CRAN: Windows UCRT patch + BayesTools version check

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: RoBMA
 Title: Robust Bayesian Meta-Analyses
-Version: 2.1.1
+Version: 2.1.2
 Maintainer: František Bartoš <[email protected]>
 Authors@R: c( 
     person("František", "Bartoš",     role = c("aut", "cre"),

NEWS.md

@@ -1,3 +1,8 @@
+## version 2.1.2
+### Fixes
+- adding Windows ucrt patch (thanks to Tomas Kalibera)
+- adding BayesTools version check
+
 ## version 2.1.1
 ### Fixes
 - incorrectly formatted citations in vignettes and capitalization

R/utilities.R

@@ -73,3 +73,48 @@ assign("options",         RoBMA.private$defaultoptions,   envir = RoBMA.private)
 assign("RoBMA_version",   "notset",                       envir = RoBMA.private)
 assign("min_jags_major",  4,                              envir = RoBMA.private)
 assign("max_jags_major",  4,                              envir = RoBMA.private)
+
+
+# check proper BayesTools package version
+.check_BayesTools <- function(){
+
+  RoBMA.version      <- try(utils::packageVersion("RoBMA"))
+  BayesTools.version <- try(utils::packageVersion("BayesTools"))
+
+  if(inherits(RoBMA.version, "try-error") | inherits(BayesTools.version, "try-error")){
+    return(invisible(FALSE))
+  }
+
+  if(is.null(RoBMA.version) | is.null(BayesTools.version)){
+    return(invisible(FALSE))
+  }
+
+  BayesTools_min <- switch(
+    paste0(RoBMA.version, collapse = "."),
+    "2.1.1" = "0.1.3",
+    "2.1.2" = "0.1.3",
+    stop("New RoBMA version needs to be defined in '.check_BayesTools' function!")
+  )
+  BayesTools_max <- switch(
+    paste0(RoBMA.version, collapse = "."),
+    "2.1.1" = "0.1.3",
+    "2.1.2" = "0.1.3",
+    stop("New RoBMA version needs to be defined in '.check_BayesTools' function!")
+  )
+
+  min_OK <- all(as.integer(strsplit(BayesTools_min, ".", fixed = TRUE)[[1]]) <= unlist(BayesTools.version))
+  max_OK <- all(as.integer(strsplit(BayesTools_max, ".", fixed = TRUE)[[1]]) >= unlist(BayesTools.version))
+
+  if(min_OK && max_OK){
+    return(invisible(TRUE))
+  }else{
+    warning(sprintf(
+      "RoBMA version %1$s requires BayesTools version higher or equal %2$s and lower or equal %3$s.",
+      paste0(RoBMA.version, collapse = "."),
+      BayesTools_min,
+      BayesTools_max
+    ), call.=FALSE)
+    return(invisible(FALSE))
+  }
+}
+

R/zzz.R

@@ -24,11 +24,13 @@
     }
   }
 
+  .check_BayesTools()
+
 }
 
 .onAttach <- function(libname, pkgname){
 
-  packageStartupMessage("This is a 2.1 version of the RoBMA package (see NEWS for detailed overview of the changes).")
+  # packageStartupMessage("This is a 2.1 version of the RoBMA package (see NEWS for detailed overview of the changes).")
 
 }
 

README.Rmd

@@ -38,6 +38,7 @@ We also prepared multiple vignettes that illustrate functionality of the package
 
  - [Reproducing Bayesian model-averaged meta-analysis (BMA)](https://fbartos.github.io/RoBMA/articles/ReproducingBMA.html)
  - [Fitting custom meta-analytic ensembles](https://fbartos.github.io/RoBMA/articles/CustomEnsembles.html)
+ - [Informed Bayesian model-averaged meta-analysis in medicine](https://fbartos.github.io/RoBMA/articles/MedicineBMA.html)
 
 
 ## Updates

README.md

@@ -25,14 +25,14 @@ heterogeneity, and publication bias components (including selection,
 PET, and PEESE style models). The package provides convenient functions
 for summary, visualizations, and fit diagnostics.
 
-See our new pre-print Bartoš et al. (2021)
+See our new pre-print Bartoš, Maier, Wagenmakers, et al. (2021)
 (<https://doi.org/10.31234/osf.io/kvsp7>) for the description of the
 newest version, RoBMA-PSMA, or our previous paper introducing the method
 Maier et al. (in press) (<https://doi.org/10.31234/osf.io/u4cns>). The
 previous version of the methods is also implemented within the the
 user-friendly graphical user interface of JASP (JASP Team, 2020) and
-accompanied by a tutorial paper with more examples (Bartoš et al., 2020)
-(<https://doi.org/10.31234/osf.io/75bqn>).
+accompanied by a tutorial paper with more examples (Bartoš, Maier,
+Quintana, et al., 2021) (<https://doi.org/10.31234/osf.io/75bqn>).
 
