensive (and widely tested) libraries such as 'OpenSSL' should be + used. + URL: |- + https://github.com/eddelbuettel/digest, + https://dirk.eddelbuettel.com/code/digest.html + BugReports: https://github.com/eddelbuettel/digest/issues + Depends: R (>= 3.3.0) + Imports: utils + License: GPL (>= 2) + Suggests: tinytest, simplermarkdown + VignetteBuilder: simplermarkdown + NeedsCompilation: 'yes' + Packaged: 2023-06-28 02:46:18 UTC; edd + Repository: RSPM + Date/Publication: 2023-07-07 14:10:02 UTC + Encoding: UTF-8 + Built: R 4.3.1; x86_64-pc-linux-gnu; 2024-02-06 18:00:16 UTC; unix + magrittr: + Type: Package + Package: magrittr + Title: A Forward-Pipe Operator for R + Version: 2.0.3 + Authors@R: |- + c( + person("Stefan Milton", "Bache", , "stefan@stefanbache.dk", role = c("aut", "cph"), + comment = "Original author and creator of magrittr"), + person("Hadley", "Wickham", , "hadley@rstudio.com", role = "aut"), + person("Lionel", "Henry", , "lionel@rstudio.com", role = "cre"), + person("RStudio", role = c("cph", "fnd")) + ) + Description: |- + Provides a mechanism for chaining commands with a new + forward-pipe operator, %>%. This operator will forward a value, or the + result of an expression, into the next function call/expression. + There is flexible support for the type of right-hand side expressions. + For more information, see package vignette. To quote Rene Magritte, + "Ceci n'est pas un pipe." + License: MIT + file LICENSE + URL: |- + https://magrittr.tidyverse.org, + https://github.com/tidyverse/magrittr + BugReports: https://github.com/tidyverse/magrittr/issues + Depends: R (>= 3.4.0) + Suggests: covr, knitr, rlang, rmarkdown, testthat + VignetteBuilder: knitr + ByteCompile: 'Yes' + Config/Needs/website: tidyverse/tidytemplate + Encoding: UTF-8 + RoxygenNote: 7.1.2 + NeedsCompilation: 'yes' + Packaged: 2022-03-29 09:34:37 UTC; lionel + Author: |- + Stefan Milton Bache [aut, cph] (Original author and creator of + magrittr), + Hadley Wickham [aut], + Lionel Henry [cre], + RStudio [cph, fnd] + Maintainer: Lionel Henry + Repository: RSPM + Date/Publication: 2022-03-30 07:30:09 UTC + Built: R 4.3.1; x86_64-pc-linux-gnu; 2024-02-06 17:54:44 UTC; unix + evaluate: + Package: evaluate + Type: Package + Title: |- + Parsing and Evaluation Tools that Provide More Details than the + Default + Version: '0.21' + Authors@R: |- + c( + person("Hadley", "Wickham", role = "aut"), + person("Yihui", "Xie", role = c("aut", "cre"), email = "xie@yihui.name", comment = c(ORCID = "0000-0003-0645-5666")), + person("Michael", "Lawrence", role = "ctb"), + person("Thomas", "Kluyver", role = "ctb"), + person("Jeroen", "Ooms", role = "ctb"), + person("Barret", "Schloerke", role = "ctb"), + person("Adam", "Ryczkowski", role = "ctb"), + person("Hiroaki", "Yutani", role = "ctb"), + person("Michel", "Lang", role = "ctb"), + person("Karolis", "Koncevičius", role = "ctb"), + person(given = "Posit Software, PBC", role = c("cph", "fnd")) + ) + Description: |- + Parsing and evaluation tools that make it easy to recreate the + command line behaviour of R. + License: MIT + file LICENSE + URL: https://github.com/r-lib/evaluate + BugReports: https://github.com/r-lib/evaluate/issues + Depends: R (>= 3.0.2) + Imports: methods + Suggests: covr, ggplot2, lattice, rlang, testthat (>= 3.0.0), withr + RoxygenNote: 7.2.3 + Encoding: UTF-8 + Config/testthat/edition: '3' + NeedsCompilation: 'no' + Packaged: 2023-05-01 21:56:45 UTC; yihui + Author: |- + Hadley Wickham [aut], + Yihui Xie [aut, cre] (), + Michael Lawrence [ctb], + Thomas Kluyver [ctb], + Jeroen Ooms [ctb], + Barret Schloerke [ctb], + Adam Ryczkowski [ctb], + Hiroaki Yutani [ctb], + Michel Lang [ctb], + Karolis Koncevičius [ctb], + Posit Software, PBC [cph, fnd] + Maintainer: Yihui Xie + Repository: RSPM + Date/Publication: 2023-05-05 23:30:02 UTC + Built: R 4.3.1; ; 2024-02-06 18:05:33 UTC; unix + grid: + Package: grid + Version: 4.3.1 + Priority: base + Title: The Grid Graphics Package + Author: Paul Murrell + Maintainer: R Core Team + Contact: R-help mailing list + Description: |- + A rewrite of the graphics layout capabilities, plus some + support for interaction. + Imports: grDevices, utils + License: Part of R 4.3.1 + NeedsCompilation: 'yes' + Built: R 4.3.1; x86_64-pc-linux-gnu; 2024-02-06 17:44:22 UTC; unix + iterators: + Package: iterators + Type: Package + Title: Provides Iterator Construct + Version: 1.0.14 + Authors@R: |- + c(person("Folashade", "Daniel", role="cre", email="fdaniel@microsoft.com"), + person("Revolution", "Analytics", role=c("aut", "cph")), + person("Steve", "Weston", role="aut")) + Description: |- + Support for iterators, which allow a programmer to traverse + through all the elements of a vector, list, or other collection of data. + URL: https://github.com/RevolutionAnalytics/iterators + Depends: R (>= 2.5.0), utils + Suggests: RUnit, foreach + License: Apache License (== 2.0) + NeedsCompilation: 'no' + Packaged: 2022-01-16 18:19:31 UTC; folashade + Author: |- + Folashade Daniel [cre], + Revolution Analytics [aut, cph], + Steve Weston [aut] + Maintainer: Folashade Daniel + Repository: RSPM + Date/Publication: 2022-02-05 00:50:08 UTC + Encoding: UTF-8 + Built: R 4.3.1; ; 2024-02-06 17:56:09 UTC; unix + mvtnorm: + Package: mvtnorm + Title: Multivariate Normal and t Distributions + Version: 1.2-3 + Date: '2023-08-17' + Authors@R: |- + c(person("Alan", "Genz", role = "aut"), + person("Frank", "Bretz", role = "aut"), + person("Tetsuhisa", "Miwa", role = "aut"), + person("Xuefei", "Mi", role = "aut"), + person("Friedrich", "Leisch", role = "ctb"), + person("Fabian", "Scheipl", role = "ctb"), + person("Bjoern", "Bornkamp", role = "ctb", comment = c(ORCID = "0000-0002-6294-8185")), + person("Martin", "Maechler", role = "ctb", comment = c(ORCID = "0000-0002-8685-9910")), + person("Torsten", "Hothorn", role = c("aut", "cre"), + email = "Torsten.Hothorn@R-project.org", comment = c(ORCID = "0000-0001-8301-0471"))) + Description: "Computes multivariate normal and t probabilities, quantiles, random + deviates, \n and densities. Log-likelihoods for multivariate Gaussian models + and Gaussian copulae \n parameterised by Cholesky factors of covariance or + precision matrices are implemented \n for interval-censored and exact data, + or a mix thereof. Score functions for these \n log-likelihoods are available. + A class representing multiple lower triangular matrices \n and corresponding + methods are part of this package." + Imports: stats + Depends: R(>= 3.5.0) + Suggests: qrng, numDeriv + License: GPL-2 + URL: http://mvtnorm.R-forge.R-project.org + NeedsCompilation: 'yes' + Packaged: 2023-08-17 08:50:49 UTC; hothorn + Author: |- + Alan Genz [aut], + Frank Bretz [aut], + Tetsuhisa Miwa [aut], + Xuefei Mi [aut], + Friedrich Leisch [ctb], + Fabian Scheipl [ctb], + Bjoern Bornkamp [ctb] (), + Martin Maechler [ctb] (), + Torsten Hothorn [aut, cre] () + Maintainer: Torsten Hothorn + Repository: RSPM + Date/Publication: 2023-08-25 14:00:02 UTC + Encoding: UTF-8 + Built: R 4.3.1; x86_64-pc-linux-gnu; 2024-02-06 18:18:41 UTC; unix + fastmap: + Package: fastmap + Title: Fast Data Structures + Version: 1.1.1 + Authors@R: |- + c( + person("Winston", "Chang", email = "winston@rstudio.com", role = c("aut", "cre")), + person(given = "RStudio", role = c("cph", "fnd")), + person(given = "Tessil", role = "cph", comment = "hopscotch_map library") + ) + Description: |- + Fast implementation of data structures, including a key-value + store, stack, and queue. Environments are commonly used as key-value stores + in R, but every time a new key is used, it is added to R's global symbol + table, causing a small amount of memory leakage. This can be problematic in + cases where many different keys are used. Fastmap avoids this memory leak + issue by implementing the map using data structures in C++. + License: MIT + file LICENSE + Encoding: UTF-8 + RoxygenNote: 7.2.3 + Suggests: testthat (>= 2.1.1) + URL: https://r-lib.github.io/fastmap/, https://github.com/r-lib/fastmap + BugReports: https://github.com/r-lib/fastmap/issues + NeedsCompilation: 'yes' + Packaged: 2023-02-24 16:01:27 UTC; winston + Author: |- + Winston Chang [aut, cre], + RStudio [cph, fnd], + Tessil [cph] (hopscotch_map library) + Maintainer: Winston Chang + Repository: RSPM + Date/Publication: 2023-02-24 16:30:02 UTC + Built: R 4.3.1; x86_64-pc-linux-gnu; 2024-02-06 18:05:08 UTC; unix + foreach: + Package: foreach + Type: Package + Title: Provides Foreach Looping Construct + Version: 1.5.2 + Authors@R: |- + c(person("Folashade", "Daniel", role="cre", email="fdaniel@microsoft.com"), + person("Hong", "Ooi", role="ctb"), + person("Rich", "Calaway", role="ctb"), + person("Microsoft", role=c("aut", "cph")), + person("Steve", "Weston", role="aut")) + Description: |- + Support for the foreach looping construct. Foreach is an + idiom that allows for iterating over elements in a collection, + without the use of an explicit loop counter. This package in + particular is intended to be used for its return value, rather + than for its side effects. In that sense, it is similar to the + standard lapply function, but doesn't require the evaluation + of a function. Using foreach without side effects also + facilitates executing the loop in parallel. + License: Apache License (== 2.0) + URL: https://github.com/RevolutionAnalytics/foreach + BugReports: https://github.com/RevolutionAnalytics/foreach/issues + Depends: R (>= 2.5.0) + Imports: codetools, utils, iterators + Suggests: randomForest, doMC, doParallel, testthat, knitr, rmarkdown + VignetteBuilder: knitr + RoxygenNote: 7.1.1 + Collate: |- + 'callCombine.R' 'foreach.R' 'do.R' 'foreach-ext.R' + 'foreach-pkg.R' 'getDoPar.R' 'getDoSeq.R' 'getsyms.R' 'iter.R' + 'nextElem.R' 'onLoad.R' 'setDoPar.R' 'setDoSeq.R' 'times.R' + 'utils.R' + NeedsCompilation: 'no' + Packaged: 2022-01-11 04:21:12 UTC; fdaniel + Author: |- + Folashade Daniel [cre], + Hong Ooi [ctb], + Rich Calaway [ctb], + Microsoft [aut, cph], + Steve Weston [aut] + Maintainer: Folashade Daniel + Repository: RSPM + Date/Publication: 2022-02-02 09:20:02 UTC + Encoding: UTF-8 + Built: R 4.3.1; ; 2024-02-06 17:56:11 UTC; unix + rprojroot: + Package: rprojroot + Title: Finding Files in Project Subdirectories + Version: 2.0.3 + Authors@R: |2- + + person(given = "Kirill", + family = "M\u00fcller", + role = c("aut", "cre"), + email = "krlmlr+r@mailbox.org", + comment = c(ORCID = "0000-0002-1416-3412")) + Description: |- + Robust, reliable and flexible paths to files below + a project root. The 'root' of a project is defined as a directory that + matches a certain criterion, e.g., it contains a certain regular file. + License: MIT + file LICENSE + URL: https://rprojroot.r-lib.org/, https://github.com/r-lib/rprojroot + BugReports: https://github.com/r-lib/rprojroot/issues + Depends: R (>= 3.0.0) + Suggests: |- + covr, knitr, lifecycle, mockr, rmarkdown, testthat (>= + 3.0.0), withr + VignetteBuilder: knitr + Config/testthat/edition: '3' + Encoding: UTF-8 + RoxygenNote: 7.1.2 + NeedsCompilation: 'no' + Packaged: 2022-04-02 16:14:00 UTC; kirill + Author: Kirill Müller [aut, cre] () + Maintainer: Kirill Müller + Repository: RSPM + Date/Publication: 2022-04-02 16:40:02 UTC + Built: R 4.3.1; ; 2024-02-06 18:17:17 UTC; unix + Matrix: + Package: Matrix + Version: 1.6-1 + Date: '2023-08-11' + Priority: recommended + Title: Sparse and Dense Matrix Classes and Methods + Description: "A rich hierarchy of sparse and dense matrix classes,\n\tincluding + general, symmetric, triangular, and diagonal matrices\n\twith numeric, logical, + or pattern entries. Efficient methods for\n\toperating on such matrices, often + wrapping the 'BLAS', 'LAPACK',\n\tand 'SuiteSparse' libraries." + License: GPL (>= 2) | file LICENCE + URL: https://Matrix.R-forge.R-project.org + BugReports: https://R-forge.R-project.org/tracker/?atid=294&group_id=61 + Contact: Matrix-authors@R-project.org + Authors@R: "\n\tc(person(\"Douglas\", \"Bates\", role = \"aut\",\n\t comment + = c(ORCID = \"0000-0001-8316-9503\")),\n\t person(\"Martin\", \"Maechler\", + role = c(\"aut\", \"cre\"),\n\t email = \"mmaechler+Matrix@gmail.com\",\n\t + \ comment = c(ORCID = \"0000-0002-8685-9910\")),\n\t person(\"Mikael\", + \"Jagan\", role = \"aut\",\n\t comment = c(ORCID = \"0000-0002-3542-2938\")),\n\t + \ person(\"Timothy A.