Merge pull request #2 from FBartos/BayesTools-rewrite

CRAN eddits

.github/workflows/R-CMD-tests.yaml

@@ -12,10 +12,10 @@ on:
       - master
       - pre-release
 
-name: R-CMD-tests
+name: R-CMD-test
 
 jobs:
-  R-CMD-check:
+  R-CMD-test:
     runs-on: ${{ matrix.config.os }}
 
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
@@ -26,6 +26,7 @@ jobs:
         config:
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-20.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04,   r: 'devel',   rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest", http-user-agent: "R/4.1.0 (ubuntu-20.04) R (4.1.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
         #  - {os: macOS-11.6.2,   r: 'release'} # the release C++ version does not compile properly
 
     env:

DESCRIPTION

@@ -10,12 +10,12 @@ Authors@R: c(
     )
 Description: An implementation of Bayesian model-averaged t-test that allows 
     users to draw inference about the presence vs absence of the effect, 
-    heterogeneity of variances, and outliers. The RoBTT packages estimates model 
+    heterogeneity of variances, and outliers. The 'RoBTT' packages estimates model 
     ensembles of models created as a combination of the competing hypotheses and uses 
     Bayesian model-averaging to combine the models using posterior model probabilities. 
     Users can obtain the model-averaged posterior distributions and inclusion Bayes 
     factors which account for the uncertainty in the data generating process 
-    (Maier et al. forthcomming).
+    (Maier et al., 2022, <doi:10.31234/osf.io/d5zwc>).
     Users can define a wide range of informative priors for all parameters 
     of interest. The package provides convenient functions for summary, visualizations, 
     and fit diagnostics.
@@ -26,7 +26,7 @@ Encoding: UTF-8
 LazyData: true
 SystemRequirements: GNU make
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.0
+RoxygenNote: 7.2.1
 NeedsCompilation: yes
 ByteCompile: true
 LinkingTo: 

R/RoBTT-package.R

@@ -3,7 +3,6 @@
 ##' RoBTT: Bayesian model-averaged t-test extends the Bayesian t-test by 
 ##' incorporating inference about heterogeneity of variances and outliers.
 ##'
-##'
 ##' @name RoBTT-package
 ##' @author František Bartoš \email{f.bartos96@@gmail.com}
 ##' @keywords package

R/check-input-and-settings.R

@@ -76,6 +76,12 @@ set_control             <- function(adapt_delta = 0.80, max_treedepth = 15, brid
   BayesTools::check_bool(silent,   "silent",                  call = call)
   BayesTools::check_int(seed,      "seed", allow_NULL = TRUE, call = call)
 
+  if(!parallel){
+    cores <- 1
+  }else if(cores > RoBTT.get_option("max_cores")){
+    cores <- RoBTT.get_option("max_cores")
+  }
+
   if(is.null(control[["adapt_delta"]])){
     control[["adapt_delta"]] <- 0.80
   }else{

R/main.R

@@ -73,15 +73,18 @@
 #' @return \code{RoBTT} returns an object of \link[base]{class} \code{"RoBTT"}.
 #'
 #' @examples
-#' # using the example data from Anderson et al. 2010 and fitting the default model
+#' # using the example data from Darwin
 #' data("fertilization", package = "RoBTT")
 #' fit <- RoBTT(
 #'   x1       = fertilization$Self,
 #'   x2       = fertilization$Crossed,
 #'   prior_delta = prior("cauchy", list(0, 1/sqrt(2))),
 #'   prior_rho   = prior("beta",   list(3, 3)),
 #'   likelihood  = "normal",
-#'   seed        = 1,
+#'   seed        = 1, 
+#'   chains      = 1,
+#'   warmup      = 1000,
+#'   iter        = 2000,
 #'   control     = set_control(adapt_delta = 0.95)
 #' )
 #'
@@ -152,7 +155,7 @@ RoBTT <- function(
     parallel::stopCluster(cl)
 
   }
-  
+
   # deal with non-converged the converged models
   object$add_info$converged <- .get_model_convergence(object)
 

