Merge pull request #620 from adokter/cran_release

bioRad 0.7.1 CRAN release
adokter · Jul 17, 2023 · 7a6cfdf · 7a6cfdf
2 parents b950303 + f85afd7
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diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -1,3 +1,3 @@
 Version: 0.7.1
-Date: 2023-07-10 19:20:10 UTC
-SHA: 3e9e916782d7e86b894e8cc04313b7ad4392c2a1
+Date: 2023-07-17 16:11:14 UTC
+SHA: bab8c99165d91822e5bacd5c62ddf4c6cc94c3d7
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: bioRad
 Title: Biological Analysis and Visualization of Weather Radar Data
-Version: 0.7.0.9617
+Version: 0.7.1
 Description: Extract, visualize and summarize aerial movements of birds and
     insects from weather radar data. See Dokter, A. M. et al. (2018) 
     "bioRad: biological analysis and visualization of weather radar data" <doi:10.1111/ecog.04028>
@@ -37,7 +37,6 @@ Imports:
     graphics,
     lubridate,
     lutz,
-    rhdf5,
     suntools,
     methods,
     raster,
@@ -52,8 +51,6 @@ Imports:
     viridis,
     rlang,
     jsonlite
-Remotes:
-    bioc::rhdf5
 Suggests:
     vol2birdR,
     aws.s3,

diff --git a/R/apply_mistnet.R b/R/apply_mistnet.R
@@ -83,19 +83,22 @@
 #' (11), pp. 1908-22. \doi{10.1111/2041-210X.13280}
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' # make sure you have installed the MistNet libraries and model, using:
-#' # vol2birdR::install_mistnet()
-#' # vol2birdR::install_mistnet_model()
-#'
+#' if(!vol2birdR::mistnet_exists()){
+#'    vol2birdR::install_mistnet()
+#'    vol2birdR::install_mistnet_model()
+#' }
+#' # start a temporary file to store polar volume
+#' tempfile=tempfile("KBGM_example")
 #' # Download a NEXRAD file and save as KBGM_example
 #' download.file(
 #'   "https://noaa-nexrad-level2.s3.amazonaws.com/2019/10/01/KBGM/KBGM20191001_000542_V06",
-#'   "~/KBGM_example"
+#'   tempfile
 #' )
 #'
 #' # Calculate MistNet segmentation
-#' mistnet_pvol <- apply_mistnet("~/KBGM_example")
+#' mistnet_pvol <- apply_mistnet(tempfile)
 #'
 #' # Print summary info for the segmented elevation scan at the 0.5 degree,
 #' # verify new parameters BIOLOGY, WEATHER, BACKGROUND and CELL have been added
@@ -120,7 +123,7 @@
 #' plot(ppi, param = "CELL")
 #'
 #' # Remove file
-#' file.remove("~/KBGM_example")
+#' file.remove(tempfile)
 #' }
 apply_mistnet <- function(file, pvolfile_out, verbose = FALSE,
                           mount = dirname(file), load = TRUE,

diff --git a/R/plot.scan.R b/R/plot.scan.R
@@ -37,12 +37,14 @@
 #' # Plot reflectivity
 #' plot(example_scan, param = "DBZH")
 #'
+#' \donttest{
 #' # Change the range of reflectivities to plot, from -10 to 10 dBZ
 #' plot(example_scan, param = "DBZH", zlim = c(-10, 10))
 #'
 #' # Change the scale name, change the color palette to Viridis colors
 #' plot(example_scan, param = "DBZH", zlim = c(-10, 10)) +
 #'   viridis::scale_fill_viridis(name = "dBZ")
+#' }
 plot.scan <- function(x, param, xlim = c(0, 100000),
                       ylim = c(0, 360), zlim = c(-20, 20), na.value = "transparent", ...) {
   stopifnot(inherits(x, "scan"))

diff --git a/R/rcs.R b/R/rcs.R
@@ -71,6 +71,8 @@ rcs.vpi <- function(x) {
 #' @inheritParams rcs
 #' @param value Numeric. The radar cross section value to assign in cm^2.
 #'
+#' @return The input object with updated density `x$data$dens` and updated radar cross section attribute.
+#'
 #' @export
 #'
 #' @seealso

diff --git a/R/read_vpfiles.R b/R/read_vpfiles.R
@@ -101,7 +101,7 @@ read_vp <- function(file) {
 #' read_vpfiles(vpfile)
 #'
 #' # to load multiple files at once:
-#' # read_vpfiles(c("my/path/profile1.h5", "my/path/profile2.h5", ...))
+#' read_vpfiles(c(vpfile, vpfile))
 read_vpfiles <- function(files) {
   if (length(files) == 1) {
     return(read_vp(files))

diff --git a/R/sd_vvp_threshold.R b/R/sd_vvp_threshold.R
@@ -64,6 +64,8 @@ sd_vvp_threshold.vpts <- function(x) {
 #' @inheritParams sd_vvp_threshold
 #' @param value Numeric. The `sd_vvp` threshold value to assign in m/s.
 #'
+#' @return The input object with updated density `x$data$dens` and `sd_vvp_thresh` attribute.
+#'
 #' @export
 #'
 #' @seealso

diff --git a/R/vp.R b/R/vp.R
@@ -67,7 +67,7 @@
 #' * [bind_into_vpts()]
 #'
 #' @return For [summary.vp()]: prints summary of the `vp` object.
-#' 
+#'
 #' @examples
 #' # Check if an object is of class vp
 #' is.vp(example_vp)
@@ -141,6 +141,10 @@ dim.vp <- function(x) {
 #'
 #' @export
 #'
+#' @examples
+#' # concatenate vp objects into a list:
+#' c(example_vp, example_vp)
+#'
 #' @seealso [bind_into_vpts()]
 c.vp <- function(...) {
   vp_list <- list(...)