 We also prepared multiple vignettes that illustrate functionality of the
 package:
@@ -41,12 +41,15 @@ package:
     (BMA)](https://fbartos.github.io/RoBMA/articles/ReproducingBMA.html)
 -   [Fitting custom meta-analytic
     ensembles](https://fbartos.github.io/RoBMA/articles/CustomEnsembles.html)
+-   [Informed Bayesian model-averaged meta-analysis in
+    medicine](https://fbartos.github.io/RoBMA/articles/MedicineBMA.html)
 
 ## Updates
 
 The package was updated to version 2.0 to provides Bayesian
 model-averaging across selection models and PET-PEESE (as described in
-Bartoš et al. (2021) at <https://doi.org/10.31234/osf.io/kvsp7>).
+Bartoš, Maier, Wagenmakers, et al. (2021) at
+<https://doi.org/10.31234/osf.io/kvsp7>).
 
 ### Backwards Compatibility
 
@@ -81,7 +84,7 @@ The 2.0 version brings several updates to the package:
     `prior_PEESE(distribution = "Cauchy", parameters = ...)`),
 -   new default prior distribution specification for the publication
     bias adjustment part of the models (corresponding to the RoBMA-PSMA
-    model from Bartoš et al. (2021)),
+    model from Bartoš, Maier, Wagenmakers, et al. (2021)),
 -   new `model_type` argument allowing to specify different “pre-canned”
     models (`"PSMA"` = RoBMA-PSMA, `"PP"` = RoBMA-PP, `"2w"` =
     corresponding to Maier et al. (in press)),
@@ -117,12 +120,12 @@ devtools::install_github("fbartos/RoBMA")
 ## Example
 
 To illustrate the functionality of the package, we fit the RoBMA-PSMA
-model from the example in Bartoš et al. (2021) to adjust for publication
-bias in the infamous Bem (2011) “Feeling the future” pre-cognition
-study. The RoBMA-PSMA model combines six selection models and PET-PEESE
-to adjust for publication bias. As in the pre-print, we analyze the data
-as described by Bem et al. (2011) in his reply to methodological
-critiques.
+model from the example in Bartoš, Maier, Wagenmakers, et al. (2021) to
+adjust for publication bias in the infamous Bem (2011) “Feeling the
+future” pre-cognition study. The RoBMA-PSMA model combines six selection
+models and PET-PEESE to adjust for publication bias. As in the
+pre-print, we analyze the data as described by Bem et al. (2011) in his
+reply to methodological critiques.
 
 First, we load the package and the data set included in the package.
 
@@ -330,9 +333,10 @@ line-spacing="2">
 
 <div id="ref-bartos2020adjusting" class="csl-entry">
 
-Bartoš, F., Maier, M., & Wagenmakers, E.-J. (2020). Adjusting for
-publication bias in JASP — selection models and robust Bayesian
-meta-analysis. In *PsyArXiv*. <https://doi.org/10.31234/osf.io/75bqn>
+Bartoš, F., Maier, M., Quintana, D. S., & Wagenmakers, E.-J. (2021).
+Adjusting for publication bias in JASP & R – selection models,
+PET-PEESE, and robust Bayesian meta-analysis. In *PsyArXiv*.
+<https://doi.org/10.31234/osf.io/75bqn>
 
