Merge pull request #107 from mrc-ide/develop

Develop

DESCRIPTION

@@ -1,42 +1,43 @@
-Package: drjacoby
-Type: Package
-Title: Flexible Markov Chain Monte Carlo via Reparameterization
-Version: 1.5.0
-Authors@R: c(
-    person("Bob", "Verity", email = "[email protected]", role = c("aut", "cre")),
-    person("Pete", "Winskill", email = "[email protected]", role = c("aut"))
-    )
-Description: drjacoby is an R package for performing Bayesian inference via
-    Markov chain monte carlo (MCMC). In addition to being highly flexible it
-    implements some advanced techniques that can improve mixing in tricky
-    situations.
-License: MIT + file LICENSE
-Encoding: UTF-8
-LazyData: true
-RoxygenNote: 7.1.1
-LinkingTo: 
-    Rcpp
-Imports: 
-    Rcpp,
-    coda,
-    parallel,
-    ggplot2,
-    RcppXPtrUtils,
-    usethis,
-    tools,
-    rlang,
-    cowplot,
-    dplyr,
-    magrittr,
-    readr
-SystemRequirements: C++11
-Suggests: 
-    testthat,
-    covr,
-    knitr,
-    rmarkdown,
-    microbenchmark,
-    gridExtra
-BugReports: https://github.com/mrc-ide/drjacoby/issues
-VignetteBuilder: knitr
-Depends: R (>= 3.1.0)
+Package: drjacoby
+Type: Package
+Title: Flexible Markov Chain Monte Carlo via Reparameterization
+Version: 1.5.2
+Authors@R: c(
+    person("Bob", "Verity", email = "[email protected]", role = c("aut", "cre")),
+    person("Pete", "Winskill", email = "[email protected]", role = c("aut"))
+    )
+Description: drjacoby is an R package for performing Bayesian inference via
+    Markov chain monte carlo (MCMC). In addition to being highly flexible it
+    implements some advanced techniques that can improve mixing in tricky
+    situations.
+License: MIT + file LICENSE
+Encoding: UTF-8
+LazyData: true
+RoxygenNote: 7.1.1
+LinkingTo: 
+    Rcpp
+Imports: 
+    Rcpp,
+    coda,
+    parallel,
+    ggplot2,
+    RcppXPtrUtils,
+    usethis,
+    tools,
+    rlang,
+    cowplot,
+    dplyr,
+    magrittr,
+    readr,
+    data.table
+SystemRequirements: C++11
+Suggests: 
+    testthat,
+    covr,
+    knitr,
+    rmarkdown,
+    microbenchmark,
+    gridExtra
+BugReports: https://github.com/mrc-ide/drjacoby/issues
+VignetteBuilder: knitr
+Depends: R (>= 3.1.0)

R/data.R

@@ -0,0 +1,11 @@
+#' Population data.
+#'
+#' Example population growth data.
+#'
+#' @format A data frame with 20 rows and 2 variables:
+#' \describe{
+#'   \item{pop}{population size}
+#'   \item{time}{time}
+#'   ...
+#' }
+"population_data"

R/main.R

@@ -184,6 +184,8 @@ check_params <- function(x) {
 #'   raised to the power \eqn{\beta[i]^\alpha}, meaning we can use the
 #'   \eqn{\alpha} parameter to concentrate rungs towards the start or the end of
 #'   the temperature scale.
+#' @param target_acceptance Target acceptance rate. Should be between 0 and 1.
+#'   Default of 0.44, set as optimum for unvariate proposal distributions.
 #' @param cluster option to pass in a cluster environment, allowing chains to be
 #'   run in parallel (see package "parallel").
 #' @param coupling_on whether to implement Metropolis-coupling over temperature
@@ -217,6 +219,7 @@ run_mcmc <- function(data,
                      chains = 5,
                      beta_manual = NULL,
                      alpha = 1.0,
+                     target_acceptance = 0.44,
                      cluster = NULL,
                      coupling_on = TRUE,
                      pb_markdown = FALSE,
@@ -250,6 +253,7 @@ run_mcmc <- function(data,
   assert_single_pos_int(chains, zero_allowed = FALSE)
   assert_single_logical(coupling_on)
   assert_single_pos(alpha)
+  assert_bounded(target_acceptance, 0, 1)
 
   # check df_params
   df_params <- check_params(df_params)
@@ -362,7 +366,8 @@ run_mcmc <- function(data,
                       beta_raised = beta_raised,
                       save_hot_draws = save_hot_draws,
                       pb_markdown = pb_markdown,
-                      silent = silent)
+                      silent = silent,
+                      target_acceptance = target_acceptance)
 
   # functions to pass to C++
   args_functions <- list(loglike = loglike,

_pkgdown.yml

@@ -17,6 +17,8 @@ navbar:
           href: articles/metropolis_coupling.html
         - text: "Running Parallel Chains"
           href: articles/parallel.html
+        - text: "Getting Model Fits"
+          href: articles/getting_model_fits.html
         - text: "Using Likelihood Blocks"
           href: articles/blocks.html
     - text: "Checks"