\", \"Davis\", role = \"ctb\",\n\t comment = c(ORCID + = \"0000-0001-7614-6899\",\n\t \"SuiteSparse libraries, + notably CHOLMOD and AMD\",\n\t \"collaborators listed in + dir(pattern=\\\"^[A-Z]+[.]txt$\\\", full.names=TRUE, system.file(\\\"doc\\\", + \\\"SuiteSparse\\\", package=\\\"Matrix\\\"))\")),\n\t person(\"Jens\", \"Oehlschlägel\", + role = \"ctb\",\n\t comment = \"initial nearPD()\"),\n\t person(\"Jason\", + \"Riedy\", role = \"ctb\",\n\t comment = c(ORCID = \"0000-0002-4345-4200\",\n\t + \ \"GNU Octave's condest() and onenormest()\",\n\t \"Copyright: + Regents of the University of California\")),\n\t person(\"R Core Team\", role + = \"ctb\",\n\t comment = \"base R's matrix implementation\"))" + Depends: R (>= 3.5.0), methods + Imports: grDevices, graphics, grid, lattice, stats, utils + Suggests: MASS, datasets, sfsmisc + Enhances: SparseM, graph + LazyData: 'no' + LazyDataNote: not possible, since we use data/*.R and our S4 classes + BuildResaveData: 'no' + Encoding: UTF-8 + NeedsCompilation: 'yes' + Packaged: 2023-08-11 10:11:59 UTC; maechler + Author: |- + Douglas Bates [aut] (), + Martin Maechler [aut, cre] (), + Mikael Jagan [aut] (), + Timothy A. Davis [ctb] (, + SuiteSparse libraries, notably CHOLMOD and AMD, collaborators + listed in dir(pattern="^[A-Z]+[.]txt$", full.names=TRUE, + system.file("doc", "SuiteSparse", package="Matrix"))), + Jens Oehlschlägel [ctb] (initial nearPD()), + Jason Riedy [ctb] (, GNU + Octave's condest() and onenormest(), Copyright: Regents of the + University of California), + R Core Team [ctb] (base R's matrix implementation) + Maintainer: Martin Maechler + Repository: RSPM + Date/Publication: 2023-08-14 07:20:02 UTC + Built: R 4.3.1; x86_64-pc-linux-gnu; 2024-02-06 17:46:39 UTC; unix + progress: + Package: progress + Title: Terminal Progress Bars + Version: 1.2.2 + Author: Gábor Csárdi [aut, cre], Rich FitzJohn [aut] + Maintainer: Gábor Csárdi + Description: |- + Configurable Progress bars, they may include percentage, + elapsed time, and/or the estimated completion time. They work in + terminals, in 'Emacs' 'ESS', 'RStudio', 'Windows' 'Rgui' and the + 'macOS' 'R.app'. The package also provides a 'C++' 'API', that works + with or without 'Rcpp'. + License: MIT + file LICENSE + LazyData: 'true' + URL: https://github.com/r-lib/progress#readme + BugReports: https://github.com/r-lib/progress/issues + Imports: hms, prettyunits, R6, crayon + Suggests: Rcpp, testthat, withr + RoxygenNote: 6.1.0 + Encoding: UTF-8 + NeedsCompilation: 'no' + Packaged: 2019-05-15 20:28:47 UTC; gaborcsardi + Repository: RSPM + Date/Publication: 2019-05-16 21:30:03 UTC + Built: R 4.3.1; ; 2024-02-06 18:41:43 UTC; unix + tidyverse: + Package: tidyverse + Title: Easily Install and Load the 'Tidyverse' + Version: 2.0.0 + Authors@R: |- + c( + person("Hadley", "Wickham", , "hadley@rstudio.com", role = c("aut", "cre")), + person("RStudio", role = c("cph", "fnd")) + ) + Description: |- + The 'tidyverse' is a set of packages that work in harmony + because they share common data representations and 'API' design. This + package is designed to make it easy to install and load multiple + 'tidyverse' packages in a single step. Learn more about the + 'tidyverse' at . + License: MIT + file LICENSE + URL: |- + https://tidyverse.tidyverse.org, + https://github.com/tidyverse/tidyverse + BugReports: https://github.com/tidyverse/tidyverse/issues + Depends: R (>= 3.3) + Imports: |- + broom (>= 1.0.3), conflicted (>= 1.2.0), cli (>= 3.6.0), + dbplyr (>= 2.3.0), dplyr (>= 1.1.0), dtplyr (>= 1.2.2), forcats + (>= 1.0.0), ggplot2 (>= 3.4.1), googledrive (>= 2.0.0), + googlesheets4 (>= 1.0.1), haven (>= 2.5.1), hms (>= 1.1.2), + httr (>= 1.4.4), jsonlite (>= 1.8.4), lubridate (>= 1.9.2), + magrittr (>= 2.0.3), modelr (>= 0.1.10), pillar (>= 1.8.1), + purrr (>= 1.0.1), ragg (>= 1.2.5), readr (>= 2.1.4), readxl (>= + 1.4.2), reprex (>= 2.0.2), rlang (>= 1.0.6), rstudioapi (>= + 0.14), rvest (>= 1.0.3), stringr (>= 1.5.0), tibble (>= 3.1.8), + tidyr (>= 1.3.0), xml2 (>= 1.3.3) + Suggests: |- + covr (>= 3.6.1), feather (>= 0.3.5), glue (>= 1.6.2), mockr + (>= 0.2.0), knitr (>= 1.41), rmarkdown (>= 2.20), testthat (>= + 3.1.6) + VignetteBuilder: knitr + Config/Needs/website: tidyverse/tidytemplate + Config/testthat/edition: '3' + Encoding: UTF-8 + RoxygenNote: 7.2.3 + NeedsCompilation: 'no' + Packaged: 2023-02-21 13:20:46 UTC; hadleywickham + Author: |- + Hadley Wickham [aut, cre], + RStudio [cph, fnd] + Maintainer: Hadley Wickham + Repository: RSPM + Date/Publication: 2023-02-22 09:20:06 UTC + Built: R 4.3.1; ; 2024-02-06 22:29:03 UTC; unix + backports: + Package: backports + Type: Package + Title: Reimplementations of Functions Introduced Since R-3.0.0 + Version: 1.4.1 + Authors@R: |- + c( + person("Michel", "Lang", NULL, "michellang@gmail.com", + role = c("cre", "aut"), comment = c(ORCID = "0000-0001-9754-0393")), + person("R Core Team", role = "aut")) + Maintainer: Michel Lang + Description: |2- + + Functions introduced or changed since R v3.0.0 are re-implemented in this + package. The backports are conditionally exported in order to let R resolve + the function name to either the implemented backport, or the respective base + version, if available. Package developers can make use of new functions or + arguments by selectively importing specific backports to + support older installations. + URL: https://github.com/r-lib/backports + BugReports: https://github.com/r-lib/backports/issues + License: GPL-2 | GPL-3 + NeedsCompilation: 'yes' + ByteCompile: 'yes' + Depends: R (>= 3.0.0) + Encoding: UTF-8 + RoxygenNote: 7.1.2 + Packaged: 2021-12-13 10:49:30 UTC; michel + Author: |- + Michel Lang [cre, aut] (), + R Core Team [aut] + Repository: RSPM + Date/Publication: 2021-12-13 11:30:02 UTC + Built: R 4.3.1; x86_64-pc-linux-gnu; 2024-02-06 18:20:58 UTC; unix + survival: + Title: Survival Analysis + Priority: recommended + Package: survival + Version: 3.5-7 + Date: '2023-08-12' + Depends: R (>= 3.5.0) + Imports: graphics, Matrix, methods, splines, stats, utils + LazyData: 'Yes' + LazyDataCompression: xz + ByteCompile: 'Yes' + Authors@R: "c(person(c(\"Terry\", \"M\"), \"Therneau\",\n email=\"therneau.terry@mayo.edu\",\n\t + \ role=c(\"aut\", \"cre\")),\n person(\"Thomas\", \"Lumley\", + role=c(\"ctb\", \"trl\"),\n\t comment=\"original S->R port and R maintainer + until 2009\"),\n\t person(\"Atkinson\", \"Elizabeth\", role=\"ctb\"),\n\t + \ person(\"Crowson\", \"Cynthia\", role=\"ctb\"))" + Description: "Contains the core survival analysis routines, including\n\t definition + of Surv objects, \n\t Kaplan-Meier and Aalen-Johansen (multi-state) curves, + Cox models,\n\t and parametric accelerated failure time models." + License: LGPL (>= 2) + URL: https://github.com/therneau/survival + NeedsCompilation: 'yes' + Packaged: 2023-08-13 13:14:48 UTC; therneau + Author: |- + Terry M Therneau [aut, cre], + Thomas Lumley [ctb, trl] (original S->R port and R maintainer until + 2009), + Atkinson Elizabeth [ctb], + Crowson Cynthia [ctb] + Maintainer: Terry M Therneau + Repository: RSPM + Date/Publication: 2023-08-14 07:10:03 UTC + Encoding: UTF-8 + Built: R 4.3.1; x86_64-pc-linux-gnu; 2024-02-06 17:49:20 UTC; unix + purrr: + Package: purrr + Title: Functional Programming Tools + Version: 1.0.2 + Authors@R: |- + c( + person("Hadley", "Wickham", , "hadley@rstudio.com", role = c("aut", "cre"), + comment = c(ORCID = "0000-0003-4757-117X")), + person("Lionel", "Henry", , "lionel@rstudio.com", role = "aut"), + person("RStudio", role = c("cph", "fnd")) + ) + Description: |- + A complete and consistent functional programming toolkit for + R. + License: MIT + file LICENSE + URL: https://purrr.tidyverse.org/, https://github.com/tidyverse/purrr + BugReports: https://github.com/tidyverse/purrr/issues + Depends: R (>= 3.5.0) + Imports: |- + cli (>= 3.6.1), lifecycle (>= 1.0.3), magrittr (>= 1.5.0), + rlang (>= 1.1.1), vctrs (>= 0.6.3) + Suggests: |- + covr, dplyr (>= 0.7.8), httr, knitr, lubridate, rmarkdown, + testthat (>= 3.0.0), tibble, tidyselect + LinkingTo: cli + VignetteBuilder: knitr + Biarch: 'true' + Config/Needs/website: tidyverse/tidytemplate, tidyr + Config/testthat/edition: '3' + Encoding: UTF-8 + RoxygenNote: 7.2.3 + NeedsCompilation: 'yes' + Packaged: 2023-08-08 16:13:31 UTC; hadleywickham + Author: |- + Hadley Wickham [aut, cre] (), + Lionel Henry [aut], + RStudio [cph, fnd] + Maintainer: Hadley Wickham + Repository: RSPM + Date/Publication: 2023-08-10 08:20:07 UTC + Built: R 4.3.1; x86_64-pc-linux-gnu; 2024-02-06 18:02:05 UTC; unix + fansi: + Package: fansi + Title: ANSI Control Sequence Aware String Functions + Description: |- + Counterparts to R string manipulation functions that account for + the effects of ANSI text formatting control sequences. + Version: 1.0.4 + Authors@R: |- + c( + person("Brodie", "Gaslam", email="brodie.gaslam@yahoo.com", + role=c("aut", "cre")), + person("Elliott", "Sales De Andrade", role="ctb"), + person(family="R Core Team", + email="R-core@r-project.org", role="cph", + comment="UTF8 byte length calcs from src/util.c" + )) + Depends: R (>= 3.1.0) + License: GPL-2 | GPL-3 + URL: https://github.com/brodieG/fansi + BugReports: https://github.com/brodieG/fansi/issues + VignetteBuilder: knitr + Suggests: unitizer, knitr, rmarkdown + Imports: grDevices, utils + RoxygenNote: 7.1.1 + Encoding: UTF-8 + Collate: |- + 'constants.R' 'fansi-package.R' 'internal.R' 'load.R' 'misc.R' + 'nchar.R' 'strwrap.R' 'strtrim.R' 'strsplit.R' 'substr2.R' + 'trimws.R' 'tohtml.R' 'unhandled.R' 'normalize.R' 'sgr.R' + NeedsCompilation: 'yes' + Packaged: 2023-01-22 17:39:01 UTC; bg + Author: |- + Brodie Gaslam [aut, cre], + Elliott Sales De Andrade [ctb], + R Core Team [cph] (UTF8 byte length calcs from src/util.c) + Maintainer: Brodie Gaslam + Repository: RSPM + Date/Publication: 2023-01-22 19:20:02 UTC + Built: R 4.3.1; x86_64-pc-linux-gnu; 2024-02-06 17:54:37 UTC; unix + scales: + Package: scales + Title: Scale Functions for Visualization + Version: 1.2.1 + Authors@R: |- + c( + person("Hadley", "Wickham", , "hadley@rstudio.com", role = c("aut", "cre")), + person("Dana", "Seidel", role = "aut"), + person("RStudio", role = c("cph", "fnd")) + ) + Description: |- + Graphical scales map data to aesthetics, and provide methods + for automatically determining breaks and labels for axes and legends. + License: MIT + file LICENSE + URL: https://scales.r-lib.org, https://github.com/r-lib/scales + BugReports: https://github.com/r-lib/scales/issues + Depends: R (>= 3.2) + Imports: |- + farver (>= 2.0.3), labeling, lifecycle, munsell (>= 0.5), R6, + RColorBrewer, rlang (>= 1.0.0), viridisLite + Suggests: |- + bit64, covr, dichromat, ggplot2, hms (>= 0.5.0), stringi, + testthat (>= 3.0.0), waldo (>= 0.4.0) + Config/Needs/website: tidyverse/tidytemplate + Encoding: UTF-8 + LazyLoad: 'yes' + RoxygenNote: 7.2.1 + Config/testthat/edition: '3' + NeedsCompilation: 'no' + Packaged: 2022-08-19 15:35:49 UTC; hadleywickham + Author: |- + Hadley Wickham [aut, cre], + Dana Seidel [aut], + RStudio [cph, fnd] + Maintainer: Hadley Wickham + Repository: RSPM + Date/Publication: 2022-08-20 00:10:11 UTC + Built: R 4.3.1; ; 2024-02-06 17:54:30 UTC; unix + codetools: + Package: codetools + Version: 0.2-19 + Priority: recommended + Author: Luke Tierney + Description: Code analysis tools for R. + Title: Code Analysis Tools for R + Depends: R (>= 2.1) + Maintainer: Luke Tierney + URL: https://gitlab.com/luke-tierney/codetools + License: GPL + NeedsCompilation: 'no' + Packaged: 2023-01-31 19:16:51 UTC; luke + Repository: RSPM + Date/Publication: 2023-02-01 13:21:59 UTC + Encoding: UTF-8 + Built: R 4.3.1; ; 2024-02-06 17:49:16 UTC; unix + AIPW: + Package: AIPW + Title: Augmented Inverse Probability Weighting + Version: 0.6.3.2 + Authors@R: |2- + + c(person(given = "Yongqi", + family = "Zhong", + role = c("aut", "cre"), + email = "yq.zhong7@gmail.com", + comment = c(ORCID = "0000-0002-4042-7450")), + person(given = "Ashley", + family = "Naimi", + role = c("aut"), + email = "ashley.naimi@emory.edu", + comment = c(ORCID = "0000-0002-1510-8175")), + person(given = "Gabriel", + family = "Conzuelo", + role = c("ctb"), + email = "gabriel.conzuelo@pitt.edu"), + person(given = "Edward", + family = "Kennedy", + role = c("ctb"), + email = "edward@stat.cmu.edu")) + Maintainer: Yongqi Zhong + Description: 'The ''AIPW'' pacakge implements the augmented inverse probability + weighting, a doubly robust estimator, for average causal effect estimation with + user-defined stacked machine learning algorithms. To cite the ''AIPW'' package, + please use: "Yongqi Zhong, Edward H. Kennedy, Lisa M. Bodnar, Ashley I. Naimi + (2021, In Press). AIPW: An R Package for Augmented Inverse Probability Weighted + Estimation of Average Causal Effects. American Journal of Epidemiology". Visit: + for more information.' + License: GPL-3 + Encoding: UTF-8 + Language: es + LazyData: 'true' + Suggests: testthat (>= 2.1.0), knitr, rmarkdown, covr, tmle + RoxygenNote: 7.1.0 + Imports: |- + stats, utils, R6, SuperLearner, ggplot2, future.apply, + progressr, Rsolnp + URL: https://github.com/yqzhong7/AIPW + BugReports: https://github.com/yqzhong7/AIPW/issues + VignetteBuilder: knitr + Depends: R (>= 2.10) + NeedsCompilation: 'no' + Packaged: 2021-06-10 14:44:41 UTC; k + Author: |- + Yongqi Zhong [aut, cre] (), + Ashley Naimi [aut] (), + Gabriel Conzuelo [ctb], + Edward Kennedy [ctb] + Repository: RSPM + Date/Publication: 2021-06-11 09:30:02 UTC + Built: R 4.3.1; ; 2024-02-06 23:35:19 UTC; unix + cli: + Package: cli + Title: Helpers for Developing Command Line Interfaces + Version: 3.6.1 + Authors@R: |- + c( + person("Gábor", "Csárdi", , "csardi.gabor@gmail.com", role = c("aut", "cre")), + person("Hadley", "Wickham", role = "ctb"), + person("Kirill", "Müller", role = "ctb"), + person("RStudio", role = c("cph", "fnd")) + ) + Description: |- + A suite of tools to build attractive command line interfaces + ('CLIs'), from semantic elements: headings, lists, alerts, paragraphs, + etc. Supports custom themes via a 'CSS'-like language. It also + contains a number of lower level 'CLI' elements: rules, boxes, trees, + and 'Unicode' symbols with 'ASCII' alternatives. It support ANSI + colors and text styles as well. + License: MIT + file LICENSE + URL: https://cli.r-lib.org, https://github.com/r-lib/cli#readme + BugReports: https://github.com/r-lib/cli/issues + Depends: R (>= 3.4) + Imports: utils + Suggests: |- + callr, covr, crayon, digest, glue (>= 1.6.0), grDevices, + htmltools, htmlwidgets, knitr, methods, mockery, processx, ps + (>= 1.3.4.9000), rlang (>= 1.0.2.9003), rmarkdown, rprojroot, + rstudioapi, testthat, tibble, whoami, withr + Config/Needs/website: |- + r-lib/asciicast, bench, brio, cpp11, decor, desc, + fansi, prettyunits, sessioninfo, tidyverse/tidytemplate, + usethis, vctrs + Config/testthat/edition: '3' + Encoding: UTF-8 + RoxygenNote: 7.2.1.9000 + NeedsCompilation: 'yes' + Packaged: 2023-03-22 13:59:32 UTC; gaborcsardi + Author: |- + Gábor Csárdi [aut, cre], + Hadley Wickham [ctb], + Kirill Müller [ctb], + RStudio [cph, fnd] + Maintainer: Gábor Csárdi + Repository: RSPM + Date/Publication: 2023-03-23 12:52:05 UTC + Built: R 4.3.1; x86_64-pc-linux-gnu; 2024-02-06 17:53:03 UTC; unix + crayon: + Package: crayon + Title: Colored Terminal Output + Version: 1.5.2 + Authors@R: |- + c( + person("Gábor", "Csárdi", , "csardi.gabor@gmail.com", + role = c("aut", "cre")), + person( + "Brodie", "Gaslam", email="brodie.gaslam@yahoo.com", + role=c("ctb")) + ) + Description: |- + The crayon package is now superseded. Please use the 'cli' package + for new projects. + Colored terminal output on terminals that support 'ANSI' + color and highlight codes. It also works in 'Emacs' 'ESS'. 