Run styler on package

NeuroShepherd · Nov 17, 2024 · 98f5c6c · 98f5c6c
1 parent a54d0aa
commit 98f5c6c
Show file tree

Hide file tree

Showing 16 changed files with 248 additions and 278 deletions.
diff --git a/.Rprofile b/.Rprofile
@@ -1,11 +1,11 @@
 source("renv/activate.R")
-options(shiny.autoload.r=FALSE)
+options(shiny.autoload.r = FALSE)
 options(
   list(
     ordinalsimr.default_iterations = 20,
     ordinalsimr.default_size_min = 30,
     ordinalsimr.default_size_max = 35,
     ordinalsimr.default_ratio = "50:50",
-    ordinalsimr.default_distributions = data.frame(c(0.4,0.3,0.3), c(0.8,0.1,0.1))
+    ordinalsimr.default_distributions = data.frame(c(0.4, 0.3, 0.3), c(0.8, 0.1, 0.1))
   )
 )
diff --git a/R/mod_distributions_page.R b/R/mod_distributions_page.R
@@ -24,7 +24,8 @@ mod_distributions_page_ui <- function(id) {
           h6("Confidence Intervals"),
           !!!mod_plot_distributions_ui("plot_distributions_1")[["ci_inputs"]],
           h6("Outlier Removal (Plot Only)"),
-          mod_plot_distributions_ui("plot_distributions_1")[["outlier_input"]]),
+          mod_plot_distributions_ui("plot_distributions_1")[["outlier_input"]]
+        ),
         nav_panel(
           title = "Power",
           mod_plot_distributions_ui("plot_distributions_1")[["output_plots"]][["power_plot"]]

diff --git a/R/mod_plot_distributions.R b/R/mod_plot_distributions.R
@@ -174,7 +174,7 @@ mod_plot_distributions_server <- function(id, p_value_table, n) {
             alpha = p_val_threshold(),
             t1_error_confidence_int = input$t1_error_group1_confidence_int
           )
-        }
+      }
     })
     output$t1_error_group1 <- DT::renderDataTable({
       validate(
@@ -195,7 +195,6 @@ mod_plot_distributions_server <- function(id, p_value_table, n) {
 
     # GROUP 2 TYPE 1 ERROR
     group2_t1_reactive_table <- reactive({
-
       if (!is.null(p_value_table$group2_results())) {
         p_value_table$group2_results() %>%
           bind_rows() %>%
@@ -212,7 +211,6 @@ mod_plot_distributions_server <- function(id, p_value_table, n) {
             t1_error_confidence_int = input$t1_error_group2_confidence_int
           )
       }
-
     })
     output$t1_error_group2 <- DT::renderDataTable({
       validate(

diff --git a/R/mod_report_generator.R b/R/mod_report_generator.R
@@ -35,7 +35,7 @@ mod_report_generator_server <- function(id, formatted_data, rng_info) {
                 run_info = formatted_data()$comparison_data$run_info,
                 distribution_statistics = formatted_data()$comparison_data$distribution_statistics,
                 distribution_plot = formatted_data()$comparison_data$distribution_plot
-                ),
+              ),
               group1_data = list(
                 run_info = formatted_data()$group1_data$run_info,
                 group1_t1error = formatted_data()$group1_data$group1_t1error
@@ -62,60 +62,59 @@ mod_report_generator_server <- function(id, formatted_data, rng_info) {
 
 
     download_counter_zip <- reactiveVal(1)
-    output$download_report <-  downloadHandler(
-        filename = function() {
-          paste0("ordinalsimr_session_", strtrim(session$token, 8),
-                 "_download_", download_counter_zip(),
-                 ".zip")
-        },
-        content = function(file) {
-
-          output_folder <- file.path(paste0("ordinalsimr_session_", strtrim(session$token, 8),
-                                            "_download_", download_counter_zip()))
-          dir.create(output_folder, showWarnings = FALSE)
-
-          try({
-            write(
-              custom_report(),
-              file.path(output_folder, "completed_report.html")
-            )
-          })
-          try({
-            saveRDS(
-              formatted_data(),
-              file.path(output_folder, "ordinalsimr_results.rds")
-            )
-          })
-          try({
-            write(
-              readLines(system.file("report_template.Rmd", package = "ordinalsimr")),
-              file.path(output_folder, "report_template.Rmd")
-            )
-          })
-
-            zip_files <- c(
-              file.path(output_folder, "completed_report.html"),
-              file.path(output_folder, "ordinalsimr_results.rds"),
-              file.path(output_folder, "report_template.Rmd")
-            )
-
-          try({
-            utils::zip(
-              zipfile = file,
-              files = zip_files
-              # flags = '-r9Xb'
-            )
-          })
-
-          unlink(output_folder, recursive = TRUE, force = TRUE)
-          download_counter_zip(download_counter_zip() + 1)
-
-        },
-        contentType = "application/zip"
-      )
+    output$download_report <- downloadHandler(
+      filename = function() {
+        paste0(
+          "ordinalsimr_session_", strtrim(session$token, 8),
+          "_download_", download_counter_zip(),
+          ".zip"
+        )
+      },
+      content = function(file) {
+        output_folder <- file.path(paste0(
+          "ordinalsimr_session_", strtrim(session$token, 8),
+          "_download_", download_counter_zip()
+        ))
+        dir.create(output_folder, showWarnings = FALSE)
+
+        try({
+          write(
+            custom_report(),
+            file.path(output_folder, "completed_report.html")
+          )
+        })
+        try({
+          saveRDS(
+            formatted_data(),
+            file.path(output_folder, "ordinalsimr_results.rds")
+          )
+        })
+        try({
+          write(
+            readLines(system.file("report_template.Rmd", package = "ordinalsimr")),
+            file.path(output_folder, "report_template.Rmd")
+          )
+        })
 
