Merge pull request #9 from AlbanSagouis/dev

Preparation for CRAN submission

.Rbuildignore

@@ -1,11 +1,15 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 cran-comments.md
+CONTRIBUTING.md
+codemeta.json
 ^revdep$
 ^README\.Rmd$
 ^README-.*\.png$
-^NEWS\.md$
 ^LICENSE\.md$
 ^examples$
 ^\.travis\.yml$
 ^\.github$
+^doc$
+^Meta$
+^codemeta\.json$

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

@@ -1,5 +1,9 @@
 # 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
+#
+# NOTE: This workflow is overkill for most R packages and
+# check-standard.yaml is likely a better choice.
+# usethis::use_github_action("check-standard") will install it.
 on:
   push:
     branches: [main, master]
@@ -18,18 +22,27 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {os: macos-latest,   r: 'release'}
+
           - {os: windows-latest, r: 'release'}
+          # Use 3.6 to trigger usage of RTools35
+          - {os: windows-latest, r: '3.6'}
+          # use 4.1 to check with rtools40's older compiler
+          - {os: windows-latest, r: '4.1'}
+
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
           - {os: ubuntu-latest,   r: 'oldrel-1'}
+          - {os: ubuntu-latest,   r: 'oldrel-2'}
+          - {os: ubuntu-latest,   r: 'oldrel-3'}
+          - {os: ubuntu-latest,   r: 'oldrel-4'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.gitignore

@@ -8,3 +8,7 @@ mobsim.Rproj
 revdep/
 .Rproj.user
 mobsim_package.Rproj
+
+.DS_Store
+/doc/
+/Meta/

DESCRIPTION

@@ -1,11 +1,16 @@
 Package: mobsim
 Type: Package
 Title: Spatial Simulation and Scale-Dependent Analysis of Biodiversity Changes
-Version: 0.2.0.9015
-Authors@R: c(person("Felix", "May", email = "[email protected]", role = c("aut","cre")),
-    person("Alban", "Sagouis", email = "[email protected]", role = c("aut"))
-    )
-Date: 2022-03-04
+Version: 0.3.0
+Authors@R: c(
+    person("Felix", "May", email = "[email protected]",
+        role = c("aut", "cre"),
+        comment = c(ORCID = "0000-0002-1106-8188")),
+    person("Alban", "Sagouis", email = "[email protected]",
+        role = "aut",
+        comment = c(ORCID = "0000-0002-3827-1063"))
+  )
+Date: 2023-12-12
 Description: Tools for the simulation, analysis and sampling of spatial
     biodiversity data (May et al. 2017) <doi:10.1101/209502>.
     In the simulation tools user define the numbers of
@@ -14,15 +19,15 @@ Description: Tools for the simulation, analysis and sampling of spatial
     and accumulation curves, species-area relationships and the distance
     decay of similarity. 
 License: GPL (>= 3)
-LazyData: TRUE
 Imports:
     Rcpp,
     vegan,
     sads (>= 0.4.1),
     grDevices,
     utils,
     graphics,
-    stats
+    stats,
+    methods
 LinkingTo:
     Rcpp
 Suggests:
@@ -31,9 +36,10 @@ Suggests:
     testthat (>= 3.0.0), mockery,
     knitr
 Config/testthat/edition: 3
+Config/testthat/parallel: true
 VignetteBuilder: knitr
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
+Language: en-GB
 Encoding: UTF-8
-Source: https://prograide.com/pregunta/73922/avertissement-concernant-lutf-8-avec-roxygen2
 URL: https://github.com/AlbanSagouis/mobsim
 BugReports: https://github.com/AlbanSagouis/mobsim

NAMESPACE

@@ -32,5 +32,7 @@ export(sim_thomas_coords)
 export(spec_sample)
 export(spec_sample_curve)
 importFrom(Rcpp,sourceCpp)
+importFrom(methods,is)
+importFrom(sads,rsad)
 useDynLib(mobsim)
 useDynLib(mobsim, .registration = TRUE)