'ANSI' + color support is automatically detected. Colors and highlighting can + be combined and nested. New styles can also be created easily. + This package was inspired by the 'chalk' 'JavaScript' project. + License: MIT + file LICENSE + URL: https://github.com/r-lib/crayon#readme + BugReports: https://github.com/r-lib/crayon/issues + Collate: |- + 'aaa-rstudio-detect.R' 'aaaa-rematch2.R' + 'aab-num-ansi-colors.R' 'aac-num-ansi-colors.R' 'ansi-256.r' + 'ansi-palette.R' 'combine.r' 'string.r' 'utils.r' + 'crayon-package.r' 'disposable.r' 'enc-utils.R' 'has_ansi.r' + 'has_color.r' 'link.R' 'styles.r' 'machinery.r' 'parts.r' + 'print.r' 'style-var.r' 'show.r' 'string_operations.r' + Imports: grDevices, methods, utils + Suggests: mockery, rstudioapi, testthat, withr + RoxygenNote: 7.1.2 + Encoding: UTF-8 + NeedsCompilation: 'no' + Packaged: 2022-09-29 06:24:10 UTC; gaborcsardi + Author: |- + Gábor Csárdi [aut, cre], + Brodie Gaslam [ctb] + Maintainer: Gábor Csárdi + Repository: RSPM + Date/Publication: 2022-09-29 16:20:24 UTC + Built: R 4.3.1; ; 2024-02-06 18:17:26 UTC; unix + rlang: + Package: rlang + Version: 1.1.1 + Title: Functions for Base Types and Core R and 'Tidyverse' Features + Description: |- + A toolbox for working with base types, core R features + like the condition system, and core 'Tidyverse' features like tidy + evaluation. + Authors@R: "c(\n person(\"Lionel\", \"Henry\", ,\"lionel@posit.co\", c(\"aut\", + \"cre\")),\n person(\"Hadley\", \"Wickham\", ,\"hadley@posit.co\", \"aut\"),\n + \ person(given = \"mikefc\",\n email = \"mikefc@coolbutuseless.com\", + \n role = \"cph\", \n comment = \"Hash implementation based + on Mike's xxhashlite\"),\n person(given = \"Yann\",\n family = + \"Collet\",\n role = \"cph\", \n comment = \"Author of the + embedded xxHash library\"),\n person(given = \"Posit, PBC\", role = c(\"cph\", + \"fnd\"))\n )" + License: MIT + file LICENSE + ByteCompile: 'true' + Biarch: 'true' + Depends: R (>= 3.5.0) + Imports: utils + Suggests: |- + cli (>= 3.1.0), covr, crayon, fs, glue, knitr, magrittr, + methods, pillar, rmarkdown, stats, testthat (>= 3.0.0), tibble, + usethis, vctrs (>= 0.2.3), withr + Enhances: winch + Encoding: UTF-8 + RoxygenNote: 7.2.3 + URL: https://rlang.r-lib.org, https://github.com/r-lib/rlang + BugReports: https://github.com/r-lib/rlang/issues + Config/testthat/edition: '3' + Config/Needs/website: dplyr, tidyverse/tidytemplate + NeedsCompilation: 'yes' + Packaged: 2023-04-28 10:48:43 UTC; lionel + Author: |- + Lionel Henry [aut, cre], + Hadley Wickham [aut], + mikefc [cph] (Hash implementation based on Mike's xxhashlite), + Yann Collet [cph] (Author of the embedded xxHash library), + Posit, PBC [cph, fnd] + Maintainer: Lionel Henry + Repository: RSPM + Date/Publication: 2023-04-28 22:30:03 UTC + Built: R 4.3.1; x86_64-pc-linux-gnu; 2024-02-06 17:53:22 UTC; unix + munsell: + Package: munsell + Type: Package + Title: Utilities for Using Munsell Colours + Version: 0.5.0 + Author: Charlotte Wickham + Maintainer: Charlotte Wickham + Description: "Provides easy access to, and manipulation of, the Munsell \n colours. + Provides a mapping between Munsell's \n original notation (e.g. \"5R 5/10\") + and hexadecimal strings suitable \n for use directly in R graphics. Also + provides utilities \n to explore slices through the Munsell colour tree, + to transform \n Munsell colours and display colour palettes." + Suggests: ggplot2, testthat + Imports: colorspace, methods + License: MIT + file LICENSE + URL: |- + https://cran.r-project.org/package=munsell, + https://github.com/cwickham/munsell/ + RoxygenNote: 6.0.1 + NeedsCompilation: 'no' + Packaged: 2018-06-11 23:15:15 UTC; wickhamc + Repository: RSPM + Date/Publication: 2018-06-12 04:29:06 UTC + Encoding: UTF-8 + Built: R 4.3.1; ; 2024-02-06 17:54:20 UTC; unix + splines: + Package: splines + Version: 4.3.1 + Priority: base + Imports: graphics, stats + Title: Regression Spline Functions and Classes + Author: |- + Douglas M. Bates and + William N. Venables + Maintainer: R Core Team + Contact: R-help mailing list + Description: Regression spline functions and classes. + License: Part of R 4.3.1 + Suggests: Matrix, methods + NeedsCompilation: 'yes' + Built: R 4.3.1; x86_64-pc-linux-gnu; 2024-02-06 17:44:27 UTC; unix + withr: + Package: withr + Title: Run Code 'With' Temporarily Modified Global State + Version: 2.5.0 + Authors@R: |2- + + c(person(given = "Jim", + family = "Hester", + role = "aut"), + person(given = "Lionel", + family = "Henry", + role = c("aut", "cre"), + email = "lionel@rstudio.com"), + person(given = "Kirill", + family = "Müller", + role = "aut", + email = "krlmlr+r@mailbox.org"), + person(given = "Kevin", + family = "Ushey", + role = "aut", + email = "kevinushey@gmail.com"), + person(given = "Hadley", + family = "Wickham", + role = "aut", + email = "hadley@rstudio.com"), + person(given = "Winston", + family = "Chang", + role = "aut"), + person(given = "Jennifer", + family = "Bryan", + role = "ctb"), + person(given = "Richard", + family = "Cotton", + role = "ctb"), + person(given = "RStudio", + role = c("cph", "fnd"))) + Description: |- + A set of functions to run code 'with' safely and + temporarily modified global state. Many of these functions were + originally a part of the 'devtools' package, this provides a simple + package with limited dependencies to provide access to these + functions. + License: MIT + file LICENSE + URL: https://withr.r-lib.org, https://github.com/r-lib/withr#readme + BugReports: https://github.com/r-lib/withr/issues + Depends: R (>= 3.2.0) + Imports: graphics, grDevices, stats + Suggests: |- + callr, covr, DBI, knitr, lattice, methods, rlang, rmarkdown + (>= 2.12), RSQLite, testthat (>= 3.0.0) + VignetteBuilder: knitr + Encoding: UTF-8 + RoxygenNote: 7.1.2 + Collate: |- + 'aaa.R' 'collate.R' 'compat-defer.R' 'connection.R' 'db.R' + 'defer.R' 'wrap.R' 'local_.R' 'with_.R' 'devices.R' 'dir.R' + 'env.R' 'file.R' 'language.R' 'libpaths.R' 'locale.R' + 'makevars.R' 'namespace.R' 'options.R' 'par.R' 'path.R' 'rng.R' + 'seed.R' 'sink.R' 'tempfile.R' 'timezone.R' 'torture.R' + 'utils.R' 'with.R' + Config/testthat/edition: '3' + Config/Needs/website: tidyverse/tidytemplate + NeedsCompilation: 'no' + Packaged: 2022-03-03 21:13:01 UTC; lionel + Author: |- + Jim Hester [aut], + Lionel Henry [aut, cre], + Kirill Müller [aut], + Kevin Ushey [aut], + Hadley Wickham [aut], + Winston Chang [aut], + Jennifer Bryan [ctb], + Richard Cotton [ctb], + RStudio [cph, fnd] + Maintainer: Lionel Henry + Repository: RSPM + Date/Publication: 2022-03-03 21:50:02 UTC + Built: R 4.3.1; ; 2024-02-06 17:55:32 UTC; unix + yaml: + Package: yaml + Type: Package + Title: Methods to Convert R Data to YAML and Back + Date: '2023-01-18' + Version: 2.3.7 + Suggests: RUnit + Author: |- + Shawn P Garbett [aut], Jeremy Stephens [aut, cre], Kirill Simonov [aut], Yihui Xie [ctb], + Zhuoer Dong [ctb], Hadley Wickham [ctb], Jeffrey Horner [ctb], reikoch [ctb], + Will Beasley [ctb], Brendan O'Connor [ctb], Gregory R. Warnes [ctb], + Michael Quinn [ctb], Zhian N. Kamvar [ctb] + Maintainer: Shawn Garbett + License: BSD_3_clause + file LICENSE + Description: |- + Implements the 'libyaml' 'YAML' 1.1 parser and emitter + () for R. + URL: https://github.com/vubiostat/r-yaml/ + BugReports: https://github.com/vubiostat/r-yaml/issues + NeedsCompilation: 'yes' + Packaged: 2023-01-18 17:20:16 UTC; garbetsp + Repository: RSPM + Date/Publication: 2023-01-23 18:40:02 UTC + Encoding: UTF-8 + Built: R 4.3.1; x86_64-pc-linux-gnu; 2024-02-06 18:05:26 UTC; unix + tools: + Package: tools + Version: 4.3.1 + Priority: base + Title: Tools for Package Development + Author: R Core Team + Maintainer: R Core Team + Contact: R-help mailing list + Description: Tools for package development, administration and documentation. + License: Part of R 4.3.1 + Suggests: codetools, methods, xml2, curl, commonmark, knitr, xfun, mathjaxr, V8 + NeedsCompilation: 'yes' + Built: R 4.3.1; x86_64-pc-linux-gnu; 2024-02-06 17:43:09 UTC; unix + colorspace: + Package: colorspace + Version: 2.1-0 + Date: '2023-01-23' + Title: A Toolbox for Manipulating and Assessing Colors and Palettes + Authors@R: "c(person(given = \"Ross\", family = \"Ihaka\", role = \"aut\", email + = \"ihaka@stat.auckland.ac.nz\"),\n person(given = \"Paul\", family + = \"Murrell\", role = \"aut\", email = \"paul@stat.auckland.ac.nz\",\n comment + = c(ORCID = \"0000-0002-3224-8858\")),\n person(given = \"Kurt\", + family = \"Hornik\", role = \"aut\", email = \"Kurt.Hornik@R-project.org\",\n\t\t + \ comment = c(ORCID = \"0000-0003-4198-9911\")),\n person(given + = c(\"Jason\", \"C.\"), family = \"Fisher\", role = \"aut\", email = \"jfisher@usgs.gov\",\n + \ comment = c(ORCID = \"0000-0001-9032-8912\")),\n person(given + = \"Reto\", family = \"Stauffer\", role = \"aut\", email = \"Reto.Stauffer@uibk.ac.at\",\n + \ comment = c(ORCID = \"0000-0002-3798-5507\")),\n person(given + = c(\"Claus\", \"O.\"), family = \"Wilke\", role = \"aut\", email = \"wilke@austin.utexas.edu\",\n + \ comment = c(ORCID = \"0000-0002-7470-9261\")),\n person(given + = c(\"Claire\", \"D.\"), family = \"McWhite\", role = \"aut\", email = \"claire.mcwhite@utmail.utexas.edu\",\n + \ comment = c(ORCID = \"0000-0001-7346-3047\")),\n person(given + = \"Achim\", family = \"Zeileis\", role = c(\"aut\", \"cre\"), email = \"Achim.Zeileis@R-project.org\",\n + \ comment = c(ORCID = \"0000-0003-0918-3766\")))" + Description: "Carries out mapping between assorted color spaces including RGB, + HSV, HLS,\n CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB, and polar + CIELAB.\n\t Qualitative, sequential, and diverging color palettes based + on HCL colors\n\t are provided along with corresponding ggplot2 color scales.\n\t + \ Color palette choice is aided by an interactive app (with either a Tcl/Tk\n\t + \ or a shiny graphical user interface) and shiny apps with an HCL color picker + and a\n\t color vision deficiency emulator. Plotting functions for displaying\n\t + \ and assessing palettes include color swatches, visualizations of the\n\t + \ HCL space, and trajectories in HCL and/or RGB spectrum. Color manipulation\n\t + \ functions include: desaturation, lightening/darkening, mixing, and\n\t + \ simulation of color vision deficiencies (deutanomaly, protanomaly, tritanomaly).\n\t + \ Details can be found on the project web page at \n\t + \ and in the accompanying scientific paper: Zeileis et al. (2020, Journal + of Statistical\n\t Software, )." + Depends: R (>= 3.0.0), methods + Imports: graphics, grDevices, stats + Suggests: |- + datasets, utils, KernSmooth, MASS, kernlab, mvtnorm, vcd, + tcltk, shiny, shinyjs, ggplot2, dplyr, scales, grid, png, jpeg, + knitr, rmarkdown, RColorBrewer, rcartocolor, scico, viridis, + wesanderson + VignetteBuilder: knitr + License: BSD_3_clause + file LICENSE + URL: https://colorspace.R-Forge.R-project.org/, https://hclwizard.org/ + BugReports: https://colorspace.R-Forge.R-project.org/contact.html + LazyData: 'yes' + Encoding: UTF-8 + RoxygenNote: 7.2.3 + NeedsCompilation: 'yes' + Packaged: 2023-01-23 08:50:11 UTC; zeileis + Author: |- + Ross Ihaka [aut], + Paul Murrell [aut] (), + Kurt Hornik [aut] (), + Jason C. Fisher [aut] (), + Reto Stauffer [aut] (), + Claus O. Wilke [aut] (), + Claire D. McWhite [aut] (), + Achim Zeileis [aut, cre] () + Maintainer: Achim Zeileis + Repository: RSPM + Date/Publication: 2023-01-23 11:40:02 UTC + Built: R 4.3.1; x86_64-pc-linux-gnu; 2024-02-06 17:54:12 UTC; unix + here: + Package: here + Title: A Simpler Way to Find Your Files + Version: 1.0.1 + Date: '2020-12-13' + Authors@R: |2- + + c(person(given = "Kirill", + family = "M\u00fcller", + role = c("aut", "cre"), + email = "krlmlr+r@mailbox.org", + comment = c(ORCID = "0000-0002-1416-3412")), + person(given = "Jennifer", + family = "Bryan", + role = "ctb", + email = "jenny@rstudio.com", + comment = c(ORCID = "0000-0002-6983-2759"))) + Description: |- + Constructs paths to your project's files. + Declare the relative path of a file within your project with 'i_am()'. + Use the 'here()' function as a drop-in replacement for 'file.path()', + it will always locate the files relative to your project root. + License: MIT + file LICENSE + URL: https://here.r-lib.org/, https://github.com/r-lib/here + BugReports: https://github.com/r-lib/here/issues + Imports: rprojroot (>= 2.0.2) + Suggests: |- + conflicted, covr, fs, knitr, palmerpenguins, plyr, readr, + rlang, rmarkdown, testthat, uuid, withr + VignetteBuilder: knitr + Encoding: UTF-8 + LazyData: 'true' + RoxygenNote: 7.1.1.9000 + Config/testthat/edition: '3' + NeedsCompilation: 'no' + Packaged: 2020-12-13 06:59:33 UTC; kirill + Author: |- + Kirill Müller [aut, cre] (), + Jennifer Bryan [ctb] () + Maintainer: Kirill Müller + Repository: RSPM + Date/Publication: 2020-12-13 07:30:02 UTC + Built: R 4.3.1; ; 2024-02-06 20:00:45 UTC; unix + broom: + Type: Package + Package: broom + Title: Convert Statistical Objects into Tidy Tibbles + Version: 1.0.5 + Authors@R: "\n c(person(given = \"David\",\n family = \"Robinson\",\n + \ role = \"aut\",\n email = \"admiral.david@gmail.com\"),\n + \ person(given = \"Alex\",\n family = \"Hayes\",\n role + = \"aut\",\n email = \"alexpghayes@gmail.com\",\n comment + = c(ORCID = \"0000-0002-4985-5160\")),\n person(given = \"Simon\",\n family + = \"Couch\",\n role = c(\"aut\", \"cre\"),\n email = + \"simon.couch@posit.co\",\n comment = c(ORCID = \"0000-0001-5676-5107\")),\n + \ person(given = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")),\n + \ person(given = \"Indrajeet\",\n family = \"Patil\",\n role + = \"ctb\",\n email = \"patilindrajeet.science@gmail.com\",\n comment + = c(ORCID = \"0000-0003-1995-6531\")),\n person(given = \"Derek\",\n family + = \"Chiu\",\n role = \"ctb\",\n email = \"dchiu@bccrc.ca\"),\n + \ person(given = \"Matthieu\",\n family = \"Gomez\",\n role + = \"ctb\",\n email = \"mattg@princeton.edu\"),\n person(given + = \"Boris\",\n family = \"Demeshev\",\n role = \"ctb\",\n + \ email = \"boris.demeshev@gmail.com\"),\n person(given = \"Dieter\",\n + \ family = \"Menne\",\n role = \"ctb\",\n email + = \"dieter.menne@menne-biomed.de\"),\n person(given = \"Benjamin\",\n family + = \"Nutter\",\n role = \"ctb\",\n email = \"nutter@battelle.org\"),\n + \ person(given = \"Luke\",\n family = \"Johnston\",\n role + = \"ctb\",\n email = \"luke.johnston@mail.utoronto.ca\"),\n person(given + = \"Ben\",\n family = \"Bolker\",\n role = \"ctb\",\n + \ email = \"bolker@mcmaster.ca\"),\n person(given = \"Francois\",\n + \ family = \"Briatte\",\n role = \"ctb\",\n