 </div>
 

src/Makevars.ucrt

@@ -0,0 +1,90 @@
+######################################################################################################
+###  This file is based on file in the runjags package (version 2.0)
+###  The previous version of the file is Copyright (C) Matthew Denwood, licensed under GPL-2.
+###
+###  The previous file is based on that in the rjags package (version 3-10)
+###  Original file is Copyright (C) Martyn Plummer, licensed under GPL-2
+###
+###  Note:  This windows makefile requires the JAGS_ROOT variable to be set
+###
+###  This file allows compilation with JAGS 4 (or later) without modifying RoBMA.
+###  To force the package to compile assuming a given JAGS version is installed, use the 
+###  JAGS_MAJOR_FORCED environmental variable.  This might be necessary on windows if you have
+###  JAGS installed in a non-standard location.
+###  
+######################################################################################################
+
+## Conditionally set the JAGS_ROOT variable (if it is not already set) to a location specified by the CRAN team:
+JAGS_ROOT ?= /c/progra~1/JAGS/JAGS-4.3.0
+
+## Use the old ABI to match JAGS 4.x compilation on Windows:
+#PKG_CXXFLAGS = -D_GLIBCXX_USE_CXX11_ABI=0
+PKG_CXXFLAGS=
+## Note: this behaviour will be changed (and RoBMA updated) before JAGS 5 is released
+## If you are trying to compile this version of RoBMA against JAGS 5 you may need to remove this PKG_CXXFLAGS line
+
+###############
+###  Flags
+###  The installed major version of JAGS is needed at this stage - we try to guess this from JAGS_ROOT
+###  If you have a non-standard JAGS install (and therefore JAGS_ROOT variable), then see the README file
+###############
+
+# We need to introduce spaces so that we can fool word into splitting the $(JAGS_ROOT) path:
+space :=
+space +=
+
+# First check to see if JAGS_MAJOR_VERSION is defined in the environment and pass that as JAGS_MAJOR_FORCED to -D
+ifneq ($(strip $(JAGS_MAJOR_VERSION)),)
+JAGS_MAJOR = $(strip $(JAGS_MAJOR_VERSION))
+JAGS_MAJOR_ASSUMED = $(strip 0)
+else
+
+# Check if the JAGS_ROOT is standard i.e. we can extract a major version:
+JAGS_VERSION_PRESENT = $(findstring JAGS-,$(JAGS_ROOT))
+
+# If we can detect and extract a JAGS major version:
+ifneq ($(strip $(JAGS_VERSION_PRESENT)),)
+# First substitute / for space:
+JAGS_ROOT_SUB = $(subst /,$(space),$(JAGS_ROOT))
+# Then isolate the JAGS-x.x.x part:
+JAGS_FULL_VERS = $(word $(words $(JAGS_ROOT_SUB)),$(JAGS_ROOT_SUB))
+# Then substitute / for space and extract the major version
+JAGS_MAJOR_ASSUMED = $(strip $(word 2,$(subst .,$(space),$(subst -,$(space),$(JAGS_FULL_VERS)))))
+else
+# Otherwise make an assumption about JAGS_MAJOR and give a warning:
+JAGS_MAJOR_ASSUMED = $(strip 4)
+$(warning The major version of JAGS could not be determined from $(JAGS_ROOT) - assuming version $(JAGS_MAJOR_ASSUMED) (otherwise the Makevars.win file may need to be modified))
+endif
+
+JAGS_MAJOR = $(strip $(JAGS_MAJOR_ASSUMED))
+
+endif
+
+# Set the CPPFLAGS accordingly
+# Prepending 0 to JAGS_MAJOR_VERSION prevents it being set as blank (the C++ code requires a number)
+JAGS_MAJOR_ASSUMED := 4 
+PKG_CPPFLAGS=-I"$(JAGS_ROOT)/include" -D JAGS_MAJOR_ASSUMED=$(JAGS_MAJOR_ASSUMED) -D JAGS_MAJOR_FORCED=0$(JAGS_MAJOR_VERSION)
+
+PKG_LIBS=-L"$(JAGS_ROOT)/${R_ARCH}/bin" -ljags-$(JAGS_MAJOR) -ljrmath-0
+
+
+###############
+### Objects to be compiled
+### NB: the objects in distributions/jags are only necessary for JAGS <=3, and are excluded by the sources when compiling against JAGS >= 4
+###############
+
+OBJECTS = distributions/DWN1.o distributions/DWN2.o distributions/DWT1.o distributions/DWT2.o transformations/z.o transformations/r.o transformations/d.o transformations/logOR.o transformations/transformations_common.o init.o RoBMA.o testRoBMA.o
+
+###############
+
+
+
+###############
+#### If you still have compilation problems (after reading README) then you can use the following code instead.  Deleting everything above this line and uncomment the two relevant lines below.
+###############
+
+# PKG_CPPFLAGS=-I"$(JAGS_ROOT)/include"
+# PKG_LIBS=-L"$(JAGS_ROOT)/${R_ARCH}/bin" -ljags-4
+# OBJECTS = distributions/DWN1.o distributions/DWN2.o distributions/DWT1.o distributions/DWT2.o transformations/z.o transformations/r.o transformations/d.o transformations/logOR.o transformations/transformations_common.o init.o RoBMA.o testRoBMA.o
+
+###############