diff --git a/README.md b/README.md
@@ -97,7 +97,7 @@ Then load the package with:
 
 ``` r
 library(bioRad)
-#> Welcome to bioRad version 0.7.0.9617
+#> Welcome to bioRad version 0.7.1
 #> using vol2birdR version 1.0.1 (MistNet installed)
 ```
 

diff --git a/codemeta.json b/codemeta.json
@@ -345,18 +345,6 @@
       "sameAs": "https://CRAN.R-project.org/package=lutz"
     },
     "11": {
-      "@type": "SoftwareApplication",
-      "identifier": "rhdf5",
-      "name": "rhdf5",
-      "provider": {
-        "@id": "https://www.bioconductor.org",
-        "@type": "Organization",
-        "name": "Bioconductor",
-        "url": "https://www.bioconductor.org"
-      },
-      "sameAs": "https://bioconductor.org/packages/release/bioc/html/rhdf5.html"
-    },
-    "12": {
       "@type": "SoftwareApplication",
       "identifier": "suntools",
       "name": "suntools",
@@ -368,12 +356,12 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=suntools"
     },
-    "13": {
+    "12": {
       "@type": "SoftwareApplication",
       "identifier": "methods",
       "name": "methods"
     },
-    "14": {
+    "13": {
       "@type": "SoftwareApplication",
       "identifier": "raster",
       "name": "raster",
@@ -385,7 +373,7 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=raster"
     },
-    "15": {
+    "14": {
       "@type": "SoftwareApplication",
       "identifier": "readr",
       "name": "readr",
@@ -397,6 +385,18 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=readr"
     },
+    "15": {
+      "@type": "SoftwareApplication",
+      "identifier": "rhdf5",
+      "name": "rhdf5",
+      "provider": {
+        "@id": "https://www.bioconductor.org",
+        "@type": "Organization",
+        "name": "Bioconductor",
+        "url": "https://www.bioconductor.org"
+      },
+      "sameAs": "https://bioconductor.org/packages/release/bioc/html/rhdf5.html"
+    },
     "16": {
       "@type": "SoftwareApplication",
       "identifier": "dplyr",
@@ -494,7 +494,7 @@
     },
     "SystemRequirements": null
   },
-  "fileSize": "4883.789KB",
+  "fileSize": "4884.754KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",

diff --git a/cran-comments.md b/cran-comments.md
@@ -2,12 +2,9 @@
 
 Addresses all CRAN instructions from the recent 0.7.1 submission:
 
-1. Updated the DESCRIPTION file with references in the suggested format.
-2. Replaced 'T' and 'F' with 'TRUE' and 'FALSE'.
-3. Added \value tags to all .Rd files that were missing it and provided thorough descriptions of function outputs.
-4. Removed all commented code lines in examples. Replaced \dontrun{} with \donttest{} for examples that take more than 5 seconds to execute and kept \dontrun{} where an external model is required 
-5. Adjusted functions to avoid writing in the user's home filespace. All examples, vignettes, and tests now write to tempdir() by default.
+1. added value tags to rcs-set.Rd and sd_vvp_threshold-set.Rd
+2. removed commented example in read_vpfiles.Rd.
+3. We could not find a commented example in c.vp.Rd as mentioned by the reviewer, since this function did not have an example. We have added an example now.
+4. changed dontrun{} example in apply_mistnet to donttest{}, and prevent write in user home directory
 
-The deprecation of spatial packages `rgdal` and `maptools`, and the evolution of `sp` led to the archiving of bioRad on 07.07.2023.  All issues arising from spatial packages have been fixed.
-
-This package will be used extensively in a summer training school next week (Jul 16 - Jul 21), we would greatly appreciate it being restored on CRAN before that time.
+This package will be used extensively in a summer training school next week (Jul 16 - Jul 21), we would greatly appreciate it being restored on CRAN as soon as possible.
diff --git a/man/apply_mistnet.Rd b/man/apply_mistnet.Rd
diff --git a/man/c.vp.Rd b/man/c.vp.Rd
diff --git a/man/plot.scan.Rd b/man/plot.scan.Rd
diff --git a/man/rcs-set.Rd b/man/rcs-set.Rd
diff --git a/man/read_vpfiles.Rd b/man/read_vpfiles.Rd
diff --git a/man/sd_vvp_threshold-set.Rd b/man/sd_vvp_threshold-set.Rd