email + = \"f.briatte@gmail.com\"),\n person(given = \"Jeffrey\",\n family + = \"Arnold\",\n role = \"ctb\",\n email = \"jeffrey.arnold@gmail.com\"),\n + \ person(given = \"Jonah\",\n family = \"Gabry\",\n role + = \"ctb\",\n email = \"jsg2201@columbia.edu\"),\n person(given + = \"Luciano\",\n family = \"Selzer\",\n role = \"ctb\",\n + \ email = \"luciano.selzer@gmail.com\"),\n person(given = \"Gavin\",\n + \ family = \"Simpson\",\n role = \"ctb\",\n email + = \"ucfagls@gmail.com\"),\n person(given = \"Jens\",\n family + = \"Preussner\",\n role = \"ctb\",\n email = \" jens.preussner@mpi-bn.mpg.de\"),\n + \ person(given = \"Jay\",\n family = \"Hesselberth\",\n role + = \"ctb\",\n email = \"jay.hesselberth@gmail.com\"),\n person(given + = \"Hadley\",\n family = \"Wickham\",\n role = \"ctb\",\n + \ email = \"hadley@posit.co\"),\n person(given = \"Matthew\",\n + \ family = \"Lincoln\",\n role = \"ctb\",\n email + = \"matthew.d.lincoln@gmail.com\"),\n person(given = \"Alessandro\",\n + \ family = \"Gasparini\",\n role = \"ctb\",\n email + = \"ag475@leicester.ac.uk\"),\n person(given = \"Lukasz\",\n family + = \"Komsta\",\n role = \"ctb\",\n email = \"lukasz.komsta@umlub.pl\"),\n + \ person(given = \"Frederick\",\n family = \"Novometsky\",\n + \ role = \"ctb\"),\n person(given = \"Wilson\",\n family + = \"Freitas\",\n role = \"ctb\"),\n person(given = \"Michelle\",\n + \ family = \"Evans\",\n role = \"ctb\"),\n person(given + = \"Jason Cory\",\n family = \"Brunson\",\n role = \"ctb\",\n + \ email = \"cornelioid@gmail.com\"),\n person(given = \"Simon\",\n + \ family = \"Jackson\",\n role = \"ctb\",\n email + = \"drsimonjackson@gmail.com\"),\n person(given = \"Ben\",\n family + = \"Whalley\",\n role = \"ctb\",\n email = \"ben.whalley@plymouth.ac.uk\"),\n + \ person(given = \"Karissa\",\n family = \"Whiting\",\n role + = \"ctb\",\n email = \"karissa.whiting@gmail.com\"),\n person(given + = \"Yves\",\n family = \"Rosseel\",\n role = \"ctb\",\n + \ email = \"yrosseel@gmail.com\"),\n person(given = \"Michael\",\n + \ family = \"Kuehn\",\n role = \"ctb\",\n email + = \"mkuehn10@gmail.com\"),\n person(given = \"Jorge\",\n family + = \"Cimentada\",\n role = \"ctb\",\n email = \"cimentadaj@gmail.com\"),\n + \ person(given = \"Erle\",\n family = \"Holgersen\",\n role + = \"ctb\",\n email = \"erle.holgersen@gmail.com\"),\n person(given + = \"Karl\",\n family = \"Dunkle Werner\",\n role = \"ctb\",\n + \ comment = c(ORCID = \"0000-0003-0523-7309\")),\n person(given + = \"Ethan\",\n family = \"Christensen\",\n role = \"ctb\",\n + \ email = \"christensen.ej@gmail.com\"),\n person(given = \"Steven\",\n + \ family = \"Pav\",\n role = \"ctb\",\n email + = \"shabbychef@gmail.com\"),\n person(given = \"Paul\",\n family + = \"PJ\",\n role = \"ctb\",\n email = \"pjpaul.stephens@gmail.com\"),\n + \ person(given = \"Ben\",\n family = \"Schneider\",\n role + = \"ctb\",\n email = \"benjamin.julius.schneider@gmail.com\"),\n + \ person(given = \"Patrick\",\n family = \"Kennedy\",\n role + = \"ctb\",\n email = \"pkqstr@protonmail.com\"),\n person(given + = \"Lily\",\n family = \"Medina\",\n role = \"ctb\",\n + \ email = \"lilymiru@gmail.com\"),\n person(given = \"Brian\",\n + \ family = \"Fannin\",\n role = \"ctb\",\n email + = \"captain@pirategrunt.com\"),\n person(given = \"Jason\",\n family + = \"Muhlenkamp\",\n role = \"ctb\",\n email = \"jason.muhlenkamp@gmail.com\"),\n + \ person(given = \"Matt\",\n family = \"Lehman\",\n role + = \"ctb\"),\n person(given = \"Bill\",\n family = \"Denney\",\n + \ role = \"ctb\",\n email = \"wdenney@humanpredictions.com\",\n + \ comment = c(ORCID = \"0000-0002-5759-428X\")),\n person(given + = \"Nic\",\n family = \"Crane\",\n role = \"ctb\"),\n + \ person(given = \"Andrew\",\n family = \"Bates\",\n role + = \"ctb\"),\n person(given = \"Vincent\",\n family = \"Arel-Bundock\",\n + \ role = \"ctb\",\n email = \"vincent.arel-bundock@umontreal.ca\",\n + \ comment = c(ORCID = \"0000-0003-2042-7063\")),\n person(given + = \"Hideaki\",\n family = \"Hayashi\",\n role = \"ctb\"),\n + \ person(given = \"Luis\",\n family = \"Tobalina\",\n role + = \"ctb\"),\n person(given = \"Annie\",\n family = \"Wang\",\n + \ role = \"ctb\",\n email = \"anniewang.uc@gmail.com\"),\n + \ person(given = \"Wei Yang\",\n family = \"Tham\",\n role + = \"ctb\",\n email = \"weiyang.tham@gmail.com\"),\n person(given + = \"Clara\",\n family = \"Wang\",\n role = \"ctb\",\n + \ email = \"clara.wang.94@gmail.com\"),\n person(given = \"Abby\",\n + \ family = \"Smith\",\n role = \"ctb\",\n email + = \"als1@u.northwestern.edu\",\n comment = c(ORCID = \"0000-0002-3207-0375\")),\n + \ person(given = \"Jasper\",\n family = \"Cooper\",\n role + = \"ctb\",\n email = \"jaspercooper@gmail.com\",\n comment + = c(ORCID = \"0000-0002-8639-3188\")),\n person(given = \"E Auden\",\n + \ family = \"Krauska\",\n role = \"ctb\",\n email + = \"krauskae@gmail.com\",\n comment = c(ORCID = \"0000-0002-1466-5850\")),\n + \ person(given = \"Alex\",\n family = \"Wang\",\n role + = \"ctb\",\n email = \"x249wang@uwaterloo.ca\"),\n person(given + = \"Malcolm\",\n family = \"Barrett\",\n role = \"ctb\",\n + \ email = \"malcolmbarrett@gmail.com\",\n comment = c(ORCID + = \"0000-0003-0299-5825\")),\n person(given = \"Charles\",\n family + = \"Gray\",\n role = \"ctb\",\n email = \"charlestigray@gmail.com\",\n + \ comment = c(ORCID = \"0000-0002-9978-011X\")),\n person(given + = \"Jared\",\n family = \"Wilber\",\n role = \"ctb\"),\n + \ person(given = \"Vilmantas\",\n family = \"Gegzna\",\n role + = \"ctb\",\n email = \"GegznaV@gmail.com\",\n comment + = c(ORCID = \"0000-0002-9500-5167\")),\n person(given = \"Eduard\",\n family + = \"Szoecs\",\n role = \"ctb\",\n email = \"eduardszoecs@gmail.com\"),\n + \ person(given = \"Frederik\",\n family = \"Aust\",\n role + = \"ctb\",\n email = \"frederik.aust@uni-koeln.de\",\n comment + = c(ORCID = \"0000-0003-4900-788X\")),\n person(given = \"Angus\",\n family + = \"Moore\",\n role = \"ctb\",\n email = \"angusmoore9@gmail.com\"),\n + \ person(given = \"Nick\",\n family = \"Williams\",\n role + = \"ctb\",\n email = \"ntwilliams.personal@gmail.com\"),\n person(given + = \"Marius\",\n family = \"Barth\",\n role = \"ctb\",\n + \ email = \"marius.barth.uni.koeln@gmail.com\",\n comment + = c(ORCID = \"0000-0002-3421-6665\")),\n person(given = \"Bruna\",\n family + = \"Wundervald\",\n role = \"ctb\",\n email = \"brunadaviesw@gmail.com\",\n + \ comment = c(ORCID = \"0000-0001-8163-220X\")),\n person(given + = \"Joyce\",\n family = \"Cahoon\",\n role = \"ctb\",\n + \ email = \"joyceyu48@gmail.com\",\n comment = c(ORCID + = \"0000-0001-7217-4702\")),\n person(given = \"Grant\",\n family + = \"McDermott\",\n role = \"ctb\",\n email = \"grantmcd@uoregon.edu\",\n + \ comment = c(ORCID = \"0000-0001-7883-8573\")),\n person(given + = \"Kevin\",\n family = \"Zarca\",\n role = \"ctb\",\n + \ email = \"kevin.zarca@gmail.com\"),\n person(given = \"Shiro\",\n + \ family = \"Kuriwaki\",\n role = \"ctb\",\n email + = \"shirokuriwaki@gmail.com\",\n comment = c(ORCID = \"0000-0002-5687-2647\")),\n + \ person(given = \"Lukas\",\n family = \"Wallrich\",\n role + = \"ctb\",\n email = \"lukas.wallrich@gmail.com\",\n comment + = c(ORCID = \"0000-0003-2121-5177\")),\n person(given = \"James\",\n family + = \"Martherus\",\n role = \"ctb\",\n email = \"james@martherus.com\",\n + \ comment = c(ORCID = \"0000-0002-8285-3300\")),\n person(given + = \"Chuliang\",\n family = \"Xiao\",\n role = \"ctb\",\n + \ email = \"cxiao@umich.edu\",\n comment = c(ORCID = + \"0000-0002-8466-9398\")),\n person(given = \"Joseph\",\n family + = \"Larmarange\",\n role = \"ctb\",\n email = \"joseph@larmarange.net\"),\n + \ person(given = \"Max\",\n family = \"Kuhn\",\n role + = \"ctb\",\n email = \"max@posit.co\"),\n person(given = \"Michal\",\n + \ family = \"Bojanowski\",\n role = \"ctb\",\n email + = \"michal2992@gmail.com\"),\n person(given = \"Hakon\",\n family + = \"Malmedal\",\n role = \"ctb\",\n email = \"hmalmedal@gmail.com\"),\n + \ person(given = \"Clara\",\n family = \"Wang\",\n role + = \"ctb\"),\n person(given = \"Sergio\",\n family = \"Oller\",\n + \ role = \"ctb\",\n email = \"sergioller@gmail.com\"),\n + \ person(given = \"Luke\",\n family = \"Sonnet\",\n role + = \"ctb\",\n email = \"luke.sonnet@gmail.com\"),\n person(given + = \"Jim\",\n family = \"Hester\",\n role = \"ctb\",\n + \ email = \"jim.hester@posit.co\"),\n person(given = \"Ben\",\n + \ family = \"Schneider\",\n role = \"ctb\",\n email + = \"benjamin.julius.schneider@gmail.com\"),\n person(given = \"Bernie\",\n + \ family = \"Gray\",\n role = \"ctb\",\n email + = \"bfgray3@gmail.com\",\n comment = c(ORCID = \"0000-0001-9190-6032\")),\n + \ person(given = \"Mara\",\n family = \"Averick\",\n role + = \"ctb\",\n email = \"mara@posit.co\"),\n person(given = \"Aaron\",\n + \ family = \"Jacobs\",\n role = \"ctb\",\n email + = \"atheriel@gmail.com\"),\n person(given = \"Andreas\",\n family + = \"Bender\",\n role = \"ctb\",\n email = \"bender.at.R@gmail.com\"),\n + \ person(given = \"Sven\",\n family = \"Templer\",\n role + = \"ctb\",\n email = \"sven.templer@gmail.com\"),\n person(given + = \"Paul-Christian\",\n family = \"Buerkner\",\n role + = \"ctb\",\n email = \"paul.buerkner@gmail.com\"),\n person(given + = \"Matthew\",\n family = \"Kay\",\n role = \"ctb\",\n + \ email = \"mjskay@umich.edu\"),\n person(given = \"Erwan\",\n + \ family = \"Le Pennec\",\n role = \"ctb\",\n email + = \"lepennec@gmail.com\"),\n person(given = \"Johan\",\n family + = \"Junkka\",\n role = \"ctb\",\n email = \"johan.junkka@umu.se\"),\n + \ person(given = \"Hao\",\n family = \"Zhu\",\n role + = \"ctb\",\n email = \"haozhu233@gmail.com\"),\n person(given + = \"Benjamin\",\n family = \"Soltoff\",\n role = \"ctb\",\n + \ email = \"soltoffbc@uchicago.edu\"),\n person(given = \"Zoe\",\n + \ family = \"Wilkinson Saldana\",\n role = \"ctb\",\n + \ email = \"zoewsaldana@gmail.com\"),\n person(given = \"Tyler\",\n + \ family = \"Littlefield\",\n role = \"ctb\",\n email + = \"tylurp1@gmail.com\"),\n person(given = \"Charles T.\",\n family + = \"Gray\",\n role = \"ctb\",\n email = \"charlestigray@gmail.com\"),\n + \ person(given = \"Shabbh E.\",\n family = \"Banks\",\n role + = \"ctb\"),\n person(given = \"Serina\",\n family = \"Robinson\",\n + \ role = \"ctb\",\n email = \"robi0916@umn.edu\"),\n + \ person(given = \"Roger\",\n family = \"Bivand\",\n role + = \"ctb\",\n email = \"Roger.Bivand@nhh.no\"),\n person(given + = \"Riinu\",\n family = \"Ots\",\n role = \"ctb\",\n + \ email = \"riinuots@gmail.com\"),\n person(given = \"Nicholas\",\n + \ family = \"Williams\",\n role = \"ctb\",\n email + = \"ntwilliams.personal@gmail.com\"),\n person(given = \"Nina\",\n family + = \"Jakobsen\",\n role = \"ctb\"),\n person(given = \"Michael\",\n + \ family = \"Weylandt\",\n role = \"ctb\",\n email + = \"michael.weylandt@gmail.com\"),\n person(given = \"Lisa\",\n family + = \"Lendway\",\n role = \"ctb\",\n email = \"llendway@macalester.edu\"),\n + \ person(given = \"Karl\",\n family = \"Hailperin\",\n role + = \"ctb\",\n email = \"khailper@gmail.com\"),\n person(given + = \"Josue\",\n family = \"Rodriguez\",\n role = \"ctb\",\n + \ email = \"jerrodriguez@ucdavis.edu\"),\n person(given = \"Jenny\",\n + \ family = \"Bryan\",\n role = \"ctb\",\n email + = \"jenny@posit.co\"),\n person(given = \"Chris\",\n family + = \"Jarvis\",\n role = \"ctb\",\n email = \"Christopher1.jarvis@gmail.com\"),\n + \ person(given = \"Greg\",\n family = \"Macfarlane\",\n role + = \"ctb\",\n email = \"gregmacfarlane@gmail.com\"),\n person(given + = \"Brian\",\n family = \"Mannakee\",\n role = \"ctb\",\n + \ email = \"bmannakee@gmail.com\"),\n person(given = \"Drew\",\n + \ family = \"Tyre\",\n role = \"ctb\",\n email + = \"atyre2@unl.edu\"),\n person(given = \"Shreyas\",\n family + = \"Singh\",\n role = \"ctb\",\n email = \"shreyas.singh.298@gmail.com\"),\n + \ person(given = \"Laurens\",\n family = \"Geffert\",\n role + = \"ctb\",\n email = \"laurensgeffert@gmail.com\"),\n person(given + = \"Hong\",\n family = \"Ooi\",\n role = \"ctb\",\n + \ email = \"hongooi@microsoft.com\"),\n person(given = \"Henrik\",\n + \ family = \"Bengtsson\",\n role = \"ctb\",\n email + = \"henrikb@braju.com\"),\n person(given = \"Eduard\",\n family + = \"Szocs\",\n role = \"ctb\",\n email = \"eduardszoecs@gmail.com\"),\n + \ person(given = \"David\",\n family = \"Hugh-Jones\",\n role + = \"ctb\",\n email = \"davidhughjones@gmail.com\"),\n person(given + = \"Matthieu\",\n family = \"Stigler\",\n role = \"ctb\",\n + \ email = \"Matthieu.Stigler@gmail.com\"),\n person(given = + \"Hugo\",\n family = \"Tavares\",\n role = \"ctb\",\n + \ email = \"hm533@cam.ac.uk\",\n comment = c(ORCID = + \"0000-0001-9373-2726\")),\n\t person(given = \"R. Willem\",\n family + = \"Vervoort\",\n role = \"ctb\",\n email = \"Willemvervoort@gmail.com\"),\n + \ person(given = \"Brenton M.\",\n family = \"Wiernik\",\n role + = \"ctb\",\n email = \"brenton@wiernik.org\"),\n person(given + = \"Josh\",\n family = \"Yamamoto\",\n role = \"ctb\",\n + \ email = \"joshuayamamoto5@gmail.com\"),\n person(given = \"Jasme\",\n + \ family = \"Lee\",\n role = \"ctb\"),\n person(given + = \"Taren\",\n family = \"Sanders\",\n role = \"ctb\",\n + \ email = \"taren.sanders@acu.edu.au\",\n comment = c(ORCID + = \"0000-0002-4504-6008\")),\n person(given = \"Ilaria\",\n family + = \"Prosdocimi\",\n role = \"ctb\",\n email = \"prosdocimi.ilaria@gmail.com\",\n + \ comment = c(ORCID = \"0000-0001-8565-094X\")),\n person(given + = \"Daniel D.