Merge pull request #533 from adokter/fix_subres_height_integration

bioRad 0.7.0.9532

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: bioRad
 Title: Biological Analysis and Visualization of Weather Radar Data
-Version: 0.7.0.9522
+Version: 0.7.0.9532
 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.
@@ -49,7 +49,8 @@ Imports:
     viridis,
     vol2birdR
 Remotes:
-    adokter/vol2birdR
+    adokter/vol2birdR,
+    bioc::rhdf5
 Suggests:
     knitr,
     rlang,

NEWS.md

@@ -13,6 +13,9 @@ bioRad 0.7 includes a major backend overhaul that deprecates the use of Docker.
 * argument `local_install` in `calculate_vp()` and `apply_mistnet()` is now deprecated.
 * functions `check_docker()` and `update_docker()` have been deprecated
 * function `vol2bird_version()` has been migrated to package vol2birdR and can be accessed by `vol2birdR::vol2bird_version()`
+* fix bug in height integration, which excluded the lowest bins for certain low altitude radars (#534)
+* fast parallel mistnet runs (https://github.com/adokter/vol2birdR/issues/16)
+* simplify installation, including automatic installation of rhdf5 from bioconductor (#464)
 
 # bioRad 0.6.1
 
@@ -32,6 +35,8 @@ Introduces a number of new functions and parameters and includes bugfixes. All i
 
 * New function `write_pvolfile()` to write polar volumes to ODIM hdf5 format (#470, #471).
 
+* New function `download_pvolfiles()` to download NEXRAD polar volume files from Amazon Web Services (#41, #487)
+
 * New functions `Math.pvol()`, `Math.scan()`, `Ops.pvol()`,`Ops.scan()`,`Ops.param()`: standard mathematical operations for `param`, `scan` and `pvol` objects.
 
 ## New features and bugfixes

R/integrate_profile.R

@@ -204,7 +204,7 @@ integrate_profile.vp <- function(x, alt_min = 0, alt_max = Inf, alpha = NA,
   # Its value is zeros for bins completly below alt_min or above alt_max, the
   # interval value for all bin completly above alt_min and below alt_max, and
   # a ratio of interval for the bins overlaping alt_min and alt_max
-  dh <- pmin(pmin(pmax(x$data$height-alt_min,0),interval),
+  dh <- pmin(pmin(pmax(x$data$height+x$attributes$where$interval-alt_min,0),interval),
              pmin(pmax(alt_max-x$data$height,0),interval)) / 1000
 
   # Vertically Integrated Density in individuals/km^2
@@ -376,7 +376,7 @@ integrate_profile.vpts <- function(x, alt_min = 0, alt_max = Inf,
   # Its value is zeros for bins completly below alt_min or above alt_max, the
   # interval value for all bin completly above alt_min and below alt_max, and
   # a ratio of interval for the bins overlaping alt_min and alt_max
-  dh <- pmin(pmin(pmax(x$height-alt_min,0),interval),
+  dh <- pmin(pmin(pmax(x$height+x$attributes$where$interval-alt_min,0),interval),
              pmin(pmax(alt_max-x$height,0),interval)) / 1000
 
   # Vertically Integrated Density in individuals/km^2

R/read_cajun.R

@@ -71,7 +71,8 @@ read_cajun <- function(file, rcs = 11, wavelength = "S") {
   attributes <- list(
     where = data.frame(
       interval = interval,
-      levels = length(height)
+      levels = length(height),
+      height = 0 # cajun altitudes are relative to antenna level
     ),
     what = data.frame(source = basename(file), stringsAsFactors = F),
     how = data.frame(wavelength = wavelength, task = "UMASS Cajun")

README.Rmd

@@ -62,13 +62,6 @@ sudo apt install libgdal-dev
 <br>
 
 ### Install bioRad
-bioRad depends on packages from both the [CRAN](https://CRAN.R-project.org) and
-[Bioconductor](https://www.bioconductor.org/) repositories. Enable both with:
-
-```{r eval = FALSE}
-setRepositories(ind = 1:2)
-```
-
 You can install the released version of bioRad from [CRAN](https://CRAN.R-project.org) with:
 
 ```{r eval = FALSE}

README.md

@@ -76,15 +76,6 @@ Linux systems. In terminal, install these with:
 
 ### Install bioRad
 
-bioRad depends on packages from both the
-[CRAN](https://CRAN.R-project.org) and
-[Bioconductor](https://www.bioconductor.org/) repositories. Enable both
-with:
-
-``` r
-setRepositories(ind = 1:2)
-```
-
 You can install the released version of bioRad from
 [CRAN](https://CRAN.R-project.org) with:
 
@@ -104,8 +95,8 @@ Then load the package with:
 
 ``` r
 library(bioRad)
-#> Welcome to bioRad version 0.7.0.9517
-#> using vol2bird version 0.5.0.9174 (MistNet not installed)
+#> Welcome to bioRad version 0.7.0.9532
+#> using vol2birdR version 0.1.1.9919 (MistNet installed)
 ```
 
 ### (optional) Enable MistNet