Merge pull request #334 from adokter/develop

bioRad 0.5.1

CRAN-RELEASE

@@ -1,2 +1,2 @@
-This package was submitted to CRAN on 2020-02-18.
-Once it is accepted, delete this file and tag the release (commit 513108933d).
+This package was submitted to CRAN on 2020-03-31.
+Once it is accepted, delete this file and tag the release (commit ea28c310b7).

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: bioRad
 Title: Biological Analysis and Visualization of Weather Radar Data
-Version: 0.5.0.9325
+Version: 0.5.1
 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.
@@ -44,4 +44,4 @@ Suggests:
 LazyData: true
 Encoding: UTF-8
 VignetteBuilder: knitr
-RoxygenNote: 7.0.2
+RoxygenNote: 7.1.0

NEWS.md

@@ -1,3 +1,22 @@
+# bioRad 0.5.1
+
+Minor bugfixes. All issues included in this release can be found [here](https://github.com/adokter/bioRad/pull/334). This release primarily fixes a bug that will become effective once R version 4.0 is released.
+
+* fixes a conflict due to new raw data format introduced in R version 4.0 (#331)
+
+* corrects incorrect values in reading of correlation coefficient values RHOHV (#328)
+
+* bugfix in `read_cajun()` which introduced incorrect height column during refactoring in bioRad 0.5.0 release ([93ad0a4](https://github.com/adokter/bioRad/commit/93ad0a4))
+
+* bugfix that fixes the mapping by `map()` of composites of composites (ppi's produced after repeated application of `composite_ppi()`) ([a5c9048](https://github.com/adokter/bioRad/commit/a5c9048), [043aa73](https://github.com/adokter/bioRad/commit/043aa73))
+* minor bug fixes, and addressing conflicts with CRAN depencies
+
+* extend the functionality of `composite_ppi()` and improve its documentation (partial fix of #59)
+
+* fix a bug in the color legend of `map()` when providing a custom color scale with palette argument (#324)
+
+* minor documentation improvements
+
 # bioRad 0.5.0
 
 New CRAN release. All issues included in this release can be found [here](https://github.com/adokter/bioRad/milestone/6?closed=1).

R/composite_ppi.R

@@ -144,7 +144,8 @@ composite_ppi <- function(x, param = "DBZH", nx = 100, ny = 100, xlim, ylim, res
     #weights<-raster::pointDistance(as.matrix(data.frame(x=lons.radar,y=lats.radar)), coordinates(raster(spGrid)),lonlat=T)
     for(i in 1:length(projs)){
       brick_data <- raster::setValues(brick_data, projs[[i]], layer=i)
-      weights<-raster::pointDistance(as.matrix(data.frame(x=lons.radar,y=lats.radar))[i,], coordinates(raster(spGrid)),lonlat=T)
+      latlon.radar <- unique(data.frame(lat=c(lats.radar), lon=c(lons.radar)))
+      weights<-raster::pointDistance(as.matrix(data.frame(x=latlon.radar$lon,y=latlon.radar$lat))[i,], coordinates(raster(spGrid)),lonlat=T)
       if(!is.na(idw_max_distance)) weights[weights>idw_max_distance]=NA
       weights = 1/(weights^idp)
 

R/filter.R

@@ -1,8 +1,8 @@
 #' Time selection in a time series of vertical profiles ('vpts')
 #'
 #' @param x A \code{vpts} object.
-#' @param min Minimum datetime to be included. POSIXct value or charater string convertable to POSIXct.
-#' @param max Maximum datetime to be included. POSIXct value or charater string convertable to POSIXct.
+#' @param min Minimum datetime to be included. POSIXct value or character string convertable to POSIXct.
+#' @param max Maximum datetime to be included. POSIXct value or character string convertable to POSIXct.
 #' @param nearest If specified, \code{min} and \code{max} are ignored and the profile nearest to the
 #' specified datetime is returned. POSIXct value or charater string convertable to POSIXct.
 #' @return An object of class '\link[=summary.vpts]{vpts}', or an object of class '\link[=summary.vp]{vp}'