\",\n family = \"Sjoberg\",\n role = \"ctb\",\n + \ email = \"danield.sjoberg@gmail.com\",\n comment = + c(ORCID = \"0000-0003-0862-2018\")),\n person(given = \"Alex\",\n family + = \"Reinhart\",\n role = \"ctb\",\n email = \"areinhar@stat.cmu.edu\",\n + \ comment = c(ORCID = \"0000-0002-6658-514X\")))" + Description: |- + Summarizes key information about statistical + objects in tidy tibbles. This makes it easy to report results, create + plots and consistently work with large numbers of models at once. + Broom provides three verbs that each provide different types of + information about a model. tidy() summarizes information about model + components such as coefficients of a regression. glance() reports + information about an entire model, such as goodness of fit measures + like AIC and BIC. augment() adds information about individual + observations to a dataset, such as fitted values or influence + measures. + License: MIT + file LICENSE + URL: https://broom.tidymodels.org/, https://github.com/tidymodels/broom + BugReports: https://github.com/tidymodels/broom/issues + Depends: R (>= 3.5) + Imports: |- + backports, dplyr (>= 1.0.0), ellipsis, generics (>= 0.0.2), + glue, lifecycle, purrr, rlang, stringr, tibble (>= 3.0.0), + tidyr (>= 1.0.0) + Suggests: |- + AER, AUC, bbmle, betareg, biglm, binGroup, boot, btergm (>= + 1.10.6), car, carData, caret, cluster, cmprsk, coda, covr, drc, + e1071, emmeans, epiR, ergm (>= 3.10.4), fixest (>= 0.9.0), gam + (>= 1.15), gee, geepack, ggplot2, glmnet, glmnetUtils, gmm, + Hmisc, irlba, interp, joineRML, Kendall, knitr, ks, Lahman, + lavaan, leaps, lfe, lm.beta, lme4, lmodel2, lmtest (>= 0.9.38), + lsmeans, maps, margins, MASS, mclust, mediation, metafor, mfx, + mgcv, mlogit, modeldata, modeltests, muhaz, multcomp, network, + nnet, orcutt (>= 2.2), ordinal, plm, poLCA, psych, quantreg, + rmarkdown, robust, robustbase, rsample, sandwich, sp, spdep (>= + 1.1), spatialreg, speedglm, spelling, survey, survival, + systemfit, testthat (>= 2.1.0), tseries, vars, zoo + VignetteBuilder: knitr + Config/Needs/website: tidyverse/tidytemplate + Encoding: UTF-8 + RoxygenNote: 7.2.3 + Language: en-US + Collate: |- + 'aaa-documentation-helper.R' 'null-and-default-tidiers.R' + 'aer-tidiers.R' 'auc-tidiers.R' 'base-tidiers.R' + 'bbmle-tidiers.R' 'betareg-tidiers.R' 'biglm-tidiers.R' + 'bingroup-tidiers.R' 'boot-tidiers.R' 'broom-package.R' + 'broom.R' 'btergm-tidiers.R' 'car-tidiers.R' 'caret-tidiers.R' + 'cluster-tidiers.R' 'cmprsk-tidiers.R' 'data-frame-tidiers.R' + 'deprecated-0-7-0.R' 'drc-tidiers.R' 'emmeans-tidiers.R' + 'epiR-tidiers.R' 'ergm-tidiers.R' 'fixest-tidiers.R' + 'gam-tidiers.R' 'geepack-tidiers.R' + 'glmnet-cv-glmnet-tidiers.R' 'glmnet-glmnet-tidiers.R' + 'gmm-tidiers.R' 'hmisc-tidiers.R' 'joinerml-tidiers.R' + 'kendall-tidiers.R' 'ks-tidiers.R' 'lavaan-tidiers.R' + 'leaps-tidiers.R' 'lfe-tidiers.R' 'list-irlba.R' + 'list-optim-tidiers.R' 'list-svd-tidiers.R' 'list-tidiers.R' + 'list-xyz-tidiers.R' 'lm-beta-tidiers.R' 'lmodel2-tidiers.R' + 'lmtest-tidiers.R' 'maps-tidiers.R' 'margins-tidiers.R' + 'mass-fitdistr-tidiers.R' 'mass-negbin-tidiers.R' + 'mass-polr-tidiers.R' 'mass-ridgelm-tidiers.R' + 'stats-lm-tidiers.R' 'mass-rlm-tidiers.R' 'mclust-tidiers.R' + 'mediation-tidiers.R' 'metafor-tidiers.R' 'mfx-tidiers.R' + 'mgcv-tidiers.R' 'mlogit-tidiers.R' 'muhaz-tidiers.R' + 'multcomp-tidiers.R' 'nnet-tidiers.R' 'nobs.R' + 'orcutt-tidiers.R' 'ordinal-clm-tidiers.R' + 'ordinal-clmm-tidiers.R' 'plm-tidiers.R' 'polca-tidiers.R' + 'psych-tidiers.R' 'stats-nls-tidiers.R' + 'quantreg-nlrq-tidiers.R' 'quantreg-rq-tidiers.R' + 'quantreg-rqs-tidiers.R' 'robust-glmrob-tidiers.R' + 'robust-lmrob-tidiers.R' 'robustbase-glmrob-tidiers.R' + 'robustbase-lmrob-tidiers.R' 'sp-tidiers.R' 'spdep-tidiers.R' + 'speedglm-speedglm-tidiers.R' 'speedglm-speedlm-tidiers.R' + 'stats-anova-tidiers.R' 'stats-arima-tidiers.R' + 'stats-decompose-tidiers.R' 'stats-factanal-tidiers.R' + 'stats-glm-tidiers.R' 'stats-htest-tidiers.R' + 'stats-kmeans-tidiers.R' 'stats-loess-tidiers.R' + 'stats-mlm-tidiers.R' 'stats-prcomp-tidiers.R' + 'stats-smooth.spline-tidiers.R' 'stats-summary-lm-tidiers.R' + 'stats-time-series-tidiers.R' 'survey-tidiers.R' + 'survival-aareg-tidiers.R' 'survival-cch-tidiers.R' + 'survival-coxph-tidiers.R' 'survival-pyears-tidiers.R' + 'survival-survdiff-tidiers.R' 'survival-survexp-tidiers.R' + 'survival-survfit-tidiers.R' 'survival-survreg-tidiers.R' + 'systemfit-tidiers.R' 'tseries-tidiers.R' 'utilities.R' + 'vars-tidiers.R' 'zoo-tidiers.R' 'zzz.R' + NeedsCompilation: 'no' + Packaged: 2023-06-09 21:21:49 UTC; simoncouch + Author: |- + David Robinson [aut], + Alex Hayes [aut] (), + Simon Couch [aut, cre] (), + Posit Software, PBC [cph, fnd], + Indrajeet Patil [ctb] (), + Derek Chiu [ctb], + Matthieu Gomez [ctb], + Boris Demeshev [ctb], + Dieter Menne [ctb], + Benjamin Nutter [ctb], + Luke Johnston [ctb], + Ben Bolker [ctb], + Francois Briatte [ctb], + Jeffrey Arnold [ctb], + Jonah Gabry [ctb], + Luciano Selzer [ctb], + Gavin Simpson [ctb], + Jens Preussner [ctb], + Jay Hesselberth [ctb], + Hadley Wickham [ctb], + Matthew Lincoln [ctb], + Alessandro Gasparini [ctb], + Lukasz Komsta [ctb], + Frederick Novometsky [ctb], + Wilson Freitas [ctb], + Michelle Evans [ctb], + Jason Cory Brunson [ctb], + Simon Jackson [ctb], + Ben Whalley [ctb], + Karissa Whiting [ctb], + Yves Rosseel [ctb], + Michael Kuehn [ctb], + Jorge Cimentada [ctb], + Erle Holgersen [ctb], + Karl Dunkle Werner [ctb] (), + Ethan Christensen [ctb], + Steven Pav [ctb], + Paul PJ [ctb], + Ben Schneider [ctb], + Patrick Kennedy [ctb], + Lily Medina [ctb], + Brian Fannin [ctb], + Jason Muhlenkamp [ctb], + Matt Lehman [ctb], + Bill Denney [ctb] (), + Nic Crane [ctb], + Andrew Bates [ctb], + Vincent Arel-Bundock [ctb] (), + Hideaki Hayashi [ctb], + Luis Tobalina [ctb], + Annie Wang [ctb], + Wei Yang Tham [ctb], + Clara Wang [ctb], + Abby Smith [ctb] (), + Jasper Cooper [ctb] (), + E Auden Krauska [ctb] (), + Alex Wang [ctb], + Malcolm Barrett [ctb] (), + Charles Gray [ctb] (), + Jared Wilber [ctb], + Vilmantas Gegzna [ctb] (), + Eduard Szoecs [ctb], + Frederik Aust [ctb] (), + Angus Moore [ctb], + Nick Williams [ctb], + Marius Barth [ctb] (), + Bruna Wundervald [ctb] (), + Joyce Cahoon [ctb] (), + Grant McDermott [ctb] (), + Kevin Zarca [ctb], + Shiro Kuriwaki [ctb] (), + Lukas Wallrich [ctb] (), + James Martherus [ctb] (), + Chuliang Xiao [ctb] (), + Joseph Larmarange [ctb], + Max Kuhn [ctb], + Michal Bojanowski [ctb], + Hakon Malmedal [ctb], + Clara Wang [ctb], + Sergio Oller [ctb], + Luke Sonnet [ctb], + Jim Hester [ctb], + Ben Schneider [ctb], + Bernie Gray [ctb] (), + Mara Averick [ctb], + Aaron Jacobs [ctb], + Andreas Bender [ctb], + Sven Templer [ctb], + Paul-Christian Buerkner [ctb], + Matthew Kay [ctb], + Erwan Le Pennec [ctb], + Johan Junkka [ctb], + Hao Zhu [ctb], + Benjamin Soltoff [ctb], + Zoe Wilkinson Saldana [ctb], + Tyler Littlefield [ctb], + Charles T. Gray [ctb], + Shabbh E. Banks [ctb], + Serina Robinson [ctb], + Roger Bivand [ctb], + Riinu Ots [ctb], + Nicholas Williams [ctb], + Nina Jakobsen [ctb], + Michael Weylandt [ctb], + Lisa Lendway [ctb], + Karl Hailperin [ctb], + Josue Rodriguez [ctb], + Jenny Bryan [ctb], + Chris Jarvis [ctb], + Greg Macfarlane [ctb], + Brian Mannakee [ctb], + Drew Tyre [ctb], + Shreyas Singh [ctb], + Laurens Geffert [ctb], + Hong Ooi [ctb], + Henrik Bengtsson [ctb], + Eduard Szocs [ctb], + David Hugh-Jones [ctb], + Matthieu Stigler [ctb], + Hugo Tavares [ctb] (), + R. Willem Vervoort [ctb], + Brenton M. Wiernik [ctb], + Josh Yamamoto [ctb], + Jasme Lee [ctb], + Taren Sanders [ctb] (), + Ilaria Prosdocimi [ctb] (), + Daniel D. Sjoberg [ctb] (), + Alex Reinhart [ctb] () + Maintainer: Simon Couch + Repository: RSPM + Date/Publication: 2023-06-09 22:50:02 UTC + Built: R 4.3.1; ; 2024-02-06 19:15:33 UTC; unix + vctrs: + Package: vctrs + Title: Vector Helpers + Version: 0.6.3 + Authors@R: |- + c( + person("Hadley", "Wickham", , "hadley@posit.co", role = "aut"), + person("Lionel", "Henry", , "lionel@posit.co", role = "aut"), + person("Davis", "Vaughan", , "davis@posit.co", role = c("aut", "cre")), + person("data.table team", role = "cph", + comment = "Radix sort based on data.table's forder() and their contribution to R's order()"), + person("Posit Software, PBC", role = c("cph", "fnd")) + ) + Description: |- + Defines new notions of prototype and size that are used to + provide tools for consistent and well-founded type-coercion and + size-recycling, and are in turn connected to ideas of type- and + size-stability useful for analysing function interfaces. + License: MIT + file LICENSE + URL: https://vctrs.r-lib.org/, https://github.com/r-lib/vctrs + BugReports: https://github.com/r-lib/vctrs/issues + Depends: R (>= 3.5.0) + Imports: cli (>= 3.4.0), glue, lifecycle (>= 1.0.3), rlang (>= 1.1.0) + Suggests: |- + bit64, covr, crayon, dplyr (>= 0.8.5), generics, knitr, + pillar (>= 1.4.4), pkgdown (>= 2.0.1), rmarkdown, testthat (>= + 3.0.0), tibble (>= 3.1.3), waldo (>= 0.2.0), withr, xml2, + zeallot + VignetteBuilder: knitr + Config/Needs/website: tidyverse/tidytemplate + Config/testthat/edition: '3' + Encoding: UTF-8 + Language: en-GB + RoxygenNote: 7.2.3 + NeedsCompilation: 'yes' + Packaged: 2023-06-14 21:04:57 UTC; davis + Author: |- + Hadley Wickham [aut], + Lionel Henry [aut], + Davis Vaughan [aut, cre], + data.table team [cph] (Radix sort based on data.table's forder() and + their contribution to R's order()), + Posit Software, PBC [cph, fnd] + Maintainer: Davis Vaughan + Repository: RSPM + Date/Publication: 2023-06-14 23:40:02 UTC + Built: R 4.3.1; x86_64-pc-linux-gnu; 2024-02-06 17:54:53 UTC; unix + fastDummies: + Package: fastDummies + Type: Package + Title: |- + Fast Creation of Dummy (Binary) Columns and Rows from + Categorical Variables + Version: 1.7.3 + Authors@R: "c(\n person(\"Jacob\", \"Kaplan\", email = \"jkkaplan6@gmail.com\", + role = c(\"aut\", \"cre\"),\n comment = c(ORCID = \"0000-0002-0601-0387\")), + \n person(\"Benjamin\", \"Schlegel\", email = \"kontakt@benjaminschlegl.ch\", + role = \"ctb\"))" + Description: Creates dummy columns from columns that have categorical variables + (character or factor types). You can also specify which columns to make dummies + out of, or which columns to ignore. Also creates dummy rows from character, + factor, and Date columns. This package provides a significant speed increase + from creating dummy variables through model.matrix(). + Depends: R (>= 2.10) + Imports: data.table, tibble, stringr + License: MIT + file LICENSE + Encoding: UTF-8 + URL: |- + https://github.com/jacobkap/fastDummies, + https://jacobkap.github.io/fastDummies/ + BugReports: https://github.com/jacobkap/fastDummies/issues + RoxygenNote: 7.2.3 + Suggests: testthat (>= 2.1.0), knitr, rmarkdown, covr, spelling + VignetteBuilder: knitr + Language: en-US + NeedsCompilation: 'no' + Packaged: 2023-07-05 13:40:13 UTC; jkkap + Author: |- + Jacob Kaplan [aut, cre] (), + Benjamin Schlegel [ctb] + Maintainer: Jacob Kaplan + Repository: RSPM + Date/Publication: 2023-07-06 13:50:06 UTC + Built: R 4.3.1; ; 2024-02-06 20:06:36 UTC; unix + R6: + Package: R6 + Title: Encapsulated Classes with Reference Semantics + Version: 2.5.1 + Authors@R: person("Winston", "Chang", role = c("aut", "cre"), email = "winston@stdout.org") + Description: |- + Creates classes with reference semantics, similar to R's built-in + reference classes. Compared to reference classes, R6 classes are simpler + and lighter-weight, and they are not built on S4 classes so they do not + require the methods package. These classes allow public and private + members, and they support inheritance, even when the classes are defined in + different packages. + Depends: R (>= 3.0) + Suggests: testthat, pryr + License: MIT + file LICENSE + URL: https://r6.r-lib.org, https://github.com/r-lib/R6/ + BugReports: https://github.com/r-lib/R6/issues + RoxygenNote: 7.1.1 + NeedsCompilation: 'no' + Packaged: 2021-08-06 20:18:46 UTC; winston + Author: Winston Chang [aut, cre] + Maintainer: Winston Chang + Repository: RSPM + Date/Publication: 2021-08-19 14:00:05 UTC + Encoding: UTF-8 + Built: R 4.3.1; ; 2024-02-06 17:54:23 UTC; unix + lifecycle: + Package: lifecycle + Title: Manage the Life Cycle of your Package Functions + Version: 1.0.3 + Authors@R: |- + c( + person("Lionel", "Henry", , "lionel@rstudio.com", role = c("aut", "cre")), + person("Hadley", "Wickham", , "hadley@rstudio.com", role = "aut", + comment = c(ORCID = "0000-0003-4757-117X")), + person("RStudio", role = c("cph", "fnd")) + ) + Description: |- + Manage the life cycle of your exported functions with shared + conventions, documentation badges, and user-friendly deprecation + warnings. + License: MIT + file LICENSE + URL: https://lifecycle.r-lib.org/, https://github.com/r-lib/lifecycle + BugReports: https://github.com/r-lib/lifecycle/issues + Depends: R (>= 3.4) + Imports: cli (>= 3.4.0), glue, rlang (>= 1.0.6) + Suggests: |- + covr, crayon, knitr, lintr, rmarkdown, testthat (>= 3.0.1), + tibble, tidyverse, tools, vctrs, withr + VignetteBuilder: knitr + Config/testthat/edition: '3' + Config/Needs/website: tidyverse/tidytemplate + Encoding: UTF-8 + RoxygenNote: 7.2.1 + NeedsCompilation: 'no' + Packaged: 2022-10-07 08:50:55 UTC; lionel + Author: |- + Lionel Henry [aut, cre], + Hadley Wickham [aut] (), + RStudio [cph, fnd] + Maintainer: Lionel Henry + Repository: RSPM + Date/Publication: 2022-10-07 09:50:02 UTC + Built: R 4.3.1; ; 2024-02-06 17:53:40 UTC; unix + MASS: + Package: MASS + Priority: recommended + Version: 7.3-60 + Date: '2023-05-02' + Revision: '$Rev: 3621 $' + Depends: R (>= 4.0), grDevices, graphics, stats, utils + Imports: methods + Suggests: lattice, nlme, nnet, survival + Authors@R: "c(person(\"Brian\", \"Ripley\", role = c(\"aut\", \"cre\", \"cph\"),\n + \ email = \"ripley@stats.ox.ac.uk\"),\n\t person(\"Bill\", + \"Venables\", role = \"ctb\"),\n\t person(c(\"Douglas\", \"M.