read_vpts()

.gitignore

@@ -44,3 +44,4 @@ pkgdown/*
 .DS_Store
 /doc/
 /Meta/
+

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: bioRad
 Title: Biological Analysis and Visualization of Weather Radar Data
-Version: 0.7.0.9602
+Version: 0.7.0.9603
 Description: Extract, visualize and summarize aerial movements of birds and
     insects from weather radar data. See <doi:10.1111/ecog.04028>
     for a software paper describing package and methodologies.
@@ -30,27 +30,28 @@ Imports:
     assertthat,
     curl,
     fields,
+    frictionless,
     ggplot2,
     glue,
     graphics,
     lubridate,
     lutz,
-    maptools,
+    suntools,
     methods,
     raster,
     readr,
     dplyr (>= 1.1.0),
     rhdf5,
     sp,
-    sf,
     stats,
     tidyr,
     utils,
     viridisLite,
     viridis,
-    rlang
+    rlang,
+    jsonlite
 Remotes:
-    bioc::rhdf5
+    bioc::rhdf5,
 Suggests:
     vol2birdR,
     aws.s3,
@@ -60,7 +61,7 @@ Suggests:
     rmarkdown,
     testthat (>= 3.0.0),
     vdiffr,
-    rgdal
+    sf
 LazyData: true
 Encoding: UTF-8
 VignetteBuilder: knitr

NAMESPACE

@@ -86,6 +86,7 @@ S3method(summary,vpts)
 export("rcs<-")
 export("sd_vvp_threshold<-")
 export(apply_mistnet)
+export(as.vpts)
 export(attribute_table)
 export(beam_distance)
 export(beam_height)
@@ -133,6 +134,7 @@ export(project_as_ppi)
 export(rcs)
 export(read_cajun)
 export(read_pvolfile)
+export(read_stdout)
 export(read_vpfiles)
 export(read_vpts)
 export(regularize_vpts)

NEWS.md

@@ -1,10 +1,4 @@
-<!--
-
-* `bind_into_vpts()` now works for vp's and vpts's with different heights (#343).
-
--->
-
-# bioRad 0.7.0.XXXX
+# bioRad 0.7.0
 
 bioRad 0.7 includes a major backend overhaul that deprecates the use of Docker. All Docker-dependent functionality is now included in the new dependency package [vol2birdR](https://cran.r-project.org/package=vol2birdR) package, which needs to be installed as part of bioRad. All bioRad functions remain the same, but several functions will run considerable faster.
 
@@ -16,15 +10,21 @@ bioRad 0.7 includes a major backend overhaul that deprecates the use of Docker.
 
 * Faster implementations of functions previously dependent on Docker, such as `calculate_vp()`, `apply_mistnet()` and `read_pvolfile()`.
 
-* Faster parallel mistnet runs (https://github.com/adokter/vol2birdR/issues/16).
+* Support for reading [VPTS CSV](https://aloftdata.eu/vpts-csv/) format through updated function `read_vpts()`. VPTS CSV table schema included to allow offline parsing of VPTS CSV files as a [frictionless](https://CRAN.R-project.org/package=frictionless) data package (#551, #590)
+
+* Updated function `read_vpts()` supports reading `vp`/`vpts` data in ODIM HDF, [VPTS CSV](https://aloftdata.eu/vpts-csv/) format (#551, #590)
 
 * New function `list_vpts_aloft()` produces a list of [aloft](https://aloftdata.eu/browse/) archive URLs for time series of vertical profiles (`vpts`). This list of URLs can then be used to bulk download data using any number of external tools (#553).
 
-* Updated function `read_vpts()` supports reading `vp`/`vpts` data in hdf5 and [VPTS CSV](https://aloftdata.eu/vpts-csv/) format.
+* New function `read_stdout()` replaces previous functionality of `read_vpts()` to read vol2bird stdout format. It also has a new `sep` argument (#536) to support both fixed-delimited and comma-separated stdout data.
 