R/map.R

@@ -216,21 +216,23 @@ map.ppi <- function(x, map, param, alpha = 0.7, xlim, ylim,
   # these declarations prevent generation of NOTE "no visible binding for
   # global variable" during package Check
   lon <- lat <- y <- z <- NA
+  # extract unique radar locations
+  latlon_radar <- unique(data.frame(lat=c(x$geo$lat), lon=c(x$geo$lon)))
   # symbols for the radar position
   # dummy is a hack to be able to include the ggplot2 color scale,
   # radarpoint is the actual plotting of radar positions.
   dummy <- geom_point(aes(x = lon, y = lat, colour = z),
     size = 0,
     data = data.frame(
-      lon = x$geo$lon,
-      lat = x$geo$lat,
+      lon = latlon_radar$lon,
+      lat = latlon_radar$lat,
       z = 0
     )
   )
   radarpoint <- geom_point(aes(x = lon, y = lat),
     colour = radar_color,
     size = radar_size,
-    data = data.frame(lon = x$geo$lon, lat = x$geo$lat)
+    data = data.frame(lon = latlon_radar$lon, lat = latlon_radar$lat)
   )
   # bounding box
   bboxlatlon <- attributes(map)$geo$bbox
@@ -248,4 +250,5 @@ map.ppi <- function(x, map, param, alpha = 0.7, xlim, ylim,
       scale_y_continuous(limits = ylim, expand = c(0, 0))
   )
   suppressWarnings(mymap)
+
 }

R/read_cajun.R

@@ -55,7 +55,7 @@ read_cajun <- function(file, rcs = 11, wavelength = "S") {
   data$n_all <- NA
 
   # remove redundant quantities
-  data$height <- NULL
+  data$height_mean <- NULL
 
   # sort into bioRad order
   data <- data[, header.names.sorted]

R/read_pvolfile.R

@@ -325,10 +325,15 @@ read_pvolfile_scan <- function(file, scan, param, radar, datetime, geo) {
 
 read_pvolfile_quantity <- function(file, quantity, radar, datetime, geo) {
   data <- h5read(file, quantity)$data
+  # convert storage mode from raw to numeric:
+  storage.mode(data) <- "numeric"
   attr <- h5readAttributes(file, paste(quantity, "/what", sep = ""))
   data <- replace(data, data == as.numeric(attr$nodata), NA)
   data <- replace(data, data == as.numeric(attr$undetect), NaN)
   data <- as.numeric(attr$offset) + as.numeric(attr$gain) * data
+  if(attr$quantity == "RHOHV"){
+    data <- replace(data, data > 10, NaN)
+  }
   class(data) <- c("param", class(data))
   attributes(data)$radar <- radar
   attributes(data)$datetime <- datetime

R/regularize_vpts.R

@@ -46,6 +46,10 @@ regularize_vpts <- function(ts, interval = "auto", date_min = ts$daterange[1],
   stopifnot(inherits(date_min, "POSIXct"))
   stopifnot(inherits(date_max, "POSIXct"))
 
+  # @param keep_datetime Logical, when \code{TRUE} keep original radar acquisition timestamps,
+  # and do not update to values of the regularized time grid.
+  keep_datetime <- FALSE # option under development
+
   if (!(units %in% c("secs", "mins", "hours", "days", "weeks"))) {
     stop(
       "Invalid 'units' argument. Should be one of",
@@ -85,6 +89,7 @@ regularize_vpts <- function(ts, interval = "auto", date_min = ts$daterange[1],
       ts$data[[x]][, index]
     }
   )
+  index2 <- integer(0)
   if (!fill) {
     index2 <- which(abs(ts$datetime[index] - grid) > as.double(dt, units = "secs"))
     if (length(index2) > 0) {
@@ -99,8 +104,14 @@ regularize_vpts <- function(ts, interval = "auto", date_min = ts$daterange[1],
     }
   }
   names(ts$data) <- quantity.names
-  ts$datetime <- grid
-  ts$timesteps <- rep(as.double(dt, units = "secs"), length(grid) - 1)
+  if(!keep_datetime){
+    ts$datetime <- grid
+    ts$timesteps <- rep(as.double(dt, units = "secs"), length(grid) - 1)
+  } else{
+    ts$datetime <- ts$datetime[index]
+    ts$timesteps <- difftime(ts$datetime[-1], ts$datetime[-length(ts$datetime)], units = "secs")
+    ts$timesteps[index2] <- dt
+  }
   ts$regular <- TRUE
   return(ts)
 }

R/vpts.R

@@ -187,7 +187,7 @@ print.vpts <- function(x, digits = max(3L, getOption("digits") - 3L), ...) {
   } else {
     stepMin <- stepMax <- NA
   }
-  if (x$regular) {
+  if (x$regular & stepMin == stepMax) {
     cat("   time step (s): ", stepMin, "\n")
   } else {
     cat("   time step (s): ", "min:", stepMin, "    max: ", stepMax, "\n")

