Merge pull request #29 from nicholasjclark/development

Updates for v1.38 CRAN release
nicholasjclark · Mar 22, 2021 · dba1ec6 · dba1ec6
2 parents 9440e81 + 1be86fe
commit dba1ec6
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,6 +1,8 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
-^README\.Rmd$
-^README-.*\.png$
-^docs$
-^cran-comments.md$
+^doc$
+^Meta$
+^CRAN-RELEASE
+^cran-comments.md
+^docs
+^CRAN-RELEASE$
diff --git a/.gitignore b/.gitignore
@@ -8,3 +8,5 @@ README-unnamed-chunk-6-1.png
 README-unnamed-chunk-7-1.png
 README-unnamed-chunk-8-1.png
 README-unnamed-chunk-9-1.png
+doc
+Meta
diff --git a/CRAN-RELEASE b/CRAN-RELEASE
@@ -0,0 +1,2 @@
+This package was submitted to CRAN on 2021-03-18.
+Once it is accepted, delete this file and tag the release (commit cb7d26c).
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: MRFcov
 Type: Package
 Title: Markov Random Fields with Additional Covariates 
-Version: 1.0.37
-Date/Publication: 2019-11-04
+Version: 1.0.38
+Date/Publication: 2021-02-25
 URL: https://github.com/nicholasjclark/MRFcov
 Authors@R: c(
     person("Nicholas J", "Clark", email = "[email protected]", role = c("aut", "cre")),
@@ -35,7 +35,7 @@ Imports: purrr,
     MASS
 License: GPL-3
 Encoding: UTF-8
-RoxygenNote: 6.1.1
+RoxygenNote: 7.1.1
 LazyData: true
 Suggests: testthat,
     knitr, 

diff --git a/NEWS.md b/NEWS.md
@@ -1,10 +1,7 @@
-# MRFcov 1.0.40
+# MRFcov 1.0.38
 *   Improved nonparanormal mapping of predictions for discrete variables
-
-# MRFcov 1.0.39
+*   Option to remove progress bar in multicore estimation, significantly speeding up analysis runs
 *   Improvement for the detection of infinite values in data and coordinates
-
-# MRFcov 1.0.38
 *   Option to prep spatial splines separately to allow efficient out-of-sample cross-validation
 
 # MRFcov 1.0.37

diff --git a/R/Bird.parasites.R b/R/Bird.parasites.R
@@ -17,5 +17,5 @@
 #' @references Clark, N.J., Wells, K., Dimitrov, D. & Clegg, S.M. (2016)
 #' Co-infections and environmental conditions drive the distributions of blood
 #' parasites in wild birds. Journal of Animal Ecology, 85, 1461-1470.
-#' @source \url{http://dx.doi.org/10.5061/dryad.pp6k4}
+#' @source \doi{10.5061/dryad.pp6k4}
 "Bird.parasites"
diff --git a/R/MRFcov.R b/R/MRFcov.R
@@ -42,6 +42,7 @@
 #'coefficients are estimated on the identity scale AFTER using a nonparanormal transformation.
 #'See \code{vignette("Gaussian_Poisson_CRFs")} for details of interpretation
 #'@param bootstrap Logical. Used by \code{\link{bootstrap_MRF}} to reduce memory usage
+#'@param progress_bar Logical. Progress bar in pbapply is used if \code{TRUE}, but this slows estimation.
 #'
 #'@return A \code{list} containing:
 #'\itemize{
@@ -120,7 +121,7 @@
 #'
 MRFcov <- function(data, symmetrise,
                    prep_covariates, n_nodes, n_cores, n_covariates,
-                   family, bootstrap = FALSE) {
+                   family, bootstrap = FALSE, progress_bar = FALSE) {
 
   #### Specify default parameter values and initiate warnings ####
   if(!(family %in% c('gaussian', 'poisson', 'binomial')))
@@ -364,6 +365,14 @@ MRFcov <- function(data, symmetrise,
 