R/plot.R

@@ -1,10 +1,10 @@
-#' @title Plots a fitted RoBTT object
+#' @title Plots a fitted 'RoBTT' object
 #'
 #' @description \code{plot.RoBTT} allows to visualize
 #' different \code{"RoBTT"} object parameters in various
 #' ways. See \code{type} for the different model types.
 #'
-#' @param x a fitted RoBTT object
+#' @param x a fitted 'RoBTT' object
 #' @param parameter a parameter to be plotted. Defaults to
 #' \code{"delta"} (for the effect size). The additional options
 #' are \code{"rho"} (for the heterogeneity),
@@ -39,7 +39,10 @@
 #'   prior_delta = prior("cauchy", list(0, 1/sqrt(2))),
 #'   prior_rho   = prior("beta",   list(3, 3)),
 #'   likelihood  = "normal",
-#'   seed        = 1,
+#'   seed        = 1, 
+#'   chains      = 1,
+#'   warmup      = 1000,
+#'   iter        = 2000,
 #'   control     = set_control(adapt_delta = 0.95)
 #' )
 #' 

R/summary.R

@@ -1,6 +1,6 @@
-#' @title Prints a fitted RoBTT object
+#' @title Prints a fitted 'RoBTT' object
 #'
-#' @param x a fitted RoBTT object.
+#' @param x a fitted 'RoBTT' object.
 #' @param ... additional arguments.
 #'
 #'
@@ -16,13 +16,13 @@ print.RoBTT <- function(x, ...){
 }
 
 
-#' @title Summarize fitted RoBTT object
+#' @title Summarize fitted 'RoBTT' object
 #'
 #' @description \code{summary.RoBTT} creates summary tables for a
 #' RoBTT object.
 #'
-#' @param object a fitted RoBTT object
-#' @param type whether to show the overall RoBTT results (\code{"ensemble"}),
+#' @param object a fitted 'RoBTT' object
+#' @param type whether to show the overall 'RoBTT' results (\code{"ensemble"}),
 #' an overview of the individual models (\code{"models"}), an overview of
 #' the individual models MCMC diagnostics (\code{"diagnostics"}), or a detailed summary
 #' of the individual models (\code{"individual"}). Can be abbreviated to first letters.
@@ -42,15 +42,18 @@ print.RoBTT <- function(x, ...){
 #' @param ... additional arguments
 #'
 #' @examples
-#' # using the example data from Anderson et al. 2010 and fitting the default model
+#' # using the example data from Darwin
 #' data("fertilization", package = "RoBTT")
 #' fit <- RoBTT(
 #'   x1       = fertilization$Self,
 #'   x2       = fertilization$Crossed,
 #'   prior_delta = prior("cauchy", list(0, 1/sqrt(2))),
 #'   prior_rho   = prior("beta",   list(3, 3)),
 #'   likelihood  = "normal",
-#'   seed        = 1,
+#'   seed        = 1, 
+#'   chains      = 1,
+#'   warmup      = 1000,
+#'   iter        = 2000,
 #'   control     = set_control(adapt_delta = 0.95)
 #' )
 #'
@@ -70,7 +73,6 @@ print.RoBTT <- function(x, ...){
 #'
 #' # summary of individual models and their parameters can be further obtained by
 #' summary(fit, type = "individual")
-#' }
 #'
 #'
 #' @return \code{summary.RoBTT} returns a list of tables of class 'BayesTools_table'.
@@ -271,9 +273,9 @@ summary.RoBTT       <- function(object, type = "ensemble", conditional = FALSE,
 }
 
 
-#' @title Prints summary object for RoBTT method
+#' @title Prints summary object for 'RoBTT' method
 #'
-#' @param x a summary of a RoBTT object
+#' @param x a summary of a 'RoBTT' object
 #' @param ... additional arguments
 #'
 #'
@@ -342,7 +344,7 @@ print.summary.RoBTT <- function(x, ...){
 }
 