README.md

@@ -71,8 +71,8 @@ Then load the package with:
 
 ``` r
 library(bioRad)
-#> Welcome to bioRad version 0.5.0
-#> Docker daemon running, Docker functionality enabled (vol2bird version 0.5.0, MistNet available)
+#> Welcome to bioRad version 0.5.1
+#> Docker daemon running, Docker functionality enabled (vol2bird version 0.5.1, MistNet available)
 ```
 
 #### Required system libraries on Linux (Ubuntu)

codemeta.json

@@ -5,7 +5,7 @@
   ],
   "@type": "SoftwareSourceCode",
   "identifier": "bioRad",
-  "description": "Extract, visualize and summarize aerial movements of birds and\n    insects from weather radar data. See <https://doi.org/10.1111/ecog.04028>\n    for a software paper describing package and methodologies.",
+  "description": "Extract, visualize and summarize aerial movements of birds and\n    insects from weather radar data. See <doi:10.1111/ecog.04028>\n    for a software paper describing package and methodologies.",
   "name": "bioRad: Biological Analysis and Visualization of Weather Radar Data",
   "codeRepository": "https://github.com/adokter/bioRad",
   "relatedLink": [
@@ -15,14 +15,14 @@
   ],
   "issueTracker": "https://github.com/adokter/bioRad/issues",
   "license": "https://spdx.org/licenses/MIT",
-  "version": "0.5.0",
+  "version": "0.5.1",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
-    "version": "3.6.2",
+    "version": "3.6.3",
     "url": "https://r-project.org"
   },
-  "runtimePlatform": "R version 3.6.2 (2019-12-12)",
+  "runtimePlatform": "R version 3.6.3 (2020-02-29)",
   "provider": {
     "@id": "https://cran.r-project.org",
     "@type": "Organization",
@@ -271,6 +271,18 @@
       "identifier": "utils",
       "name": "utils"
     },
+    {
+      "@type": "SoftwareApplication",
+      "identifier": "viridisLite",
+      "name": "viridisLite",
+      "provider": {
+        "@id": "https://cran.r-project.org",
+        "@type": "Organization",
+        "name": "Comprehensive R Archive Network (CRAN)",
+        "url": "https://cran.r-project.org"
+      },
+      "sameAs": "https://CRAN.R-project.org/package=viridisLite"
+    },
     {
       "@type": "SoftwareApplication",
       "identifier": "viridis",
@@ -394,5 +406,5 @@
   ],
   "releaseNotes": "https://github.com/adokter/bioRad/blob/master/NEWS.md",
   "readme": "https://github.com/adokter/bioRad/blob/master/README.md",
-  "fileSize": "5887.639KB"
+  "fileSize": "4947.408KB"
 }

cran-comments.md

@@ -1,7 +1,14 @@
+## bioRad 0.5.1
+This version includes a minor bugfix associated with the
+upcoming R 0.4.0 release. I only found out today that our
+package had been removed from CRAN because of this, without
+any notice, is there a way for me to subscribe to a notification
+when my package is pending to be removed?
+
 ## Test environments
-* local OS X install, R 3.6.2
-* local Ubuntu 18.04 LTS, R 3.6.2
-* local Windows 10 Enterprise, R 3.6.2
+* local OS X install, R 3.6.3
+* local Ubuntu 18.04 LTS, R 3.6.3
+* local Windows 10 Enterprise, R 3.6.3
 
 ## R CMD check results
 There were no ERRORs or WARNINGs. 
@@ -18,20 +25,10 @@ There was 1 NOTE:
 The tarball is however below the required 5 Mb
 
 ## r-hub builder
-Building bioRad with r-hub (using `check_rhub()` fails because gdal is
-not available on the r-hub build system. The rgdal package is a
-dependency of bioRad. rgdal documentations explains in detail
-how to install gdal on all platforms, so this seems more an
-rgdal issue than a bioRad issue.
-
-Resulting PREPERROR:
-```
-#> configure: GDAL: 1.11.3
-#> checking GDAL version >= 1.11.4... no
-#> configure: error: upgrade GDAL to 1.11.4 or later
-#> ERROR: configuration failed for package ‘rgdal’
-#> * removing ‘/home/docker/R/rgdal’
-```
+There was one warning:
+
+* checking package dependencies ... WARNING
+Requires orphaned package: 'ggmap'
 
 ## Downstream dependencies
 There are currently no downstream dependencies for this package