   #### If n_cores > 1, check for parallel loading before initiating parallel clusters ####
   if(n_cores > 1){
+
+    # Progress bar significantly slows estimation, set to FALSE unless specified
+    if(progress_bar){
+      pbapply::pboptions(style = 1, char = "+", type = 'timer')
+    } else {
+      pbapply::pboptions(type="none")
+    }
+
     #Initiate the n_cores parallel clusters
     cl <- makePSOCKcluster(n_cores)
     setDefaultCluster(cl)

diff --git a/R/MRFcov_spatial.R b/R/MRFcov_spatial.R
@@ -61,6 +61,7 @@
 #'@param prep_splines Logical. If spatial splines are already included in  \code{data}, set to
 #'\code{FALSE}. Default is \code{TRUE}
 #'@param bootstrap Logical. Used by \code{\link{bootstrap_MRF}} to reduce memory usage
+#'@param progress_bar Logical. Progress bar in pbapply is used if \code{TRUE}, but this slows estimation.
 #'
 #'@return A \code{list} of all elements contained in a returned \code{\link{MRFcov}} object, with
 #'the inclusion of a \code{dataframe} called \code{mrf_data}. This contains all prepped covariates
@@ -86,7 +87,7 @@
 #'@export
 #'
 MRFcov_spatial <- function(data, symmetrise, prep_covariates, n_nodes, n_cores, n_covariates,
-                   family, coords, prep_splines = TRUE, bootstrap = FALSE) {
+                   family, coords, prep_splines = TRUE, bootstrap = FALSE, progress_bar = FALSE) {
 
   #### Specify default parameter values and initiate warnings ####
   if(!(family %in% c('gaussian', 'poisson', 'binomial')))
@@ -381,6 +382,14 @@ MRFcov_spatial <- function(data, symmetrise, prep_covariates, n_nodes, n_cores,
 
   #### If n_cores > 1, check for parallel loading before initiating parallel clusters ####
   if(n_cores > 1){
+
+    # Progress bar significantly slows estimation, set to FALSE unless specified
+    if(progress_bar){
+      pbapply::pboptions(style = 1, char = "+", type = 'timer')
+    } else {
+      pbapply::pboptions(type="none")
+    }
+
     #Initiate the n_cores parallel clusters
     cl <- makePSOCKcluster(n_cores)
     setDefaultCluster(cl)

diff --git a/R/predict_MRF.R b/R/predict_MRF.R
@@ -15,6 +15,7 @@
 #'by cross-multiplication (\code{TRUE} by default; \code{FALSE} when used in other functions)
 #'@param n_cores Positive integer stating the number of processing cores to split the job across.
 #'Default is \code{1} (no parallelisation)
+#'@param progress_bar Logical. Progress bar in pbapply is used if \code{TRUE}, but this slows estimation.
 #'@return A \code{matrix} containing predictions for each observation in \code{data}. If
 #'\code{family = "binomial"}, a second element containing binary
 #'predictions for nodes is returned.
@@ -59,14 +60,23 @@
 #'
 #'@export
 #'
-predict_MRF <- function(data, MRF_mod, prep_covariates = TRUE, n_cores){
+predict_MRF <- function(data, MRF_mod, prep_covariates = TRUE, n_cores,
+                        progress_bar = FALSE){
 
   if(missing(n_cores)){
     n_cores <- 1
   }
 
   #### If n_cores > 1, check parallel library loading ####
   if(n_cores > 1){
+
+    # Progress bar significantly slows estimation, set to FALSE unless specified
+    if(progress_bar){
+      pbapply::pboptions(style = 1, char = "+", type = 'timer')
+    } else {
+      pbapply::pboptions(type="none")
+    }
+
     #Initiate the n_cores parallel clusters
     cl <- makePSOCKcluster(n_cores)
     setDefaultCluster(cl)

diff --git a/R/predict_MRFnetworks.R b/R/predict_MRFnetworks.R
@@ -30,6 +30,7 @@
 #'networks from \code{\link{MRFcov_spatial}} objects)
 #'@param n_cores Positive integer stating the number of processing cores to split the job across.
 #'Default is \code{1} (no parallelisation)
+#'@param progress_bar Logical. Progress bar in pbapply is used if \code{TRUE}, but this slows estimation.
 #'
 #'@return Either a \code{matrix} with \code{nrow = nrow(data)},
 #'containing each species' predicted network metric at each observation in \code{data}, or
@@ -64,7 +65,7 @@
 #'
 predict_MRFnetworks = function(data, MRF_mod, cutoff, omit_zeros, metric,
                                cached_predictions = NULL, prep_covariates,
-                               n_cores){
+                               n_cores, progress_bar = FALSE){
 
