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bioRad 0.7.1 CRAN release #620

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Jul 17, 2023
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4 changes: 2 additions & 2 deletions CRAN-SUBMISSION
Original file line number Diff line number Diff line change
@@ -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
5 changes: 1 addition & 4 deletions DESCRIPTION
Original file line number Diff line number Diff line change
@@ -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>
Expand Down Expand Up @@ -37,7 +37,6 @@ Imports:
graphics,
lubridate,
lutz,
rhdf5,
suntools,
methods,
raster,
Expand All @@ -52,8 +51,6 @@ Imports:
viridis,
rlang,
jsonlite
Remotes:
bioc::rhdf5
Suggests:
vol2birdR,
aws.s3,
Expand Down
17 changes: 10 additions & 7 deletions R/apply_mistnet.R
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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,
Expand Down
2 changes: 2 additions & 0 deletions R/plot.scan.R
Original file line number Diff line number Diff line change
Expand Up @@ -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"))
Expand Down
2 changes: 2 additions & 0 deletions R/rcs.R
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
2 changes: 1 addition & 1 deletion R/read_vpfiles.R
Original file line number Diff line number Diff line change
Expand Up @@ -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))
Expand Down
2 changes: 2 additions & 0 deletions R/sd_vvp_threshold.R
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
6 changes: 5 additions & 1 deletion R/vp.R
Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand Down Expand Up @@ -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(...)
Expand Down
2 changes: 1 addition & 1 deletion README.md
Original file line number Diff line number Diff line change
Expand Up @@ -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)
```

Expand Down
32 changes: 16 additions & 16 deletions codemeta.json
Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand All @@ -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",
Expand All @@ -385,7 +373,7 @@
},
"sameAs": "https://CRAN.R-project.org/package=raster"
},
"15": {
"14": {
"@type": "SoftwareApplication",
"identifier": "readr",
"name": "readr",
Expand All @@ -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",
Expand Down Expand Up @@ -494,7 +494,7 @@
},
"SystemRequirements": null
},
"fileSize": "4883.789KB",
"fileSize": "4884.754KB",
"citation": [
{
"@type": "ScholarlyArticle",
Expand Down
13 changes: 5 additions & 8 deletions cran-comments.md
Original file line number Diff line number Diff line change
Expand Up @@ -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.
17 changes: 10 additions & 7 deletions man/apply_mistnet.Rd

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5 changes: 5 additions & 0 deletions man/c.vp.Rd

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2 changes: 2 additions & 0 deletions man/plot.scan.Rd

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3 changes: 3 additions & 0 deletions man/rcs-set.Rd

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2 changes: 1 addition & 1 deletion man/read_vpfiles.Rd

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3 changes: 3 additions & 0 deletions man/sd_vvp_threshold-set.Rd

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