+        zip_files <- c(
+          file.path(output_folder, "completed_report.html"),
+          file.path(output_folder, "ordinalsimr_results.rds"),
+          file.path(output_folder, "report_template.Rmd")
+        )
 
+        try({
+          utils::zip(
+            zipfile = file,
+            files = zip_files
+            # flags = '-r9Xb'
+          )
+        })
 
+        unlink(output_folder, recursive = TRUE, force = TRUE)
+        download_counter_zip(download_counter_zip() + 1)
+      },
+      contentType = "application/zip"
+    )
   })
 }
 

diff --git a/R/mod_sample_probabilities.R b/R/mod_sample_probabilities.R
@@ -11,7 +11,7 @@ mod_sample_probabilities_ui <- function(id) {
   ns <- NS(id)
 
   default_ratio <- tryCatch(
-    getOption("ordinalsimr.default_ratio", default = "50:50") ,
+    getOption("ordinalsimr.default_ratio", default = "50:50"),
     error = function(e) {
       "50:50"
     }

diff --git a/R/mod_save_data.R b/R/mod_save_data.R
@@ -65,34 +65,39 @@ mod_save_data_server <- function(id, input_data, processed_data, rng_info, input
           h5("Excel Download:"),
           p("Please install the {writexl} package.")
         )
-        }
-      })
+      }
+    })
 
     download_counter_excel <- reactiveVal(1)
     output$save_xlsx <- downloadHandler(
-        filename = function() {
-          paste0("data-", Sys.Date(), "-", strtrim(session$token, 6), "-", download_counter_excel(), ".xlsx")
-        },
-        content = function(file) {
-          writexl::write_xlsx(
-            list(
-              distribution_statistics = data_to_save()$comparison_data$distribution_statistics,
-              comparison_run_info = data_to_save()$comparison_data$run_info,
-              group1_type1_error = data_to_save()$group1_data$group1_t1error,
-              group1_run_info = data_to_save()$group1_data$run_info,
-              group2_type1_error = data_to_save()$group2_data$group2_t1error,
-              group2_run_info = data_to_save()$group2_data$run_info
-            ) %>%
-              lapply(function(x) {if (is.null(x)) {data.frame()} else {x}}),
-            path = file
-          )
-          # increment download number
-          download_counter_excel(download_counter_excel() + 1)
-        }
-      )
+      filename = function() {
+        paste0("data-", Sys.Date(), "-", strtrim(session$token, 6), "-", download_counter_excel(), ".xlsx")
+      },
+      content = function(file) {
+        writexl::write_xlsx(
+          list(
+            distribution_statistics = data_to_save()$comparison_data$distribution_statistics,
+            comparison_run_info = data_to_save()$comparison_data$run_info,
+            group1_type1_error = data_to_save()$group1_data$group1_t1error,
+            group1_run_info = data_to_save()$group1_data$run_info,
+            group2_type1_error = data_to_save()$group2_data$group2_t1error,
+            group2_run_info = data_to_save()$group2_data$run_info
+          ) %>%
+            lapply(function(x) {
+              if (is.null(x)) {
+                data.frame()
+              } else {
+                x
+              }
+            }),
+          path = file
+        )
+        # increment download number
+        download_counter_excel(download_counter_excel() + 1)
+      }
+    )
 
