Update feedr v1.0.0

.github/workflows/R-CMD-check.yaml

@@ -1,9 +1,15 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
-on: [push, pull_request]
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
 
 name: R-CMD-check
 
+permissions: read-all
+
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
@@ -14,7 +20,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
@@ -25,23 +31,22 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
-
-      - name: macOS dependencies
-        if: runner.os == 'macOS'
-        run: |
-          brew install gdal proj
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: rcmdcheck
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - uses: r-lib/actions/check-r-package@v1
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: feedr
 Type: Package
 Title: Transforming Raw RFID Data
-Version: 0.11.0
+Version: 0.11.0.9000
 Authors@R: person("Steffi", "LaZerte", email = "[email protected]", role = c("aut","cre"))
 URL: https://github.com/animalnexus/feedr
 Description: Load, clean, transform, and visualize raw RFID data for looking at a variety of
@@ -16,25 +16,24 @@ Imports:
     leaflet (>= 2.0.4.1),
     lubridate (>= 1.7.10),
     magrittr (>= 2.0.1),
-    maptools (>= 1.1.1),
     rlang (>= 0.4.12),
     purrr (>= 0.3.4),
     scales (>= 1.1.1),
     stringr (>= 1.4.0),
     tibble (>= 3.1.2),
-    tidyr (>= 1.1.3)
+    tidyr (>= 1.1.3),
+    suncalc (>= 0.5.1)
 Suggests:
     activity,
     aniDom,
     asnipe,
-    Dominance,
     knitr,
     Perc,
     png,
     rmarkdown,
     sp,
     testthat (>= 3.0.0)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.3.1
 VignetteBuilder: knitr
 Roxygen: list(markdown = TRUE)
 Encoding: UTF-8

NAMESPACE

@@ -19,7 +19,6 @@ export(map_ggmap)
 export(map_leaflet)
 export(move)
 export(presence)
-export(sun)
 export(tz_offset)
 export(visits)
 import(leaflet)

R/convert.R

@@ -153,10 +153,13 @@ convert_anidom <- function(d){
 }
 
 
-#' Convert displacements for use by functions from the Dominance package
+#' DEFUNCT - Convert displacements for use by functions from the Dominance package
+#'
+#' **The Dominance package is no longer available therefore this function
+#'   is defunct**
 #'
 #' Converts displacements RFID data into a format for easy use by either the
-#' [Dominance::ADI()] or the [Dominance::Sociogram()]
+#' `Dominance::ADI()` or the `Dominance::Sociogram()`
 #' functions included in the Dominance package for calculating average
 #' dominance indices and drawing sociograms. Only includes individuals that
 #' participated in at least one interaction.
@@ -177,29 +180,14 @@ convert_anidom <- function(d){
 #'   vector indicating that the action type "displacement" should be included in
 #'   the calculation. See examples for specific application.
 #'
-#' @seealso Dominance package and it's functions: [Dominance::ADI] and [Dominance::Sociogram]. <https://cran.r-project.org/package=Dominance>
-#'
-#' @examples
-#' # Calculate displacements
-#' d <- disp(visits(finches_lg))
-#'
-#' # Format for use by Dominance package
-#' i <- convert_dominance(d)
-#' i <- convert_dominance(d$displacements) # Equivalent
-#'
-#' \dontrun{
-#' # Use Dominance package:
-#' library(Dominance)
-#'
-#' # Calculate the Average Dominance Index
-#' ADI(data_sheet = i$data_sheet, items = i$items, actions = i$actions, bytes = i$bytes)
-#'
-#' # Construct social network graphs
-#' Sociogram(data_sheet = i$data_sheet, items = i$items, actions = i$actions, bits = i$bytes)
-#' }
-#'
 #' @export
+
 convert_dominance <- function(d) {
+
+  stop("The Dominance package is no longer available therefore this function ",
+       "is defunct", call. = FALSE)
+
+
   # Function takes either the whole output of disp() or just the displacements
   if(!is.data.frame(d)) d <- d$displacements
 