\"), \"Bates\", + role = \"ctb\"),\n\t person(\"Kurt\", \"Hornik\", role = \"trl\",\n comment + = \"partial port ca 1998\"),\n\t person(\"Albrecht\", \"Gebhardt\", role + = \"trl\",\n comment = \"partial port ca 1998\"),\n\t person(\"David\", + \"Firth\", role = \"ctb\"))" + Description: |- + Functions and datasets to support Venables and Ripley, + "Modern Applied Statistics with S" (4th edition, 2002). + Title: Support Functions and Datasets for Venables and Ripley's MASS + LazyData: 'yes' + ByteCompile: 'yes' + License: GPL-2 | GPL-3 + URL: http://www.stats.ox.ac.uk/pub/MASS4/ + Contact: + NeedsCompilation: 'yes' + Packaged: 2023-05-02 16:42:41 UTC; ripley + Author: |- + Brian Ripley [aut, cre, cph], + Bill Venables [ctb], + Douglas M. Bates [ctb], + Kurt Hornik [trl] (partial port ca 1998), + Albrecht Gebhardt [trl] (partial port ca 1998), + David Firth [ctb] + Maintainer: Brian Ripley + Repository: RSPM + Date/Publication: 2023-05-04 07:32:21 UTC + Encoding: UTF-8 + Built: R 4.3.1; x86_64-pc-linux-gnu; 2024-02-06 17:46:03 UTC; unix + SuperLearner: + Package: SuperLearner + Type: Package + Title: Super Learner Prediction + Version: 2.0-28.1 + Date: '2021-05-04' + Authors@R: c(person("Eric", "Polley", email = "epolley@uchicago.edu", role = c("aut", + "cre")), person("Erin", "LeDell", role = c("aut")), person("Chris", "Kennedy", + role = c("aut")), person("Sam", "Lendle", role = c("ctb")), person("Mark", "van + der Laan", role = c("aut", "ths"))) + Maintainer: Eric Polley + Description: |- + Implements the super learner prediction method and contains a + library of prediction algorithms to be used in the super learner. + License: GPL-3 + URL: https://github.com/ecpolley/SuperLearner + Depends: R (>= 2.14.0), nnls, gam (>= 1.15) + Imports: cvAUC + Suggests: |- + arm, bartMachine, biglasso, bigmemory, caret, class, + devtools, e1071, earth, extraTrees, gbm, genefilter, ggplot2, + glmnet, ipred, KernelKnn, kernlab, knitr, lattice, LogicReg, + MASS, mlbench, nloptr, nnet, party, polspline, prettydoc, + quadprog, randomForest, ranger, RhpcBLASctl, ROCR, rmarkdown, + rpart, SIS, speedglm, spls, sva, testthat, xgboost (>= 0.6) + LazyLoad: 'yes' + VignetteBuilder: knitr, rmarkdown + RoxygenNote: 6.0.1 + NeedsCompilation: 'no' + Packaged: 2023-07-18 08:11:41 UTC; hornik + Author: |- + Eric Polley [aut, cre], + Erin LeDell [aut], + Chris Kennedy [aut], + Sam Lendle [ctb], + Mark van der Laan [aut, ths] + Repository: RSPM + Date/Publication: 2023-07-18 11:46:38 UTC + Encoding: UTF-8 + Built: R 4.3.1; ; 2024-02-06 23:35:05 UTC; unix + pkgconfig: + Package: pkgconfig + Title: Private Configuration for 'R' Packages + Version: 2.0.3 + Author: Gábor Csárdi + Maintainer: Gábor Csárdi + Description: |- + Set configuration options on a per-package basis. + Options set by a given package only apply to that package, + other packages are unaffected. + License: MIT + file LICENSE + LazyData: 'true' + Imports: utils + Suggests: covr, testthat, disposables (>= 1.0.3) + URL: https://github.com/r-lib/pkgconfig#readme + BugReports: https://github.com/r-lib/pkgconfig/issues + Encoding: UTF-8 + NeedsCompilation: 'no' + Packaged: 2019-09-22 08:42:40 UTC; gaborcsardi + Repository: RSPM + Date/Publication: 2019-09-22 09:20:02 UTC + Built: R 4.3.1; ; 2024-02-06 17:55:24 UTC; unix + gtable: + Package: gtable + Title: Arrange 'Grobs' in Tables + Version: 0.3.4 + Authors@R: |2- + + c(person(given = "Hadley", + family = "Wickham", + role = "aut", + email = "hadley@posit.co"), + person(given = "Thomas Lin", + family = "Pedersen", + role = c("aut", "cre"), + email = "thomas.pedersen@posit.co"), + person(given = "Posit Software, PBC", + role = "cph")) + Description: "Tools to make it easier to work with \"tables\" of\n 'grobs'. + The 'gtable' package defines a 'gtable' grob class that specifies a\n grid + along with a list of grobs and their placement in the grid. Further the\n package + makes it easy to manipulate and combine 'gtable' objects so that \n complex + compositions can be built up sequentially." + License: MIT + file LICENSE + Depends: R (>= 3.5) + Imports: cli, glue, grid, lifecycle, rlang (>= 1.1.0) + Suggests: covr, ggplot2, knitr, profvis, rmarkdown, testthat (>= 3.0.0) + VignetteBuilder: knitr + Encoding: UTF-8 + RoxygenNote: 7.2.3 + URL: https://gtable.r-lib.org, https://github.com/r-lib/gtable + BugReports: https://github.com/r-lib/gtable/issues + Config/testthat/edition: '3' + Config/Needs/website: tidyverse/tidytemplate + NeedsCompilation: 'no' + Packaged: 2023-08-21 10:36:53 UTC; thomas + Author: |- + Hadley Wickham [aut], + Thomas Lin Pedersen [aut, cre], + Posit Software, PBC [cph] + Maintainer: Thomas Lin Pedersen + Repository: RSPM + Date/Publication: 2023-08-21 11:20:02 UTC + Built: R 4.3.1; ; 2024-02-06 17:53:43 UTC; unix + pillar: + Package: pillar + Title: Coloured Formatting for Columns + Version: 1.9.0 + Authors@R: |2- + + c(person(given = "Kirill", + family = "M\u00fcller", + role = c("aut", "cre"), + email = "kirill@cynkra.com", + comment = c(ORCID = "0000-0002-1416-3412")), + person(given = "Hadley", + family = "Wickham", + role = "aut"), + person(given = "RStudio", + role = "cph")) + Description: |- + Provides 'pillar' and 'colonnade' generics designed + for formatting columns of data using the full range of colours + provided by modern terminals. + License: MIT + file LICENSE + URL: https://pillar.r-lib.org/, https://github.com/r-lib/pillar + BugReports: https://github.com/r-lib/pillar/issues + Imports: |- + cli (>= 2.3.0), fansi, glue, lifecycle, rlang (>= 1.0.2), utf8 + (>= 1.1.0), utils, vctrs (>= 0.5.0) + Suggests: |- + bit64, DBI, debugme, DiagrammeR, dplyr, formattable, ggplot2, + knitr, lubridate, nanotime, nycflights13, palmerpenguins, + rmarkdown, scales, stringi, survival, testthat (>= 3.1.1), + tibble, units (>= 0.7.2), vdiffr, withr + VignetteBuilder: knitr + Encoding: UTF-8 + RoxygenNote: 7.2.3 + Config/testthat/edition: '3' + Config/testthat/parallel: 'true' + Config/testthat/start-first: |- + format_multi_fuzz, format_multi_fuzz_2, + format_multi, ctl_colonnade, ctl_colonnade_1, ctl_colonnade_2 + Config/autostyle/scope: line_breaks + Config/autostyle/strict: 'true' + Config/gha/extra-packages: DiagrammeR=?ignore-before-r=3.5.0 + Config/Needs/website: tidyverse/tidytemplate + NeedsCompilation: 'no' + Packaged: 2023-03-21 08:42:46 UTC; kirill + Author: |- + Kirill Müller [aut, cre] (), + Hadley Wickham [aut], + RStudio [cph] + Maintainer: Kirill Müller + Repository: RSPM + Date/Publication: 2023-03-22 08:10:02 UTC + Built: R 4.3.1; ; 2024-02-06 17:55:18 UTC; unix + glue: + Package: glue + Title: Interpreted String Literals + Version: 1.6.2 + Authors@R: |- + c( + person("Jim", "Hester", role = "aut", + comment = c(ORCID = "0000-0002-2739-7082")), + person("Jennifer", "Bryan", , "jenny@rstudio.com", role = c("aut", "cre"), + comment = c(ORCID = "0000-0002-6983-2759")), + person("RStudio", role = c("cph", "fnd")) + ) + Description: |- + An implementation of interpreted string literals, inspired by + Python's Literal String Interpolation + and Docstrings + and Julia's Triple-Quoted + String Literals + . + License: MIT + file LICENSE + URL: https://github.com/tidyverse/glue, https://glue.tidyverse.org/ + BugReports: https://github.com/tidyverse/glue/issues + Depends: R (>= 3.4) + Imports: methods + Suggests: |- + covr, crayon, DBI, dplyr, forcats, ggplot2, knitr, magrittr, + microbenchmark, R.utils, rmarkdown, rprintf, RSQLite, stringr, + testthat (>= 3.0.0), vctrs (>= 0.3.0), waldo (>= 0.3.0), withr + VignetteBuilder: knitr + ByteCompile: 'true' + Config/Needs/website: hadley/emo, tidyverse/tidytemplate + Config/testthat/edition: '3' + Encoding: UTF-8 + RoxygenNote: 7.1.2 + NeedsCompilation: 'yes' + Packaged: 2022-02-23 22:50:40 UTC; jenny + Author: |- + Jim Hester [aut] (), + Jennifer Bryan [aut, cre] (), + RStudio [cph, fnd] + Maintainer: Jennifer Bryan + Repository: RSPM + Date/Publication: 2022-02-24 07:50:20 UTC + Built: R 4.3.1; x86_64-pc-linux-gnu; 2024-02-06 17:53:18 UTC; unix + data.table: + Package: data.table + Version: 1.14.8 + Title: Extension of `data.frame` + Authors@R: |- + c( + person("Matt","Dowle", role=c("aut","cre"), email="mattjdowle@gmail.com"), + person("Arun","Srinivasan", role="aut", email="asrini@pm.me"), + person("Jan","Gorecki", role="ctb"), + person("Michael","Chirico", role="ctb"), + person("Pasha","Stetsenko", role="ctb"), + person("Tom","Short", role="ctb"), + person("Steve","Lianoglou", role="ctb"), + person("Eduard","Antonyan", role="ctb"), + person("Markus","Bonsch", role="ctb"), + person("Hugh","Parsonage", role="ctb"), + person("Scott","Ritchie", role="ctb"), + person("Kun","Ren", role="ctb"), + person("Xianying","Tan", role="ctb"), + person("Rick","Saporta", role="ctb"), + person("Otto","Seiskari", role="ctb"), + person("Xianghui","Dong", role="ctb"), + person("Michel","Lang", role="ctb"), + person("Watal","Iwasaki", role="ctb"), + person("Seth","Wenchel", role="ctb"), + person("Karl","Broman", role="ctb"), + person("Tobias","Schmidt", role="ctb"), + person("David","Arenburg", role="ctb"), + person("Ethan","Smith", role="ctb"), + person("Francois","Cocquemas", role="ctb"), + person("Matthieu","Gomez", role="ctb"), + person("Philippe","Chataignon", role="ctb"), + person("Nello","Blaser", role="ctb"), + person("Dmitry","Selivanov", role="ctb"), + person("Andrey","Riabushenko", role="ctb"), + person("Cheng","Lee", role="ctb"), + person("Declan","Groves", role="ctb"), + person("Daniel","Possenriede", role="ctb"), + person("Felipe","Parages", role="ctb"), + person("Denes","Toth", role="ctb"), + person("Mus","Yaramaz-David", role="ctb"), + person("Ayappan","Perumal", role="ctb"), + person("James","Sams", role="ctb"), + person("Martin","Morgan", role="ctb"), + person("Michael","Quinn", role="ctb"), + person("@javrucebo","", role="ctb"), + person("@marc-outins","", role="ctb"), + person("Roy","Storey", role="ctb"), + person("Manish","Saraswat", role="ctb"), + person("Morgan","Jacob", role="ctb"), + person("Michael","Schubmehl", role="ctb"), + person("Davis","Vaughan", role="ctb"), + person("Toby","Hocking", role="ctb"), + person("Leonardo","Silvestri", role="ctb"), + person("Tyson","Barrett", role="ctb"), + person("Jim","Hester", role="ctb"), + person("Anthony","Damico", role="ctb"), + person("Sebastian","Freundt", role="ctb"), + person("David","Simons", role="ctb"), + person("Elliott","Sales de Andrade", role="ctb"), + person("Cole","Miller", role="ctb"), + person("Jens Peder","Meldgaard", role="ctb"), + person("Vaclav","Tlapak", role="ctb"), + person("Kevin","Ushey", role="ctb"), + person("Dirk","Eddelbuettel", role="ctb"), + person("Ben","Schwen", role="ctb")) + Depends: R (>= 3.1.0) + Imports: methods + Suggests: |- + bit64 (>= 4.0.0), bit (>= 4.0.4), curl, R.utils, xts, + nanotime, zoo (>= 1.8-1), yaml, knitr, rmarkdown + SystemRequirements: zlib + Description: Fast aggregation of large data (e.g. 100GB in RAM), fast ordered + joins, fast add/modify/delete of columns by group using no copies at all, list + columns, friendly and fast character-separated-value read/write. Offers a natural + and flexible syntax, for faster development. + License: MPL-2.0 | file LICENSE + URL: |- + https://r-datatable.com, https://Rdatatable.gitlab.io/data.table, + https://github.com/Rdatatable/data.table + BugReports: https://github.com/Rdatatable/data.table/issues + VignetteBuilder: knitr + ByteCompile: 'TRUE' + NeedsCompilation: 'yes' + Packaged: 2023-02-16 16:37:18 UTC; mdowle + Author: |- + Matt Dowle [aut, cre], + Arun Srinivasan [aut], + Jan Gorecki [ctb], + Michael Chirico [ctb], + Pasha Stetsenko [ctb], + Tom Short [ctb], + Steve Lianoglou [ctb], + Eduard Antonyan [ctb], + Markus Bonsch [ctb], + Hugh Parsonage [ctb], + Scott Ritchie [ctb], + Kun Ren [ctb], + Xianying Tan [ctb], + Rick Saporta [ctb], + Otto Seiskari [ctb], + Xianghui Dong [ctb], + Michel Lang [ctb], + Watal Iwasaki [ctb], + Seth Wenchel [ctb], + Karl Broman [ctb], + Tobias Schmidt [ctb], + David Arenburg [ctb], + Ethan Smith [ctb], + Francois Cocquemas [ctb], + Matthieu Gomez [ctb], + Philippe Chataignon [ctb], + Nello Blaser [ctb], + Dmitry Selivanov [ctb], + Andrey Riabushenko [ctb], + Cheng Lee [ctb], + Declan Groves [ctb], + Daniel Possenriede [ctb], + Felipe Parages [ctb], + Denes Toth [ctb], + Mus Yaramaz-David [ctb], + Ayappan Perumal [ctb], + James Sams [ctb], + Martin Morgan [ctb], + Michael Quinn [ctb], + @javrucebo [ctb], + @marc-outins [ctb], + Roy Storey [ctb], + Manish Saraswat [ctb], + Morgan Jacob [ctb], + Michael Schubmehl [ctb], + Davis Vaughan [ctb], + Toby Hocking [ctb], + Leonardo Silvestri [ctb], + Tyson Barrett [ctb], + Jim Hester [ctb], + Anthony Damico [ctb], + Sebastian Freundt [ctb], + David Simons [ctb], + Elliott Sales de Andrade [ctb], + Cole Miller [ctb], + Jens Peder Meldgaard [ctb], + Vaclav Tlapak [ctb], + Kevin Ushey [ctb], + Dirk Eddelbuettel [ctb], + Ben Schwen [ctb] + Maintainer: Matt Dowle + Repository: RSPM + Date/Publication: 2023-02-17 12:20:12 UTC + Encoding: UTF-8 + Built: R 4.3.1; x86_64-pc-linux-gnu; 2024-02-06 17:56:43 UTC; unix + Rcpp: + Package: Rcpp + Title: Seamless R and C++ Integration + Version: 1.0.11 + Date: '2023-07-03' + Author: |- + Dirk Eddelbuettel, Romain Francois, JJ Allaire, Kevin Ushey, Qiang Kou, + Nathan Russell, Inaki Ucar, Douglas Bates and John Chambers + Maintainer: Dirk Eddelbuettel + Description: |- + The 'Rcpp' package provides R functions as well as C++ classes which + offer a seamless integration of R and C++. Many R data types and objects can be + mapped back and forth to C++ equivalents which facilitates both writing of new + code as well as easier integration of third-party libraries. Documentation + about 'Rcpp' is provided by several vignettes included in this package, via the + 'Rcpp Gallery' site at , the paper by Eddelbuettel and + Francois (2011, ), the book by Eddelbuettel (2013, + ) and the paper by Eddelbuettel and Balamuta (2018, + ); see 'citation("Rcpp")' for details. + Imports: methods, utils + Suggests: tinytest, inline, rbenchmark, pkgKitten (>= 0.1.2) + URL: |- + https://www.rcpp.org, + https://dirk.eddelbuettel.com/code/rcpp.html, + https://github.com/RcppCore/Rcpp + License: GPL (>= 2) + BugReports: https://github.com/RcppCore/Rcpp/issues + MailingList: rcpp-devel@lists.r-forge.r-project.org + RoxygenNote: 6.1.1 + Encoding: UTF-8 + NeedsCompilation: 'yes' + Packaged: 2023-07-03 15:56:55 UTC; edd + Repository: RSPM + Date/Publication: 2023-07-06 07:33:14 UTC + Built: R 4.3.1; x86_64-pc-linux-gnu; 2024-02-06 17:56:14 UTC; unix + xfun: + Package: xfun + Type: Package + Title: Supporting Functions for Packages Maintained by 'Yihui Xie' + Version: '0.39' + Authors@R: |- + c( + person("Yihui", "Xie", role = c("aut", "cre", "cph"), email = "xie@yihui.name", comment = c(ORCID = "0000-0003-0645-5666")), + person("Wush", "Wu", role = "ctb"), + person("Daijiang", "Li", role = "ctb"), + person("Xianying", "Tan", role = "ctb"), + person("Salim", "Brüggemann", role = "ctb", email = "salim-b@pm.me", comment = c(ORCID = "0000-0002-5329-5987")), + person("Christophe", "Dervieux", role = "ctb"), + person(given = "Posit