-* New function `read_stdout()` replaces previous functionality of `read_vpts()` to read vol2bird stdout format. It also has a new `sep` argument (#536).
+* New function `as.vpts` converts a data.frame originating from a VPTS CSV file into a vpts object (#555). Inverse operation of as.data.frame.vpts
 
-* `read_pvolfiles()` now allows ODIM_H5 files with missing `source` attribute. The functionality is similar to `read_vpfiles()`, i.e. using the NOD identifier in the source attribute, if missing try RAD, if also missing try WMO, if nothing found use `unknown` (2f6935c).
+* `read_pvolfiles()` now allows ODIM H5 files with missing `source` attribute. The functionality is similar to `read_vpfiles()`, i.e. extracting the NOD, RAD or WMO identifier, otherwise using `unknown` (2f6935c).
+
+* `bind_into_vpts()` now works for vp and vpts objects with different heights (#343)
+
+* Faster parallel mistnet runs (https://github.com/adokter/vol2birdR/issues/16).
 
 ## Bugfixes
 
@@ -38,6 +38,8 @@ bioRad 0.7 includes a major backend overhaul that deprecates the use of Docker.
 
 * Function `vol2bird_version()` has been migrated to package vol2birdR and can be accessed by `vol2birdR::vol2bird_version()`.
 
+* Dependency `maptools` has been replaced with [suntools](https://github.com/adokter/suntools), `rgdal` has been removed in accordance with the evoltion of `sp` and the [imminent archiving](https://r-spatial.org/r/2023/05/15/evolution4.html) of `rgdal` 
+
 # bioRad 0.6.1
 
 Rebuilds the documentation using roxygen2 for compability with HTML5 (a CRAN requirement).

R/as.vpts.R

@@ -0,0 +1,96 @@
+
+#' Convert a dataframe into a vpts object
+#'
+#' @param data a dataframe created from a VPTS CSV file
+#' @returns a bioRad vpts object
+#' @examples
+#' # locate example file in VPTS CSV format:
+#' df <- read.csv(system.file("extdata", "example_vpts.csv", package = "bioRad"))
+#' # convert the data.frame to a vpts object:
+#' as.vpts(df)
+#' @export
+as.vpts <- function(data) {
+  height <- datetime <- source_file <- radar <- NULL
+
+  # Throw error if nrows per height are not identical
+
+  assertthat::assert_that(
+    isFactor(dim(data)[1], length(unique(data$height))) > 0,
+    msg = "Number of rows per height variable must be identical"
+  )
+
+  radar <- unique(data[["radar"]])
+
+  # Check radar is unique
+  assertthat::assert_that(
+    length(radar) == 1,
+    msg = "`files` must contain data of a single radar."
+  )
+
+  if (!exists("cached_schema")) {
+    # Load the schema from the data directory and cache it
+    cached_schema <- jsonlite::fromJSON(system.file("extdata", "vpts-csv-table-schema.json", package = "bioRad"),
+      simplifyDataFrame = FALSE, simplifyVector = TRUE
+    )
+  }
+
+  data <- dplyr::mutate(
+    data,
+    radar = as.factor(radar),
+    source_file = as.factor(source_file),
+    datetime = as.POSIXct(datetime, format = "%Y-%m-%dT%H:%M:%SZ", tz = "UTC")
+  )
+
+  # Check whether time series is regular
+  heights <- as.integer(unique(data[["height"]]))
+
+  # Subset timestamps by first sampled height
+  datetime <- data[data[["height"]] == heights[1], ][["datetime"]]
+  datetime <- as.POSIXct(datetime, format = "%Y-%m-%dT%H:%M:%SZ", tz = "UTC")
+
+
+  # Determine regularity
+  difftimes <- difftime(datetime[-1], datetime[-length(datetime)], units = "secs")
+  if (length(unique(difftimes)) == 1) {
+    regular <- TRUE
+  } else {
+    regular <- FALSE
+  }
+
+  # Get attributes
+  radar_height <- data[["radar_height"]][1]
+  interval <- unique(heights[-1] - heights[-length(heights)])
+  wavelength <- data[["radar_wavelength"]][1]
+  lon <- data[["radar_longitude"]][1]
+  lat <- data[["radar_latitude"]][1]
+  rcs <- data[["rcs"]][1]
+  sd_vvp_threshold <- data[["sd_vvp_threshold"]][1]
+
+  # Convert dataframe
+  maskvars <- c("radar", "radar_latitude", "radar_longitude", "radar_height", "radar_wavelength", "source_file", "datetime", "height")
+
+  data <- df_to_mat_list(data, maskvars, cached_schema)
+
+  # Create vpts object
+  output <- list(
+    radar = as.character(radar),
+    datetime = datetime,
+    height = heights,
+    daterange = c(min(datetime), max(datetime)),
+    timesteps = difftimes,
+    data = data,
+    attributes = list(
+      where = data.frame(
+        interval = as.integer(interval),
+        levels = length(heights),
+        height = as.integer(radar_height),
+        lon = lon,
+        lat = lat
+      ),
+      how = data.frame(wavelength = wavelength, rcs_bird = rcs, sd_vvp_thresh = sd_vvp_threshold)
+    ),
+    regular = regular
+  )
+  class(output) <- "vpts"
+  return(output)
+}