R/maps.R

@@ -112,9 +112,9 @@ map_leaflet_base <- function(locs, marker = "logger_id",
     options = leaflet::leafletOptions(minZoom = minZoom,
                                       maxZoom = maxZoom)) %>%
     leaflet::addTiles(group = "Open Street Map") %>%
-    leaflet::addProviderTiles("Stamen.Toner", group = "Black and White") %>%
-    leaflet::addProviderTiles("Esri.WorldImagery", group = "Satellite") %>%
-    leaflet::addProviderTiles("Esri.WorldTopoMap", group = "Terrain") %>%
+    leaflet::addProviderTiles(providers$Stadia.StamenToner, group = "Black and White") %>%
+    leaflet::addProviderTiles(providers$Esri.WorldImagery, group = "Satellite") %>%
+    leaflet::addProviderTiles(providers$Esri.WorldTopoMap, group = "Terrain") %>%
     leaflet::addCircleMarkers(~lon, ~lat,
                               popup  = htmltools::htmlEscape(
                                 paste("Logger:",
@@ -467,6 +467,7 @@ map_ggmap <- function() {
   .Defunct()
 }
 
+
 map.ggmap <- function() {
- .Defunct()
+  .Defunct()
 }

R/transformations.R

@@ -841,6 +841,7 @@ disp <- function(v, bw = 2, pass = TRUE){
                c("animal_id", "logger_id", "date", "start", "end")])
 
   if(nrow(d) > 0) {
+
     d <- d %>%
       dplyr::arrange(.data$start) %>%
       dplyr::mutate(role = rep(c("displacee", "displacer"), dplyr::n()/2)) %>%
@@ -859,6 +860,7 @@ disp <- function(v, bw = 2, pass = TRUE){
     s <- d %>%
       dplyr::group_by(role, animal_id) %>%
       dplyr::summarize(n = length(animal_id)) %>%
+      dplyr::ungroup() %>%
       tidyr::complete(animal_id, role, fill = list("n" = 0)) %>%
       tidyr::spread(role, n) %>%
       dplyr::mutate(p_win = displacer / (displacee + displacer)) %>%
@@ -1098,11 +1100,13 @@ activity_single <- function(p1, loggers, res = 15, by_logger = FALSE, missing =
           message(paste0(p1$animal_id[1], ": Skipping sunrise/sunset, no lat/lon information"))
         } else {
 
-          s <- expand.grid(logger_id = loggers$logger_id,
-                           date = lubridate::as_date(seq(start, end, by = "1 day"))) %>%
-            dplyr::left_join(unique(loggers[, c("logger_id", "lon", "lat")]), by = "logger_id")
-
-          s <- dplyr::bind_cols(s, sun(s[, c("lon", "lat")], s$date, tz = tz))
+          s <- tidyr::expand_grid(
+            date = lubridate::as_date(seq(start, end, by = "1 day")),
+            dplyr::distinct(loggers[, c("lon", "lat")])) |>
+            suncalc::getSunlightTimes(data = _, keep = c("sunrise", "sunset")) |>
+            dplyr::rename("rise" = "sunrise", "set" = "sunset") |>
+            dplyr::left_join(x = loggers, y = _, by = c("lat", "lon"),
+                             relationship = "many-to-many")
 
           if(by_logger == TRUE) {
             a <- dplyr::left_join(a, s[, c("logger_id", "date", "rise", "set")],
@@ -1209,23 +1213,3 @@ daily_single <- function(a1, pass = TRUE){
   dplyr::select(d, dplyr::all_of(n)) %>%
     dplyr::arrange(animal_id, time)
 }
-
-#' Get sunrise/sunset times
-#'
-#' Calculate times of sunrise and sunset depending on the location and the date.
-#'
-#' @param loc Vector/Data frame. Longitude and Latitude coordinates for location
-#'   of sun rise/set
-#' @param date Vector. Date(s) to cacluate sun rise/set for.
-#' @param tz Timezone of the dates.
-#'
-#' @export
-sun <- function(loc, date, tz) {
-  if(class(loc) == "numeric") loc <- matrix(loc, nrow = 1)
-  if(class(loc) %in% c("data.frame", "matrix")) loc <- as.matrix(loc)
-  date <- as.POSIXct(as.character(date), tz = tz)
-  s <- data.frame(rise = maptools::sunriset(loc, date, direction = "sunrise", POSIXct.out = TRUE)$time,
-                  set = maptools::sunriset(loc, date, direction = "sunset", POSIXct.out = TRUE)$time)
-
-  return(s)
-}

tests/testthat.R

@@ -1,3 +1,11 @@
+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
+# * https://testthat.r-lib.org/articles/special-files.html
+
 library(testthat)
 library(feedr)