 
-#' @title Reports whether x is a RoBTT object
+#' @title Reports whether x is a 'RoBTT' object
 #'
 #' @param x an object to test
 #'
@@ -355,10 +357,11 @@ is.RoBTT            <- function(x){
 }
 
 
-#' @title Interprets results of a RoBTT model.
+
+#' @title Interprets results of a 'RoBTT' model.
 #'
 #' @description \code{interpret} creates a brief textual summary
-#' of a fitted RoBTT object.
+#' of a fitted 'RoBTT' object.
 #'
 #' @inheritParams summary.RoBTT
 #'

R/tools.R

@@ -1,10 +1,10 @@
-#' @title Check fitted RoBTT object for errors and warnings
+#' @title Check fitted 'RoBTT' object for errors and warnings
 #'
-#' @description Checks fitted RoBTT object
+#' @description Checks fitted 'RoBTT' object
 #' for warnings and errors and prints them to the
 #' console.
 #'
-#' @param fit a fitted RoBTT object.
+#' @param fit a fitted 'RoBTT' object.
 #'
 #'
 #' @return \code{check_RoBTT} returns a vector of error and

R/utilities.R

@@ -1,14 +1,14 @@
-#' @title Options for the RoBTT package
+#' @title Options for the 'RoBTT' package
 #'
-#' @description A placeholder object and functions for the RoBTT package.
+#' @description A placeholder object and functions for the 'RoBTT' package.
 #' (adapted from the runjags R package).
 #'
 #' @param name the name of the option to get the current value of - for a list of
 #' available options, see details below.
 #' @param ... named option(s) to change - for a list of available options, see
 #' details below.
 #'
-#' @return The current value of all available RoBTT options (after applying any
+#' @return The current value of all available 'RoBTT' options (after applying any
 #' changes specified) is returned invisibly as a named list.
 #'
 #' @export RoBTT.options

README.Rmd

@@ -51,7 +51,7 @@ install.packages("RoBTT")
 and the development version of the package can be installed from GitHub:
 
 ``` r
-devtools::install_github("fbartos/RoBTT")
+devtools::install_github("FBartos/RoBTT")
 ```
 
 

README.md

@@ -28,7 +28,7 @@ define a wide range of informative priors for all parameters of
 interest. The package provides convenient functions for summary,
 visualizations, and fit diagnostics.
 
-See our pre-print Maier et al. (forthcoming) introducing the method.
+See our pre-print Maier et al. (2022) introducing the method.
 
 We also prepared a vignette that illustrate functionality of the
 package:
@@ -47,7 +47,7 @@ install.packages("RoBTT")
 and the development version of the package can be installed from GitHub:
 
 ``` r
-devtools::install_github("fbartos/RoBTT")
+devtools::install_github("FBartos/RoBTT")
 ```
 
 ### References
@@ -58,8 +58,8 @@ line-spacing="2">
 <div id="ref-maier2022bayesian" class="csl-entry">
 
 Maier, M., Bartoš, F., Quintana, D. S., Bergh, D. van den, Marsman, M.,
-Ly, A., & Wagenmakers, E.-J. (forthcoming). Bayesian model-averaged
-t-tests. In *PsyArxiv*.
+Ly, A., & Wagenmakers, E.-J. (2022). *Model-averaged Bayesian t-tests*.
+<https://doi.org/10.31234/osf.io/d5zwc>
 
 </div>
 

inst/REFERENCES.bib

@@ -1,9 +1,9 @@
 @unpublished{maier2022bayesian,
-  title     = {Bayesian model-averaged t-tests},
+  title     = {Model-averaged {B}ayesian t-tests},
   author    = {Maier, Maximilian and Barto{\v{s}}, Franti{\v{s}}ek and Quintana, Daniel S and van den Bergh, Don and Marsman, Maarten and Ly, Alexander and Wagenmakers, Eric-Jan},
-  year      = {forthcoming},
-  journal   = {PsyArxiv},
-  note      = {(will be preprinted shorty)}
+  year      = {2022},
+  note      = {PsyArxiv Preprint},
+  doi       = {10.31234/osf.io/d5zwc}
 }
 
 @book{fisher1937design,