     return(data_to_save)
-
   })
 }
 

diff --git a/R/mod_simulation_inputs_page.R b/R/mod_simulation_inputs_page.R
@@ -15,9 +15,8 @@ mod_simulation_inputs_page_ui <- function(id) {
     layout_columns(
       fill = TRUE,
       fillable = TRUE,
-      col_widths = c(-1,10,-1,-1,10,-1),
+      col_widths = c(-1, 10, -1, -1, 10, -1),
       row_heights = c(9, 7),
-
       card(
         card_header("Data Entry", class = "bg-dark"),
         layout_sidebar(
@@ -37,29 +36,27 @@ mod_simulation_inputs_page_ui <- function(id) {
           "Core Inputs",
           card_title("Iterations, Samples, and Tests"),
           layout_column_wrap(
-            width = 1/3,
-              mod_iterations_ui("iterations_1"),
-              mod_sample_size_ui("sample_size_1"),
-              mod_sample_probabilities_ui("sample_probabilities_1")
+            width = 1 / 3,
+            mod_iterations_ui("iterations_1"),
+            mod_sample_size_ui("sample_size_1"),
+            mod_sample_probabilities_ui("sample_probabilities_1")
           ),
           layout_column_wrap(
             width = 1,
-              mod_select_tests_ui("select_tests_1")
-            )
+            mod_select_tests_ui("select_tests_1")
+          )
         ),
-
         nav_panel(
           "Type I Erorr",
           card_title("TI Error by Group"),
           mod_type_one_error_ui("type_one_error_1")
         ),
-
         nav_panel(
           "RNG Options",
           card_title("Advanced: Random Number Generator Adjustments"),
           markdown("These Random Number Generators are advanced options, and they use the default values employed by R as of version 4.4. Run `?RNGkind` in an R session to see the associated help file."),
           layout_column_wrap(
-            width = 1/3,
+            width = 1 / 3,
             !!!mod_rng_option_ui("rng_option_1")
           )
         )

diff --git a/R/mod_start_simulation.R b/R/mod_start_simulation.R
@@ -11,7 +11,7 @@ mod_start_simulation_ui <- function(id) {
   ns <- NS(id)
   tagList(
     actionButton(ns("run_button"), "Run Tests") %>%
-      tagAppendAttributes(class="btn btn-success")
+      tagAppendAttributes(class = "btn btn-success")
   )
 }
 

diff --git a/R/run_simulations.R b/R/run_simulations.R
@@ -50,43 +50,42 @@ run_simulations <- function(sample_size, sample_prob, prob0, prob1, niter, inclu
   )
 
 
-    lapply(sample_size, function(x) {
-      sample_size_nested <- x
-      initial_groups <- lapply(1:niter, function(x) {
-        assign_groups(
-          sample_size = sample_size_nested,
-          sample_prob = sample_prob,
-          prob0 = prob0, prob1 = prob1,
-          seed = x,
-          .rng_kind = .rng_kind,
-          .rng_normal_kind = .rng_normal_kind,
-          .rng_sample_kind = .rng_sample_kind
-        )
-      })
+  lapply(sample_size, function(x) {
+    sample_size_nested <- x
+    initial_groups <- lapply(1:niter, function(x) {
+      assign_groups(
+        sample_size = sample_size_nested,
+        sample_prob = sample_prob,
+        prob0 = prob0, prob1 = prob1,
+        seed = x,
+        .rng_kind = .rng_kind,
+        .rng_normal_kind = .rng_normal_kind,
+        .rng_sample_kind = .rng_sample_kind
+      )
+    })
 
-      p_values <- initial_groups %>%
-        sapply(., function(x) ordinal_tests(x[["x"]], x[["y"]], included = included)) %>%
-        t()
+    p_values <- initial_groups %>%
+      sapply(., function(x) ordinal_tests(x[["x"]], x[["y"]], included = included)) %>%
+      t()
 
-      initial_groups_formatted <- lapply(initial_groups, function(groups) {
-        tibble(
-          y = list(groups[["y"]]), x = list(groups[["x"]]),
-          n_null = groups[["n_null"]], n_intervene = groups[["n_intervene"]],
-          sample_size = groups[["sample_size"]], K = groups[["K"]]
-        )
-      }) %>%
-        bind_rows() %>%
-        mutate(run = row_number(), .before = .data$y)
-
-      if (shiny::isRunning()) {
-        incProgress(
-          1/(max(sample_size)-min(sample_size)),
-          detail = paste("Sample size", sample_size_nested, "completed.")
-        )
-      }
-
-      return(sim_results_table = bind_cols(p_values, initial_groups_formatted))
+    initial_groups_formatted <- lapply(initial_groups, function(groups) {
+      tibble(
+        y = list(groups[["y"]]), x = list(groups[["x"]]),
+        n_null = groups[["n_null"]], n_intervene = groups[["n_intervene"]],
+        sample_size = groups[["sample_size"]], K = groups[["K"]]
+      )
     }) %>%
-      magrittr::set_names(paste0("sample_size_", sample_size))
+      bind_rows() %>%
+      mutate(run = row_number(), .before = .data$y)
+
+    if (shiny::isRunning()) {
+      incProgress(
+        1 / (max(sample_size) - min(sample_size)),
+        detail = paste("Sample size", sample_size_nested, "completed.")
+      )
+    }
 
+    return(sim_results_table = bind_cols(p_values, initial_groups_formatted))
+  }) %>%
+    magrittr::set_names(paste0("sample_size_", sample_size))
 }