From ca86920eb96a0a8bf22da888fb7e00206e7632eb Mon Sep 17 00:00:00 2001 From: Adriaan Dokter Date: Fri, 14 Jul 2023 06:28:09 -0400 Subject: [PATCH 1/5] Update README.md add warning message that bioRad is unavailable on CRAN --- README.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/README.md b/README.md index de0004836..ff814e6cf 100644 --- a/README.md +++ b/README.md @@ -12,6 +12,11 @@ status](https://www.r-pkg.org/badges/version/bioRad)](https://cran.r-project.org [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3370004.svg)](https://doi.org/10.5281/zenodo.3370004) +**bioRad is temporarily unavailable on CRAN - please install from GitHub** + +*bioRad will be released as soon as CRAN has resolved infrastructure issues +(see 'Submitting to CRAN' at https://cran.r-project.org/)* + bioRad provides standardized methods for extracting and reporting biological signals from weather radars. It includes functionality to inspect low-level radar data, process these data into meaningful From eac7f1a086c12f3306b467897f719e765923986b Mon Sep 17 00:00:00 2001 From: Adriaan Dokter Date: Fri, 14 Jul 2023 10:09:27 -0400 Subject: [PATCH 2/5] add remotes to DESCRIPTION --- DESCRIPTION | 2 ++ 1 file changed, 2 insertions(+) diff --git a/DESCRIPTION b/DESCRIPTION index d248c84af..0b2454367 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -51,6 +51,8 @@ Imports: viridis, rlang, jsonlite +Remotes: + bioc::rhdf5 Suggests: vol2birdR, aws.s3, From 212399b0b061b93341848e010cda4fda18345090 Mon Sep 17 00:00:00 2001 From: Adriaan Dokter Date: Fri, 14 Jul 2023 09:34:46 -0400 Subject: [PATCH 3/5] Revert "change to dev version for merging on master" This reverts commit d9af3242f60f1fac4890c63cf733866202e3a18b. --- DESCRIPTION | 2 +- README.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 0b2454367..ab32a245f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: bioRad Title: Biological Analysis and Visualization of Weather Radar Data -Version: 0.7.0.9614 +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" diff --git a/README.md b/README.md index 7a02094a3..69daa7cc8 100644 --- a/README.md +++ b/README.md @@ -102,7 +102,7 @@ Then load the package with: ``` r library(bioRad) -#> Welcome to bioRad version 0.7.0.9614 +#> Welcome to bioRad version 0.7.1 #> using vol2birdR version 1.0.1 (MistNet not installed) ``` From cbcfad5f17fb90828b17e06a4ebe0c7aa3988074 Mon Sep 17 00:00:00 2001 From: iskandari Date: Fri, 14 Jul 2023 14:00:45 -0400 Subject: [PATCH 4/5] bugfix for NA values in as.vpts --- R/utils.R | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/R/utils.R b/R/utils.R index 549765d63..61bdbc1aa 100644 --- a/R/utils.R +++ b/R/utils.R @@ -290,7 +290,11 @@ tibble_to_mat <- function(tibble) { #' @noRd df_to_mat_list <- function(data, maskvars, schema) { datetime <- height <- variable <- fields <- NULL - radvars <- extract_names(schema$fields) + radvars <- extract_names(schema$fields) #allow DBZH as alternative to dbz_all + alt_radvar <- "DBZH" + insert_index <- which(radvars == "dbz_all") + 1 + radvars <- append(radvars, alt_radvar, after = insert_index) + radvars <- radvars[!radvars %in% maskvars] tbls_lst <- data %>% @@ -303,7 +307,10 @@ df_to_mat_list <- function(data, maskvars, schema) { var_names <- sapply(unnamed_mat_list, function(x) x$variable) named_mat_list <- lapply(unnamed_mat_list, `[[`, "matrix") names(named_mat_list) <- var_names - ordered_mat_list <- named_mat_list[radvars] + subset_indices <- match(var_names, radvars) + ordered_subset <- var_names[order(subset_indices)] + + ordered_mat_list <- named_mat_list[ordered_subset] return(ordered_mat_list) } From 1f3d4f03d4afde8902ace83022af65a4675bd8f1 Mon Sep 17 00:00:00 2001 From: iskandari Date: Fri, 14 Jul 2023 14:09:26 -0400 Subject: [PATCH 5/5] bugfix for NA values in as.vpts --- codemeta.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/codemeta.json b/codemeta.json index b5ee0c2f4..37091dce5 100644 --- a/codemeta.json +++ b/codemeta.json @@ -14,7 +14,7 @@ "name": "R", "url": "https://r-project.org" }, - "runtimePlatform": "R version 4.3.1 (2023-06-16)", + "runtimePlatform": "R version 4.3.0 (2023-04-21)", "author": [ { "@type": "Person", @@ -494,7 +494,7 @@ }, "SystemRequirements": null }, - "fileSize": "4883.507KB", + "fileSize": "4883.789KB", "citation": [ { "@type": "ScholarlyArticle",