Software, PBC", role = c("cph", "fnd")), + person() + ) + Description: Miscellaneous functions commonly used in other packages maintained + by 'Yihui Xie'. + Imports: stats, tools + Suggests: |- + testit, parallel, codetools, rstudioapi, tinytex (>= 0.30), + mime, markdown (>= 1.5), knitr (>= 1.42), htmltools, remotes, + pak, rhub, renv, curl, jsonlite, magick, yaml, rmarkdown + License: MIT + file LICENSE + URL: https://github.com/yihui/xfun + BugReports: https://github.com/yihui/xfun/issues + Encoding: UTF-8 + RoxygenNote: 7.2.3 + VignetteBuilder: knitr + NeedsCompilation: 'yes' + Packaged: 2023-04-19 22:17:10 UTC; yihui + Author: |- + Yihui Xie [aut, cre, cph] (), + Wush Wu [ctb], + Daijiang Li [ctb], + Xianying Tan [ctb], + Salim Brüggemann [ctb] (), + Christophe Dervieux [ctb], + Posit Software, PBC [cph, fnd] + Maintainer: Yihui Xie + Repository: RSPM + Date/Publication: 2023-04-20 12:50:02 UTC + Built: R 4.3.1; x86_64-pc-linux-gnu; 2024-02-06 18:05:36 UTC; unix + tibble: + Package: tibble + Title: Simple Data Frames + Version: 3.2.1 + Authors@R: |2- + + c(person(given = "Kirill", + family = "M\u00fcller", + role = c("aut", "cre"), + email = "kirill@cynkra.com", + comment = c(ORCID = "0000-0002-1416-3412")), + person(given = "Hadley", + family = "Wickham", + role = "aut", + email = "hadley@rstudio.com"), + person(given = "Romain", + family = "Francois", + role = "ctb", + email = "romain@r-enthusiasts.com"), + person(given = "Jennifer", + family = "Bryan", + role = "ctb", + email = "jenny@rstudio.com"), + person(given = "RStudio", + role = c("cph", "fnd"))) + Description: |- + Provides a 'tbl_df' class (the 'tibble') with stricter checking and better formatting than the traditional + data frame. + License: MIT + file LICENSE + URL: https://tibble.tidyverse.org/, https://github.com/tidyverse/tibble + BugReports: https://github.com/tidyverse/tibble/issues + Depends: R (>= 3.4.0) + Imports: |- + fansi (>= 0.4.0), lifecycle (>= 1.0.0), magrittr, methods, + pillar (>= 1.8.1), pkgconfig, rlang (>= 1.0.2), utils, vctrs + (>= 0.4.2) + Suggests: |- + bench, bit64, blob, brio, callr, cli, covr, crayon (>= + 1.3.4), DiagrammeR, dplyr, evaluate, formattable, ggplot2, + here, hms, htmltools, knitr, lubridate, mockr, nycflights13, + pkgbuild, pkgload, purrr, rmarkdown, stringi, testthat (>= + 3.0.2), tidyr, withr + VignetteBuilder: knitr + Encoding: UTF-8 + RoxygenNote: 7.2.3 + Config/testthat/edition: '3' + Config/testthat/parallel: 'true' + Config/testthat/start-first: |- + vignette-formats, as_tibble, add, + invariants + Config/autostyle/scope: line_breaks + Config/autostyle/strict: 'true' + Config/autostyle/rmd: 'false' + Config/Needs/website: tidyverse/tidytemplate + NeedsCompilation: 'yes' + Packaged: 2023-03-19 09:23:10 UTC; kirill + Author: |- + Kirill Müller [aut, cre] (), + Hadley Wickham [aut], + Romain Francois [ctb], + Jennifer Bryan [ctb], + RStudio [cph, fnd] + Maintainer: Kirill Müller + Repository: RSPM + Date/Publication: 2023-03-20 06:30:02 UTC + Built: R 4.3.1; x86_64-pc-linux-gnu; 2024-02-06 17:55:26 UTC; unix + tidyselect: + Package: tidyselect + Title: Select from a Set of Strings + Version: 1.2.0 + Authors@R: |- + c( + person("Lionel", "Henry", , "lionel@rstudio.com", role = c("aut", "cre")), + person("Hadley", "Wickham", , "hadley@rstudio.com", role = "aut"), + person("RStudio", role = c("cph", "fnd")) + ) + Description: |- + A backend for the selecting functions of the 'tidyverse'. It + makes it easy to implement select-like functions in your own packages + in a way that is consistent with other 'tidyverse' interfaces for + selection. + License: MIT + file LICENSE + URL: https://tidyselect.r-lib.org, https://github.com/r-lib/tidyselect + BugReports: https://github.com/r-lib/tidyselect/issues + Depends: R (>= 3.4) + Imports: |- + cli (>= 3.3.0), glue (>= 1.3.0), lifecycle (>= 1.0.3), rlang + (>= 1.0.4), vctrs (>= 0.4.1), withr + Suggests: |- + covr, crayon, dplyr, knitr, magrittr, rmarkdown, stringr, + testthat (>= 3.1.1), tibble (>= 2.1.3) + VignetteBuilder: knitr + ByteCompile: 'true' + Config/testthat/edition: '3' + Config/Needs/website: tidyverse/tidytemplate + Encoding: UTF-8 + RoxygenNote: 7.2.1 + NeedsCompilation: 'no' + Packaged: 2022-10-10 14:09:03 UTC; hadleywickham + Author: |- + Lionel Henry [aut, cre], + Hadley Wickham [aut], + RStudio [cph, fnd] + Maintainer: Lionel Henry + Repository: RSPM + Date/Publication: 2022-10-10 19:00:02 UTC + Built: R 4.3.1; ; 2024-02-06 17:58:06 UTC; unix + rstudioapi: + Package: rstudioapi + Title: Safely Access the RStudio API + Description: |- + Access the RStudio API (if available) and provide informative error + messages when it's not. + Version: 0.15.0 + Authors@R: |- + c( + person("Kevin", "Ushey", role = c("aut", "cre"), email = "kevin@rstudio.com"), + person("JJ", "Allaire", role = c("aut"), email = "jj@posit.co"), + person("Hadley", "Wickham", role = c("aut"), email = "hadley@posit.co"), + person("Gary", "Ritchie", role = c("aut"), email = "gary@posit.co"), + person(family = "RStudio", role = "cph") + ) + Maintainer: Kevin Ushey + License: MIT + file LICENSE + URL: |- + https://rstudio.github.io/rstudioapi/, + https://github.com/rstudio/rstudioapi + BugReports: https://github.com/rstudio/rstudioapi/issues + RoxygenNote: 7.2.3 + Suggests: testthat, knitr, rmarkdown, clipr, covr + VignetteBuilder: knitr + Encoding: UTF-8 + NeedsCompilation: 'no' + Packaged: 2023-07-07 17:59:12 UTC; jacquelinegutman + Author: |- + Kevin Ushey [aut, cre], + JJ Allaire [aut], + Hadley Wickham [aut], + Gary Ritchie [aut], + RStudio [cph] + Repository: RSPM + Date/Publication: 2023-07-07 19:10:02 UTC + Built: R 4.3.1; ; 2024-02-06 18:43:39 UTC; unix + knitr: + Package: knitr + Type: Package + Title: A General-Purpose Package for Dynamic Report Generation in R + Version: '1.44' + Authors@R: |- + c( + person("Yihui", "Xie", role = c("aut", "cre"), email = "xie@yihui.name", comment = c(ORCID = "0000-0003-0645-5666")), + person("Abhraneel", "Sarma", role = "ctb"), + person("Adam", "Vogt", role = "ctb"), + person("Alastair", "Andrew", role = "ctb"), + person("Alex", "Zvoleff", role = "ctb"), + person("Amar", "Al-Zubaidi", role = "ctb"), + person("Andre", "Simon", role = "ctb", comment = "the CSS files under inst/themes/ were derived from the Highlight package http://www.andre-simon.de"), + person("Aron", "Atkins", role = "ctb"), + person("Aaron", "Wolen", role = "ctb"), + person("Ashley", "Manton", role = "ctb"), + person("Atsushi", "Yasumoto", role = "ctb", comment = c(ORCID = "0000-0002-8335-495X")), + person("Ben", "Baumer", role = "ctb"), + person("Brian", "Diggs", role = "ctb"), + person("Brian", "Zhang", role = "ctb"), + person("Bulat", "Yapparov", role = "ctb"), + person("Cassio", "Pereira", role = "ctb"), + person("Christophe", "Dervieux", role = "ctb"), + person("David", "Hall", role = "ctb"), + person("David", "Hugh-Jones", role = "ctb"), + person("David", "Robinson", role = "ctb"), + person("Doug", "Hemken", role = "ctb"), + person("Duncan", "Murdoch", role = "ctb"), + person("Elio", "Campitelli", role = "ctb"), + person("Ellis", "Hughes", role = "ctb"), + person("Emily", "Riederer", role = "ctb"), + person("Fabian", "Hirschmann", role = "ctb"), + person("Fitch", "Simeon", role = "ctb"), + person("Forest", "Fang", role = "ctb"), + person(c("Frank", "E", "Harrell", "Jr"), role = "ctb", comment = "the Sweavel package at inst/misc/Sweavel.sty"), + person("Garrick", "Aden-Buie", role = "ctb"), + person("Gregoire", "Detrez", role = "ctb"), + person("Hadley", "Wickham", role = "ctb"), + person("Hao", "Zhu", role = "ctb"), + person("Heewon", "Jeon", role = "ctb"), + person("Henrik", "Bengtsson", role = "ctb"), + person("Hiroaki", "Yutani", role = "ctb"), + person("Ian", "Lyttle", role = "ctb"), + person("Hodges", "Daniel", role = "ctb"), + person("Jacob", "Bien", role = "ctb"), + person("Jake", "Burkhead", role = "ctb"), + person("James", "Manton", role = "ctb"), + person("Jared", "Lander", role = "ctb"), + person("Jason", "Punyon", role = "ctb"), + person("Javier", "Luraschi", role = "ctb"), + person("Jeff", "Arnold", role = "ctb"), + person("Jenny", "Bryan", role = "ctb"), + person("Jeremy", "Ashkenas", role = c("ctb", "cph"), comment = "the CSS file at inst/misc/docco-classic.css"), + person("Jeremy", "Stephens", role = "ctb"), + person("Jim", "Hester", role = "ctb"), + person("Joe", "Cheng", role = "ctb"), + person("Johannes", "Ranke", role = "ctb"), + person("John", "Honaker", role = "ctb"), + person("John", "Muschelli", role = "ctb"), + person("Jonathan", "Keane", role = "ctb"), + person("JJ", "Allaire", role = "ctb"), + person("Johan", "Toloe", role = "ctb"), + person("Jonathan", "Sidi", role = "ctb"), + person("Joseph", "Larmarange", role = "ctb"), + person("Julien", "Barnier", role = "ctb"), + person("Kaiyin", "Zhong", role = "ctb"), + person("Kamil", "Slowikowski", role = "ctb"), + person("Karl", "Forner", role = "ctb"), + person(c("Kevin", "K."), "Smith", role = "ctb"), + person("Kirill", "Mueller", role = "ctb"), + person("Kohske", "Takahashi", role = "ctb"), + person("Lorenz", "Walthert", role = "ctb"), + person("Lucas", "Gallindo", role = "ctb"), + person("Marius", "Hofert", role = "ctb"), + person("Martin", "Modrák", role = "ctb"), + person("Michael", "Chirico", role = "ctb"), + person("Michael", "Friendly", role = "ctb"), + person("Michal", "Bojanowski", role = "ctb"), + person("Michel", "Kuhlmann", role = "ctb"), + person("Miller", "Patrick", role = "ctb"), + person("Nacho", "Caballero", role = "ctb"), + person("Nick", "Salkowski", role = "ctb"), + person("Niels Richard", "Hansen", role = "ctb"), + person("Noam", "Ross", role = "ctb"), + person("Obada", "Mahdi", role = "ctb"), + person("Pavel N.", "Krivitsky", role = "ctb", comment=c(ORCID = "0000-0002-9101-3362")), + person("Pedro", "Faria", role = "ctb"), + person("Qiang", "Li", role = "ctb"), + person("Ramnath", "Vaidyanathan", role = "ctb"), + person("Richard", "Cotton", role = "ctb"), + person("Robert", "Krzyzanowski", role = "ctb"), + person("Rodrigo", "Copetti", role = "ctb"), + person("Romain", "Francois", role = "ctb"), + person("Ruaridh", "Williamson", role = "ctb"), + person("Sagiru", "Mati", role = "ctb", comment = c(ORCID = "0000-0003-1413-3974")), + person("Scott", "Kostyshak", role = "ctb"), + person("Sebastian", "Meyer", role = "ctb"), + person("Sietse", "Brouwer", role = "ctb"), + person(c("Simon", "de"), "Bernard", role = "ctb"), + person("Sylvain", "Rousseau", role = "ctb"), + person("Taiyun", "Wei", role = "ctb"), + person("Thibaut", "Assus", role = "ctb"), + person("Thibaut", "Lamadon", role = "ctb"), + person("Thomas", "Leeper", role = "ctb"), + person("Tim", "Mastny", role = "ctb"), + person("Tom", "Torsney-Weir", role = "ctb"), + person("Trevor", "Davis", role = "ctb"), + person("Viktoras", "Veitas", role = "ctb"), + person("Weicheng", "Zhu", role = "ctb"), + person("Wush", "Wu", role = "ctb"), + person("Zachary", "Foster", role = "ctb"), + person("Zhian N.", "Kamvar", role = "ctb", comment = c(ORCID = "0000-0003-1458-7108")), + person(given = "Posit Software, PBC", role = c("cph", "fnd")) + ) + Description: |- + Provides a general-purpose tool for dynamic report generation in R + using Literate Programming techniques. + Depends: R (>= 3.3.0) + Imports: |- + evaluate (>= 0.15), highr, methods, tools, xfun (>= 0.39), + yaml (>= 2.1.19) + Suggests: |- + bslib, codetools, DBI (>= 0.4-1), digest, formatR, gifski, + gridSVG, htmlwidgets (>= 0.7), curl, jpeg, JuliaCall (>= + 0.11.1), magick, markdown (>= 1.3), png, ragg, reticulate (>= + 1.4), rgl (>= 0.95.1201), rlang, rmarkdown, sass, showtext, + styler (>= 1.2.0), targets (>= 0.6.0), testit, tibble, + tikzDevice (>= 0.10), tinytex (>= 0.46), webshot, rstudioapi, + svglite, xml2 (>= 1.2.0) + License: GPL + URL: https://yihui.org/knitr/ + BugReports: https://github.com/yihui/knitr/issues + Encoding: UTF-8 + VignetteBuilder: knitr + SystemRequirements: |- + Package vignettes based on R Markdown v2 or + reStructuredText require Pandoc (http://pandoc.org). The + function rst2pdf() requires rst2pdf + (https://github.com/rst2pdf/rst2pdf). + Collate: |- + 'block.R' 'cache.R' 'utils.R' 'citation.R' 'hooks-html.R' + 'plot.R' 'defaults.R' 'concordance.R' 'engine.R' 'highlight.R' + 'themes.R' 'header.R' 'hooks-asciidoc.R' 'hooks-chunk.R' + 'hooks-extra.R' 'hooks-latex.R' 'hooks-md.R' 'hooks-rst.R' + 'hooks-textile.R' 'hooks.R' 'output.R' 'package.R' 'pandoc.R' + 'params.R' 'parser.R' 'pattern.R' 'rocco.R' 'spin.R' 'table.R' + 'template.R' 'utils-conversion.R' 'utils-rd2html.R' + 'utils-string.R' 'utils-sweave.R' 'utils-upload.R' + 'utils-vignettes.R' 'zzz.R' + RoxygenNote: 7.2.3 + NeedsCompilation: 'no' + Packaged: 2023-09-08 19:55:48 UTC; yihui + Author: |- + Yihui Xie [aut, cre] (), + Abhraneel Sarma [ctb], + Adam Vogt [ctb], + Alastair Andrew [ctb], + Alex Zvoleff [ctb], + Amar Al-Zubaidi [ctb], + Andre Simon [ctb] (the CSS files under inst/themes/ were derived from + the Highlight package http://www.andre-simon.de), + Aron Atkins [ctb], + Aaron Wolen [ctb], + Ashley Manton [ctb], + Atsushi Yasumoto [ctb] (), + Ben Baumer [ctb], + Brian Diggs [ctb], + Brian Zhang [ctb], + Bulat Yapparov [ctb], + Cassio Pereira [ctb], + Christophe Dervieux [ctb], + David Hall [ctb], + David Hugh-Jones [ctb], + David Robinson [ctb], + Doug Hemken [ctb], + Duncan Murdoch [ctb], + Elio Campitelli [ctb], + Ellis Hughes [ctb], + Emily Riederer [ctb], + Fabian Hirschmann [ctb], + Fitch Simeon [ctb], + Forest Fang [ctb], + Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty), + Garrick Aden-Buie [ctb], + Gregoire Detrez [ctb], + Hadley Wickham [ctb], + Hao Zhu [ctb], + Heewon Jeon [ctb], + Henrik Bengtsson [ctb], + Hiroaki Yutani [ctb], + Ian Lyttle [ctb], + Hodges Daniel [ctb], + Jacob Bien [ctb], + Jake Burkhead [ctb], + James Manton [ctb], + Jared Lander [ctb], + Jason Punyon [ctb], + Javier Luraschi [ctb], + Jeff Arnold [ctb], + Jenny Bryan [ctb], + Jeremy Ashkenas [ctb, cph] (the CSS file at + inst/misc/docco-classic.css), + Jeremy Stephens [ctb], + Jim Hester [ctb], + Joe Cheng [ctb], + Johannes Ranke [ctb], + John Honaker [ctb], + John Muschelli [ctb], + Jonathan Keane [ctb], + JJ Allaire [ctb], + Johan Toloe [ctb], + Jonathan Sidi [ctb], + Joseph Larmarange [ctb], + Julien Barnier [ctb], + Kaiyin Zhong [ctb], + Kamil Slowikowski [ctb], + Karl Forner [ctb], + Kevin K. Smith [ctb], + Kirill Mueller [ctb], + Kohske Takahashi [ctb], + Lorenz Walthert [ctb], + Lucas Gallindo [ctb], + Marius Hofert [ctb], + Martin Modrák [ctb], + Michael Chirico [ctb], + Michael Friendly [ctb], + Michal Bojanowski [ctb], + Michel Kuhlmann [ctb], + Miller Patrick [ctb], + Nacho Caballero [ctb], + Nick Salkowski [ctb], + Niels Richard Hansen [ctb], + Noam Ross [ctb], + Obada Mahdi [ctb], + Pavel N. Krivitsky [ctb] (), + Pedro Faria [ctb], + Qiang Li [ctb], + Ramnath Vaidyanathan [ctb], + Richard Cotton [ctb], + Robert Krzyzanowski [ctb], + Rodrigo Copetti [ctb], + Romain Francois [ctb], + Ruaridh Williamson [ctb], + Sagiru Mati [ctb] (), + Scott Kostyshak [ctb], + Sebastian Meyer [ctb], + Sietse Brouwer [ctb], + Simon de Bernard [ctb], + Sylvain Rousseau [ctb], + Taiyun Wei [ctb], + Thibaut Assus [ctb], + Thibaut Lamadon [ctb], + Thomas Leeper [ctb], + Tim Mastny [ctb], + Tom Torsney-Weir [ctb], + Trevor Davis [ctb], + Viktoras Veitas [ctb], + Weicheng Zhu [ctb], + Wush Wu [ctb], + Zachary Foster [ctb], + Zhian N. Kamvar [ctb] (), + Posit Software, PBC [cph, fnd] + Maintainer: Yihui Xie + Repository: RSPM + Date/Publication: 2023-09-11 17:20:19 UTC + Built: R 4.3.1; ; 2024-02-06 18:05:45 UTC; unix + emulator: + Package: emulator + Type: Package + Title: Bayesian Emulation of Computer Programs + Version: 1.2-21 + Authors@R: person(given=c("Robin", "K. S."), family="Hankin", role = c("aut","cre"), + email="hankin.robin@gmail.com", comment = c(ORCID = "0000-0001-5982-0415")) + VignetteBuilder: knitr + Depends: R (>= 3.0.1), mvtnorm + Suggests: knitr,rmarkdown + Maintainer: Robin K. S. Hankin + Description: "\n Allows one to estimate the output of a computer program,\n as + a function of the input parameters, without actually running it.