R/calculate_vp.R

@@ -15,7 +15,7 @@
 #'   library](https://trmm-fc.gsfc.nasa.gov/trmm_gv/software/rsl/) or 3) Vaisala
 #'   IRIS (IRIS RAW) format.
 #' @param vpfile Character. File name. When provided, writes a vertical profile
-#'   file (`vpfile`) in the ODIM HDF5 format to disk.
+#'   file (`vpfile`) either in the VPTS CSV or ODIM HDF5 format to disk.
 #' @param pvolfile_out Character. File name. When provided, writes a polar
 #'   volume (`pvol`) file in the ODIM HDF5 format to disk. Useful for converting
 #'   RSL formats to ODIM.
@@ -336,7 +336,11 @@ calculate_vp <- function(file, vpfile = "", pvolfile_out = "",
   filedir <- dirname(normalizePath(file[1], winslash = "/"))
   assertthat::assert_that(assertthat::is.writeable(filedir))
 
-  profile.tmp <- tempfile()
+  if (vpfile != '' && tools::file_ext(vpfile) == "csv"){
+    profile.tmp <- tempfile(fileext = ".csv")
+  } else {
+    profile.tmp <- tempfile(fileext = ".h5")
+  }
 
   config <- vol2birdR::vol2bird_config()
   if (!autoconf) {
@@ -388,7 +392,7 @@ calculate_vp <- function(file, vpfile = "", pvolfile_out = "",
   )
 
   # read output into a vp object
-  output <- read_vpfiles(profile.tmp)
+  output <- vpts_to_vp(read_vpts(profile.tmp))
 
   # read output and clean up
   if (vpfile != "") {

R/download_pvolfiles.R

@@ -19,7 +19,7 @@
 #'
 #' @examples
 #' \dontrun{
-#' create temporary directory
+#' # create temporary directory
 #' temp_dir <- paste0(tempdir(),"/bioRad_tmp_files")
 #' dir.create(temp_dir)
 #' download_pvolfiles(

R/hooks.R

@@ -6,9 +6,4 @@
   if (rlang::is_installed("vol2birdR")) {
     packageStartupMessage(paste("using vol2birdR version ", utils::packageVersion("vol2birdR"), ifelse(vol2birdR::mistnet_exists(), " (MistNet installed)", " (MistNet not installed)"), sep = ""))
   }
-  if (requireNamespace("sp", quietly = TRUE)) {
-    sp::set_evolution_status(2L)
-    packageStartupMessage("Assigning sp_evolution_status to 2. See sp::get_evolution_status()")
-    packageStartupMessage("This is required until the 'sp' package deprecates 'rgdal'")
-  }
 }