version 1.7.0

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: kirby21.base
 Type: Package
 Title: Example Data from the Multi-Modal MRI 'Reproducibility' Resource
-Version: 1.6.0
-Date: 2017-10-10
+Version: 1.7.0
+Date: 2018-08-13
 Author: John Muschelli <muschellij2@gmail.com>
 Maintainer: John Muschelli <muschellij2@gmail.com>
 Description: Multi-modal magnetic resonance imaging ('MRI')
@@ -13,11 +13,11 @@ License: GPL-2
 LazyData: true
 LazyLoad: true
 Imports: utils, stats, git2r
-RoxygenNote: 6.0.1.9000
+RoxygenNote: 6.1.0
 URL: https://www.nitrc.org/projects/multimodal/,
         http://dx.doi.org/10.1016/j.neuroimage.2010.11.047
 Encoding: UTF-8
 NeedsCompilation: no
-Packaged: 2017-10-10 15:47:59 UTC; johnmuschelli
+Packaged: 2018-08-13 15:38:48 UTC; johnmuschelli
 Repository: CRAN
-Date/Publication: 2017-10-11 10:30:08 UTC
+Date/Publication: 2018-08-13 16:00:03 UTC

MD5

@@ -1,11 +1,12 @@
-0b5f46ca021a492564cbae88d92933c2 *DESCRIPTION
-2771c376a0fd6a0ef9c3574b0dfff669 *NAMESPACE
-ec2d168c139813ea91698a9714ad1859 *NEWS.md
+680d95f5b08e3fde31a0bbe599514561 *DESCRIPTION
+842959f5a65c65e7d526ff99c0c9d95b *NAMESPACE
+9f99cd179b335821e44e589b8d00fd2f *NEWS.md
 fb3e2ffb85ea7152093c9957c9055d5e *R/all_modalities.R
 1a8d4083060c1826c6a178f2d2d4a20c *R/copy_kirby21_data.R
-0341f7a80b040e589e8ee367e8d5411c *R/download_kirby21_data.R
+7ec94da3fcd1e5d4b5525415c94b7321 *R/delete_kirby21_data.R
+87bc58add0dfc531671acd223781f585 *R/download_kirby21_data.R
 0a7065b1cdf0d8b5af4a490fc17e26d8 *R/get_ids.R
-064695f3876bc517b1e0dde3dc18f335 *R/get_image_filenames.R
+ea8d002c5f03d34a8657fd9692db9634 *R/get_image_filenames.R
 4292e61f49e4f9e82c7ce7ed6b3611ac *R/get_par_filenames.R
 9dd958acf733d2c88c37cb4a6fc96356 *R/kirby21_demog.R
 baf061417d9e5cbf22217bb77d161369 *R/modality_df.R
@@ -15,11 +16,12 @@ b9807347392fceecad9e148fe1a17335 *data/subject_id_to_visit_id.rda
 ae7db4099be276e1cdcb1e96d92af51a *inst/CITATION
 b30671fc022fd2dae26186285057be36 *man/all_modalities.Rd
 ab7062fb18c57e22f71dc138d7960ae3 *man/copy_kirby21_data.Rd
-c7373161636558920def16543d66827a *man/download_kirby21_data.Rd
+0b9f1a180e51dc3f9eb2da3b7d494023 *man/delete_kirby21_data.Rd
+42bf314cc76513a8add8d72f0685d5b6 *man/download_kirby21_data.Rd
 f7a607c07a59712c921dc3c95f40ca66 *man/get_ids.Rd
 eaa5db5b8ad10dac75ebd990c11444ae *man/get_image_filenames.Rd
-c1437bc9239af54cf55cb77b9ea82c90 *man/get_image_filenames_df.Rd
-f40d6828276b4037abb2a028f1c49f16 *man/get_par_filenames.Rd
+40eb7f79eb82fd3c8afdda41921cf10a *man/get_image_filenames_df.Rd
+fd0cac41994b4d9e2ebddc1c966efa93 *man/get_par_filenames.Rd
 fa7b4abb0dc2361174afc7fa7c812fa2 *man/kirby21_demog.Rd
 9dd5bacfb252c30db714051996af881c *man/modality_df.Rd
 365975275fcdabca8ca7a2823ef31f47 *man/subject_id_to_visit_id.Rd