   if(missing(n_cores)){
     n_cores <- 1
@@ -157,15 +158,17 @@ predict_MRFnetworks = function(data, MRF_mod, cutoff, omit_zeros, metric,
   if(MRF_mod$mod_family == "binomial"){
     if(is.null(cached_predictions)){
     preds <- predict_MRF(pred.prepped.dat, MRF_mod_booted,
-                         prep_covariates = FALSE, n_cores = n_cores)$Probability_predictions
+                         prep_covariates = FALSE, n_cores = n_cores,
+                         progress_bar = progress_bar)$Probability_predictions
     } else {
       preds <- cached_predictions$Probability_predictions
     }
 
   } else {
     if(is.null(cached_predictions)){
     preds <- predict_MRF(pred.prepped.dat, MRF_mod_booted,
-                         prep_covariates = FALSE, n_cores = n_cores)
+                         prep_covariates = FALSE, n_cores = n_cores,
+                         progress_bar = progress_bar)
     } else {
       preds <- cached_predictions
       }

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,4 +1,4 @@
-## Patch updates for release v1.0.40
+## Patch updates for release v1.0.38
 This update contains improvments to the nonparanormal mapping of predictions for discrete variables
 
 ## Test environments
@@ -8,8 +8,21 @@ This update contains improvments to the nonparanormal mapping of predictions for
 ## R CMD check results
 There were no ERRORs or WARNINGs. 
 
-The following NOTE appeared in the win-builder check:
-* checking CRAN incoming feasibility ... NOTE
+An ERROR appears in the win-builder check for r-devel-windows-ix86+x86_64, likely owing to failures on r-devel-windows-ix86+x86_64 due to missing dependencies that need compilation. A test using `rhub::check( platform="windows-x86_64-devel", env_vars=c(R_COMPILE_AND_INSTALL_PACKAGES = "always"))` passes the win-builder check
+
+Previously three top level files were non-standard. These have been moved to .Rbuildignore and now are not flagged in R RMD checks
+
+Previously the version of this update was not sufficient for CRAN requirements: Insufficient package version (submitted: 1.0.4, existing: 1.0.37). This has been changed (new version is 1.0.38)
+
+A URL in the one of the vignettes previously did not have https. The CRAN note was
+* Found the following (possibly) invalid URLs: URL: http://www.jmlr.org/papers/v10/liu09a.html (moved to https://www.jmlr.org/papers/v10/liu09a.html) From: inst/doc/Gaussian_Poisson_CRFs.html Status: 200
+
+This has been changed to the suggested https format
+
+Previously a DOI was not formatted according to CRAN requirements: Found the following URLs which should use \doi (with the DOI name only): File 'Bird.parasites.Rd': http://dx.doi.org/10.5061/dryad.pp6k4
+
+This has been fixed
+
+
 Maintainer: 'Nicholas J Clark <[email protected]>'
 
-No action was taken, as this note apparently reminds CRAN maintainers to check that the submission actually comes from myself and not anybody else.
diff --git a/docs/README.Rmd b/docs/README.Rmd
@@ -94,7 +94,7 @@ MRF_mod$key_coefs$Plas
 MRF_mod$key_coefs$Microfilaria
 ```
 
-To work through more in-depth tutorials and examples, see the vignettes in the package and check out papers that have been published using the method
+To work through more in-depth tutorials and examples, see the vignettes in the package and check out some of the papers that have been published using the method
 ```{r eval=FALSE}
 vignette("Bird_Parasite_CRF")
 vignette("Gaussian_Poisson_CRFs")

diff --git a/man/Bird.parasites.Rd b/man/Bird.parasites.Rd
diff --git a/man/MRFcov.Rd b/man/MRFcov.Rd
diff --git a/man/MRFcov_spatial.Rd b/man/MRFcov_spatial.Rd
diff --git a/man/bootstrap_MRF.Rd b/man/bootstrap_MRF.Rd
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		This package was submitted to CRAN on 2021-03-18.
		Once it is accepted, delete this file and tag the release (commit cb7d26c).