NEWS.md

@@ -1,4 +1,4 @@
-mobsim 0.2.1
+mobsim 0.3.0
 ================================================================================
 
 ### POTENTIAL CODE BREAK

R/Diversity_Area_Relationships.R

@@ -64,12 +64,12 @@ div_rect <- function(x0, y0, xsize, ysize, comm)
    abund <- abund[abund > 0]
    relabund <- abund/sum(abund)
 
-   shannon <- - sum(relabund * log(relabund))
+   shannon <- -sum(relabund * log(relabund))
 
    n <- sum(abund)
    if (n > 1)
       #simpson <- (n/(n-1)) * (1 - sum(relabund^2))
-      simpson <- 1- sum(relabund^2)
+      simpson <- 1 - sum(relabund^2)
    else
       simpson <- NA
 
@@ -123,12 +123,11 @@ div_rand_rect <- function(prop_area = 0.25, comm, n_rect = 100,
    area <- dx_plot * dy_plot * prop_area
    square_size <- sqrt(area)
 
-   if (square_size <= min(c(dx_plot, dy_plot))){
+   if (square_size <= min(c(dx_plot, dy_plot))) {
       dx_rect <- square_size
       dy_rect <- square_size
-   } else
-   {
-      if (dx_plot >= dy_plot){
+   } else {
+      if (dx_plot >= dy_plot) {
          dx_rect <- dx_plot*prop_area
          dy_rect <- dy_plot
       } else {
@@ -143,7 +142,7 @@ div_rand_rect <- function(prop_area = 0.25, comm, n_rect = 100,
                                 max = comm$y_min_max[2] - dy_rect)
 
    div_plots <- mapply(div_rect, xpos, ypos,
-                       MoreArgs=list(xsize = dx_rect, ysize = dy_rect,
+                       MoreArgs = list(xsize = dx_rect, ysize = dy_rect,
                                      comm = comm))
    if (exclude_zeros == T)
       div_plots <- div_plots[, div_plots["n_species",] > 0]
@@ -204,7 +203,7 @@ divar <- function(comm, prop_area = seq(0.1, 1, by = 0.1), n_samples = 100,
       warning("Subplot areas larger than the community size are ignored!")
    prop_area <- prop_area[prop_area <= 1]
 
-   if (class(comm) != "community")
+   if (!is(comm, "community"))
       stop("DiVAR requires a community object as input. See ?community.")
 
    n_scales <- length(prop_area)
@@ -292,7 +291,7 @@ abund_rect <- function(x0, y0, xsize, ysize, comm)
    y <- comm$census$y
 
    # logical vector which trees are in the sampling rectangle
-   in_rect <- (x >= x0 & x < (x0+xsize) & y >= y0 & y < (y0+ysize))
+   in_rect <- (x >= x0 & x < (x0 + xsize) & y >= y0 & y < (y0 + ysize))
 
    abund <- table(comm$census$species[in_rect])
    return(abund)
@@ -318,6 +317,7 @@ abund_rect <- function(x0, y0, xsize, ysize, comm)
 #' dd1 <- dist_decay(sim_com1, prop_area = 0.005, n_samples = 20)
 #' plot(dd1)
 #'
+#' @importFrom methods is
 #'@export
 #'
 dist_decay <- function(comm, prop_area = 0.005, n_samples = 20,
@@ -329,14 +329,15 @@ dist_decay <- function(comm, prop_area = 0.005, n_samples = 20,
    if (length(prop_area) != 1L)
       stop("prop_area has to be of length 1")
 
-   if (class(comm) != "community")
+   if (!is(comm, "community"))
       stop("dist_decay requires a community object as input. See ?community.")
 
    dx_plot <- comm$x_min_max[2] - comm$x_min_max[1]
    dy_plot <- comm$y_min_max[2] - comm$y_min_max[1]
    area <- dx_plot * dy_plot * prop_area
 