NAMESPACE

@@ -2,6 +2,7 @@
 
 export(all_modalities)
 export(copy_kirby21_data)
+export(delete_kirby21_data)
 export(download_kirby21_data)
 export(get_ids)
 export(get_image_filenames)

NEWS.md

@@ -1,3 +1,10 @@
+# kirby21.base 1.7.0
+
+* Added options for deleting data with `delete_kirby21_data`.  
+
+* Added option for `outdir` so that you can download the data to a different
+  directory than the package path as per CRAN rules.
+
 # kirby21.base 1.6
 
 * Data is now downloaded and directories are created if necessary versus 

R/delete_kirby21_data.R

@@ -0,0 +1,25 @@
+#' @title Delete Kirby21 Imaging Data
+#' @description This function allows users to remove specific
+#' modalities for Kirby21 data sets.  This allows this package to be 
+#' on CRAN
+#'
+#' @param modality modality of images that are to be downloaded.  You
+#' must have the package downloaded for that modality.
+#'
+#' @return Nothing is returned
+#' @export
+delete_kirby21_data =  function(
+  modality = kirby21.base::all_modalities()
+  ){
+
+  modality = match.arg(modality)
+  fnames = get_image_filenames(
+    modalities = modality,
+    ids = get_ids(),
+    FALSE)
+  if (!is.null(fnames)) {
+    file.remove(fnames) 
+  }
+  return(invisible(NULL))
+}
+

R/download_kirby21_data.R

@@ -10,20 +10,24 @@
 #' @param force If the package of that modality is not installed stop.  If
 #' \code{force = FALSE}, then this will download the data but not
 #' really install the package.
+#' @param outdir output directory for files to download.  It will
+#' default to the directory of the corresponding package for the data.
 #'
 #' @return A logical indicating the data is there.
 #' @export
 #' @importFrom git2r clone
 download_kirby21_data =  function(
   modality = kirby21.base::all_modalities(),
   progress = TRUE,
-  force = FALSE){
+  force = FALSE,
+  outdir = NULL){
 
   modality = match.arg(modality)
   fnames = get_image_filenames(
     modalities = modality,
     ids = get_ids(),
-    warn = !force)
+    warn = !force,
+    outdir = outdir)
 
   mod_df = kirby21.base::modality_df()
   pkg = mod_df[ mod_df$modality %in% modality, "package"]  
@@ -84,7 +88,11 @@ download_kirby21_data =  function(
     files = list.files(path = datadir, recursive = TRUE)
     files = files[ !(files %in% "CITATION")]
     if (length(files) > 0) {
-      pkg_dir = system.file(package = pkg)
+      if (is.null(outdir)) {
+        pkg_dir = system.file(package = pkg)
+      } else {
+        pkg_dir = outdir
+      }
       infiles = file.path(datadir, files)
       outfiles = file.path(pkg_dir, files)
       dn = dirname(outfiles)
@@ -98,7 +106,8 @@ download_kirby21_data =  function(
   good = tryCatch({
     fnames = get_image_filenames(modalities = modality,
                                  ids = get_ids(),
-                                 warn = !force)
+                                 warn = !force,
+                                 outdir = outdir)
     TRUE
   }, warning = function(w) FALSE)
   return(good)

R/get_image_filenames.R

@@ -8,6 +8,8 @@
 #' @param long if \code{TRUE}, each row is a subject, visit, modality pair
 #' @param warn if \code{TRUE}, warnings will be produced when packages
 #' are not installed
+#' @param outdir output directory for files to download.  It will
+#' default to the directory of the corresponding package for the data.
 #' 
 #' @return Data.frame of filenames
 #' 
@@ -22,7 +24,8 @@ get_image_filenames_df = function(
   modalities = all_modalities(), 
   visits = c(1,2),
   long = TRUE,
-  warn = TRUE){
+  warn = TRUE,
+  outdir = NULL){
 
 
   ##########################################
@@ -75,7 +78,16 @@ get_image_filenames_df = function(
     }
   }
   df$filename = mapply(function(fname, pkg){
-    system.file( fname, package = pkg)
+    if (is.null(outdir)) {
+      file = system.file( fname, package = pkg)
+      return(file)
+    } else {
+      file = file.path(outdir, fname)
+      if (!file.exists(file)) {
+        file = ""
+      }
+      return(file)
+    }    
   }, df$filename, df$package)
 
   df = df[ !(df$filename %in% ""), , drop = FALSE]