\n The computer + program is assumed to be a Gaussian process, whose\n parameters are estimated + using Bayesian techniques that give a PDF of\n expected program output. This + PDF is conditional on a training set\n of runs, each consisting of a point in + parameter space and the model\n output at that point. The emphasis is on complex + codes that take\n weeks or months to run, and that have a large number of undetermined\n + input parameters; many climate prediction models fall into this\n class. The + emulator essentially determines Bayesian posterior\n estimates of the PDF of + the output of a model, conditioned on results\n from previous runs and a user-specified + prior linear model. The\n package includes functionality to evaluate quadratic + forms \n efficiently. " + License: GPL + URL: https://github.com/RobinHankin/emulator + BugReports: https://github.com/RobinHankin/emulator/issues + NeedsCompilation: 'no' + Packaged: 2021-04-24 20:28:41 UTC; rhankin + Author: Robin K. S. Hankin [aut, cre] () + Repository: RSPM + Date/Publication: 2021-04-25 04:20:02 UTC + Encoding: UTF-8 + Built: R 4.3.1; ; 2024-02-06 22:58:22 UTC; unix + htmltools: + Package: htmltools + Type: Package + Title: Tools for HTML + Version: 0.5.6 + Authors@R: |- + c( + person("Joe", "Cheng", role = "aut", email = "joe@posit.co"), + person("Carson", "Sievert", role = c("aut", "cre"), email = "carson@posit.co", comment = c(ORCID = "0000-0002-4958-2844")), + person("Barret", "Schloerke", role = "aut", email = "barret@posit.co", comment = c(ORCID = "0000-0001-9986-114X")), + person("Winston", "Chang", role = "aut", email = "winston@posit.co", comment = c(ORCID = "0000-0002-1576-2126")), + person("Yihui", "Xie", role = "aut", email = "yihui@posit.co"), + person("Jeff", "Allen", role = "aut"), + person("Posit Software, PBC", role = c("cph", "fnd")) + ) + Description: Tools for HTML generation and output. + Depends: R (>= 2.14.1) + Imports: |- + utils, digest, grDevices, base64enc, rlang (>= 0.4.12), + fastmap (>= 1.1.0), ellipsis + Suggests: markdown, testthat, withr, Cairo, ragg, shiny + Enhances: knitr + License: GPL (>= 2) + URL: |- + https://github.com/rstudio/htmltools, + https://rstudio.github.io/htmltools/ + BugReports: https://github.com/rstudio/htmltools/issues + RoxygenNote: 7.2.3 + Encoding: UTF-8 + Collate: |- + 'colors.R' 'fill.R' 'html_dependency.R' 'html_escape.R' + 'html_print.R' 'htmltools-package.R' 'images.R' 'known_tags.R' + 'selector.R' 'staticimports.R' 'tag_query.R' 'utils.R' 'tags.R' + 'template.R' + Config/Needs/check: knitr + Config/Needs/website: rstudio/quillt, bench + NeedsCompilation: 'yes' + Packaged: 2023-08-10 21:52:43 UTC; cpsievert + Author: |- + Joe Cheng [aut], + Carson Sievert [aut, cre] (), + Barret Schloerke [aut] (), + Winston Chang [aut] (), + Yihui Xie [aut], + Jeff Allen [aut], + Posit Software, PBC [cph, fnd] + Maintainer: Carson Sievert + Repository: RSPM + Date/Publication: 2023-08-10 23:40:02 UTC + Built: R 4.3.1; x86_64-pc-linux-gnu; 2024-02-06 18:05:13 UTC; unix + rmarkdown: + Type: Package + Package: rmarkdown + Title: Dynamic Documents for R + Version: '2.24' + Authors@R: "c(\n person(\"JJ\", \"Allaire\", , \"jj@posit.co\", role = \"aut\"),\n + \ person(\"Yihui\", \"Xie\", , \"xie@yihui.name\", role = c(\"aut\", \"cre\"), + comment = c(ORCID = \"0000-0003-0645-5666\")),\n person(\"Christophe\", \"Dervieux\", + , \"cderv@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4474-2498\")),\n + \ person(\"Jonathan\", \"McPherson\", , \"jonathan@posit.co\", role = \"aut\"),\n + \ person(\"Javier\", \"Luraschi\", role = \"aut\"),\n person(\"Kevin\", + \"Ushey\", , \"kevin@posit.co\", role = \"aut\"),\n person(\"Aron\", \"Atkins\", + , \"aron@posit.co\", role = \"aut\"),\n person(\"Hadley\", \"Wickham\", , + \"hadley@posit.co\", role = \"aut\"),\n person(\"Joe\", \"Cheng\", , \"joe@posit.co\", + role = \"aut\"),\n person(\"Winston\", \"Chang\", , \"winston@posit.co\", + role = \"aut\"),\n person(\"Richard\", \"Iannone\", , \"rich@posit.co\", + role = \"aut\", comment = c(ORCID = \"0000-0003-3925-190X\")),\n person(\"Andrew\", + \"Dunning\", role = \"ctb\", comment = c(ORCID = \"0000-0003-0464-5036\")),\n + \ person(\"Atsushi\", \"Yasumoto\", role = c(\"ctb\", \"cph\"), comment = + c(ORCID = \"0000-0002-8335-495X\", cph = \"Number sections Lua filter\")),\n + \ person(\"Barret\", \"Schloerke\", role = \"ctb\"),\n person(\"Carson\", + \"Sievert\", role = \"ctb\", comment = c(ORCID = \"0000-0002-4958-2844\")), + \n person(\"Devon\", \"Ryan\", , \"dpryan79@gmail.com\", role = \"ctb\", + comment = c(ORCID = \"0000-0002-8549-0971\")),\n person(\"Frederik\", \"Aust\", + , \"frederik.aust@uni-koeln.de\", role = \"ctb\", comment = c(ORCID = \"0000-0003-4900-788X\")),\n + \ person(\"Jeff\", \"Allen\", , \"jeff@posit.co\", role = \"ctb\"), \n person(\"JooYoung\", + \"Seo\", role = \"ctb\", comment = c(ORCID = \"0000-0002-4064-6012\")),\n person(\"Malcolm\", + \"Barrett\", role = \"ctb\"),\n person(\"Rob\", \"Hyndman\", , \"Rob.Hyndman@monash.edu\", + role = \"ctb\"),\n person(\"Romain\", \"Lesur\", role = \"ctb\"),\n person(\"Roy\", + \"Storey\", role = \"ctb\"),\n person(\"Ruben\", \"Arslan\", , \"ruben.arslan@uni-goettingen.de\", + role = \"ctb\"),\n person(\"Sergio\", \"Oller\", role = \"ctb\"),\n person(given + = \"Posit Software, PBC\", role = c(\"cph\", \"fnd\")),\n person(, \"jQuery + UI contributors\", role = c(\"ctb\", \"cph\"), comment = \"jQuery UI library; + authors listed in inst/rmd/h/jqueryui/AUTHORS.txt\"),\n person(\"Mark\", + \"Otto\", role = \"ctb\", comment = \"Bootstrap library\"),\n person(\"Jacob\", + \"Thornton\", role = \"ctb\", comment = \"Bootstrap library\"),\n person(, + \"Bootstrap contributors\", role = \"ctb\", comment = \"Bootstrap library\"),\n + \ person(, \"Twitter, Inc\", role = \"cph\", comment = \"Bootstrap library\"),\n + \ person(\"Alexander\", \"Farkas\", role = c(\"ctb\", \"cph\"), comment = + \"html5shiv library\"),\n person(\"Scott\", \"Jehl\", role = c(\"ctb\", \"cph\"), + comment = \"Respond.js library\"),\n person(\"Ivan\", \"Sagalaev\", role + = c(\"ctb\", \"cph\"), comment = \"highlight.js library\"),\n person(\"Greg\", + \"Franko\", role = c(\"ctb\", \"cph\"), comment = \"tocify library\"),\n person(\"John\", + \"MacFarlane\", role = c(\"ctb\", \"cph\"), comment = \"Pandoc templates\"),\n + \ person(, \"Google, Inc.\", role = c(\"ctb\", \"cph\"), comment = \"ioslides + library\"),\n person(\"Dave\", \"Raggett\", role = \"ctb\", comment = \"slidy + library\"),\n person(, \"W3C\", role = \"cph\", comment = \"slidy library\"),\n + \ person(\"Dave\", \"Gandy\", role = c(\"ctb\", \"cph\"), comment = \"Font-Awesome\"),\n + \ person(\"Ben\", \"Sperry\", role = \"ctb\", comment = \"Ionicons\"),\n person(, + \"Drifty\", role = \"cph\", comment = \"Ionicons\"),\n person(\"Aidan\", + \"Lister\", role = c(\"ctb\", \"cph\"), comment = \"jQuery StickyTabs\"),\n + \ person(\"Benct Philip\", \"Jonsson\", role = c(\"ctb\", \"cph\"), comment + = \"pagebreak Lua filter\"),\n person(\"Albert\", \"Krewinkel\", role = c(\"ctb\", + \"cph\"), comment = \"pagebreak Lua filter\")\n )" + Maintainer: Yihui Xie + Description: Convert R Markdown documents into a variety of formats. + License: GPL-3 + URL: |- + https://github.com/rstudio/rmarkdown, + https://pkgs.rstudio.com/rmarkdown/ + BugReports: https://github.com/rstudio/rmarkdown/issues + Depends: R (>= 3.0) + Imports: |- + bslib (>= 0.2.5.1), evaluate (>= 0.13), fontawesome (>= + 0.5.0), htmltools (>= 0.5.1), jquerylib, jsonlite, knitr (>= + 1.22), methods, stringr (>= 1.2.0), tinytex (>= 0.31), tools, + utils, xfun (>= 0.36), yaml (>= 2.1.19) + Suggests: |- + digest, dygraphs, fs, rsconnect, downlit (>= 0.4.0), katex + (>= 1.4.0), sass (>= 0.4.0), shiny (>= 1.6.0), testthat (>= + 3.0.3), tibble, vctrs, cleanrmd, withr (>= 2.4.2) + VignetteBuilder: knitr + Config/Needs/website: rstudio/quillt, pkgdown + Encoding: UTF-8 + RoxygenNote: 7.2.3 + SystemRequirements: pandoc (>= 1.14) - http://pandoc.org + NeedsCompilation: 'no' + Packaged: 2023-08-08 08:58:47 UTC; yihui + Author: |- + JJ Allaire [aut], + Yihui Xie [aut, cre] (), + Christophe Dervieux [aut] (), + Jonathan McPherson [aut], + Javier Luraschi [aut], + Kevin Ushey [aut], + Aron Atkins [aut], + Hadley Wickham [aut], + Joe Cheng [aut], + Winston Chang [aut], + Richard Iannone [aut] (), + Andrew Dunning [ctb] (), + Atsushi Yasumoto [ctb, cph] (, + Number sections Lua filter), + Barret Schloerke [ctb], + Carson Sievert [ctb] (), + Devon Ryan [ctb] (), + Frederik Aust [ctb] (), + Jeff Allen [ctb], + JooYoung Seo [ctb] (), + Malcolm Barrett [ctb], + Rob Hyndman [ctb], + Romain Lesur [ctb], + Roy Storey [ctb], + Ruben Arslan [ctb], + Sergio Oller [ctb], + Posit Software, PBC [cph, fnd], + jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in + inst/rmd/h/jqueryui/AUTHORS.txt), + Mark Otto [ctb] (Bootstrap library), + Jacob Thornton [ctb] (Bootstrap library), + Bootstrap contributors [ctb] (Bootstrap library), + Twitter, Inc [cph] (Bootstrap library), + Alexander Farkas [ctb, cph] (html5shiv library), + Scott Jehl [ctb, cph] (Respond.js library), + Ivan Sagalaev [ctb, cph] (highlight.js library), + Greg Franko [ctb, cph] (tocify library), + John MacFarlane [ctb, cph] (Pandoc templates), + Google, Inc. [ctb, cph] (ioslides library), + Dave Raggett [ctb] (slidy library), + W3C [cph] (slidy library), + Dave Gandy [ctb, cph] (Font-Awesome), + Ben Sperry [ctb] (Ionicons), + Drifty [cph] (Ionicons), + Aidan Lister [ctb, cph] (jQuery StickyTabs), + Benct Philip Jonsson [ctb, cph] (pagebreak Lua filter), + Albert Krewinkel [ctb, cph] (pagebreak Lua filter) + Repository: RSPM + Date/Publication: 2023-08-14 08:40:06 UTC + Built: R 4.3.1; ; 2024-02-06 18:09:00 UTC; unix + gam: + Package: gam + Type: Package + Title: Generalized Additive Models + Date: '2023-03-27' + Version: 1.22-2 + Author: Trevor Hastie + Description: "Functions for fitting and working with generalized\n\t\tadditive + models, as described in chapter 7 of \"Statistical Models in S\" (Chambers and + Hastie (eds), 1991), and \"Generalized Additive Models\" (Hastie and Tibshirani, + 1990)." + Maintainer: Trevor Hastie + Depends: R (>= 4.0), stats, splines, foreach + Suggests: interp, testthat + License: GPL-2 + RoxygenNote: 7.2.1 + Encoding: UTF-8 + Imports: methods + NeedsCompilation: 'yes' + Packaged: 2023-03-27 22:47:20 UTC; hastie + Repository: RSPM + Date/Publication: 2023-03-28 02:50:02 UTC + Built: R 4.3.1; x86_64-pc-linux-gnu; 2024-02-06 20:17:24 UTC; unix + compiler: + Package: compiler + Version: 4.3.1 + Priority: base + Title: The R Compiler Package + Author: Luke Tierney + Maintainer: R Core Team + Contact: R-help mailing list + Description: Byte code compiler for R. + License: Part of R 4.3.1 + Built: R 4.3.1; ; 2024-02-06 17:43:10 UTC; unix + prettyunits: + Package: prettyunits + Title: Pretty, Human Readable Formatting of Quantities + Version: 1.1.1 + Author: Gabor Csardi + Maintainer: Gabor Csardi + Description: |- + Pretty, human readable formatting of quantities. + Time intervals: '1337000' -> '15d 11h 23m 20s'. + Vague time intervals: '2674000' -> 'about a month ago'. + Bytes: '1337' -> '1.34 kB'. + License: MIT + file LICENSE + LazyData: 'true' + URL: https://github.com/gaborcsardi/prettyunits + BugReports: https://github.com/gaborcsardi/prettyunits/issues + Suggests: codetools, covr, testthat + RoxygenNote: 7.0.2 + Encoding: UTF-8 + NeedsCompilation: 'no' + Packaged: 2020-01-24 02:16:46 UTC; gaborcsardi + Repository: RSPM + Date/Publication: 2020-01-24 06:50:07 UTC + Built: R 4.3.1; ; 2024-02-06 18:41:41 UTC; unix + nnls: + Package: nnls + Type: Package + Title: |- + The Lawson-Hanson algorithm for non-negative least squares + (NNLS) + Version: '1.4' + Author: Katharine M. Mullen and Ivo H. M. van Stokkum + Maintainer: Katharine Mullen + Description: |- + An R interface to the Lawson-Hanson implementation of an + algorithm for non-negative least squares (NNLS). Also allows + the combination of non-negative and non-positive constraints. + License: GPL (>= 2) + Packaged: 2012-03-19 16:06:34 UTC; kmullen + Repository: RSPM + Date/Publication: 2012-03-19 16:28:59 + Encoding: UTF-8 + Built: R 4.3.1; x86_64-pc-linux-gnu; 2024-02-06 21:04:17 UTC; unix +matprod: default +LA_version: 3.9.0