-   samples1 <- sample_quadrats(comm, n_quadrats = n_samples, quadrat_area = area,
+   samples1 <- sample_quadrats(comm, n_quadrats = n_samples,
+                               quadrat_area = area,
                                avoid_overlap = T, plot = F)
    com_mat <- samples1$spec_dat[rowSums(samples1$spec_dat) > 0,]
    d <- stats::dist(samples1$xy_dat[rowSums(samples1$spec_dat) > 0,])

R/RcppExports.R

@@ -6,13 +6,13 @@ sSAC1_C <- function(x, y, id_spec) {
 }
 
 #' Thomas process individual distribution simulation for one species
-#' 
+#'
 #' Usually used internally inside \code{\link{sim_thomas_coords}}
 #' This function randomly draws points (individuals) around one or several mother points using Rcpp.
 #' The function is an efficient re-implementation of the rThomas function from the spatstat package.
-#' 
+#'
 #' @name rThomas_rcpp
-#' 
+#'
 #' @param n_points The total number of points (individuals).
 #' @param n_mother_points Number of mother points (= cluster centres).
 #' @param xmother Vector of \code{n_mother_points} x coordinates for the mother points.

R/SAC_spatial.R

@@ -108,22 +108,23 @@ rare_curve <- function(abund_vec)
 #' plot(sac1)
 #'
 #' @export
+#' @importFrom methods is
 #'
 spec_sample_curve <- function(comm, method = c("accumulation" ,"rarefaction"))
 {
-   if (class(comm) != "community")
+   if (!is(comm, "community"))
       stop("spec_sample_curve requires a community object as input. See ?community.")
 
    out_dat <- data.frame(n = 1:nrow(comm$census))
 
    method <- match.arg(method, several.ok = TRUE)
 
-   if ("accumulation" %in% method){
+   if ("accumulation" %in% method) {
       out_dat$spec_accum <- sSAC1_C(comm$census$x, comm$census$y,
                                     as.integer(comm$census$species))
    }
 
-   if ("rarefaction" %in% method){
+   if ("rarefaction" %in% method) {
       abund <- community_to_sad(comm)
       out_dat$spec_rarefied <- rare_curve(abund)
 
@@ -156,19 +157,19 @@ plot.spec_sample_curve <- function(x, ...)
                   ylab = "Expected no.of species",
                   main = "Species sampling curves", ...)
 
-   if (ncol(x) == 2){
-      if (names(x)[2] == "spec_accum"){
+   if (ncol(x) == 2) {
+      if (names(x)[2] == "spec_accum") {
          legend_text <- c("Accumulation")
          line_col <- "red"
       }
-      if (names(x)[2] == "spec_rarefied"){
+      if (names(x)[2] == "spec_rarefied") {
          legend_text <- c("Rarefaction")
          line_col <- "blue"
       }
       graphics::lines(x[[1]], x[[2]], col = line_col)
    }
 
-   if (ncol(x) == 3){
+   if (ncol(x) == 3) {
       legend_text <- c("Accumulation","Rarefaction")
       line_col <- c("red","blue")
       graphics::lines(x[[1]], x[[2]], col = line_col[1])
@@ -177,4 +178,3 @@ plot.spec_sample_curve <- function(x, ...)
 
    graphics::legend("bottomright", legend = legend_text, lty = 1, col = line_col)
 }
-

R/Sample_quadrats.R

@@ -33,7 +33,7 @@
 #' specnumber(comm_mat1$spec_dat)
 #' diversity(comm_mat1$spec_dat, index = "shannon")
 #'
-#'
+#' @importFrom methods is
 #' @export
 #'
 sample_quadrats <- function(comm, n_quadrats = 20, quadrat_area = 0.01,
@@ -42,7 +42,7 @@ sample_quadrats <- function(comm, n_quadrats = 20, quadrat_area = 0.01,
                             x0 = 0, y0 = 0, delta_x = 0.1, delta_y = 0.1,
                             seed = NULL)
 {
-   if (class(comm) != "community")
+   if (!is(comm, "community"))
       stop("comm has to be a community object")
    if (round(n_quadrats, 0) != n_quadrats) stop("n_quadrats has to be an integer")