Fixing pkgkdown and some other warnings #110

.github/workflows/Deploy-pkgdown.yaml

@@ -32,10 +32,8 @@ jobs:
 
       - name: Install additional package dependencies
         run: |
-          repos.orig <- getOption('repos')
-          options(repos = c(PE = "https://predictiveecology.r-universe.dev")) ## TODO: use ropensci universe
-          pak::pkg_install("RandomFields")
-          options(repos = repos.orig)
+          pak::pkg_install("cran/RandomFieldsUtils")
+          pak::pkg_install("cran/RandomFields")
         shell: Rscript {0}
 
       - name: Build site

DESCRIPTION

@@ -34,7 +34,7 @@ License: GPL-3
 URL: https://ropensci.github.io/NLMR/
 BugReports: https://github.com/ropensci/NLMR/issues/
 Depends:
-    R (>= 3.1.0)
+    R (>= 3.6)
 Imports: 
     checkmate,
     dplyr,
@@ -49,6 +49,7 @@ Imports:
 Suggests:
     ggplot2,
     highcharter,
+    igraph,
     knitr,
     kableExtra,
     landscapemetrics,
@@ -63,7 +64,7 @@ Suggests:
     rayshader,
     rgl,
     rmarkdown,
-    testthat,
+    testthat (>= 3.0.0),
     viridis
 LinkingTo: 
     Rcpp
@@ -76,5 +77,6 @@ Config/Needs/website: bindrcpp, igraph, landscapemetrics, rasterVis, pals,
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(roclets = c("rd", "namespace", "collate"))
-RoxygenNote: 7.2.1
+RoxygenNote: 7.3.2
+Config/testthat/edition: 3
 SystemRequirements: C++11

NLMR.Rproj

@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: c60b485c-12be-40a7-be11-f785e3cf8c20
 
 RestoreWorkspace: Default
 SaveWorkspace: Default

R/nlm_mpd.R

@@ -7,14 +7,14 @@
 #' algorithm.
 #' It performs the following steps:
 #'
-#' \itemize{
-#'  \item{Initialization: }{ Determine the smallest fit of
-#'  \code{max(ncol, nrow)} in \emph{n^2 + 1} and assign value to n.
-#'  Setup matrix of size (n^2 + 1)*(n^2 + 1).
-#'  Afterwards, assign a random value to the four corners of the matrix.}
-#'  \item{Square Step: }{ For each square in the matrix, assign the average of
+#' \describe{
+#'  \item{Initialization:}{Determine the smallest fit of
+#'  \code{max(ncol, nrow)} in \emph{n^2 + 1} and assign value to n. Setup matrix of
+#'  size (n^2 + 1)*(n^2 + 1). Afterwards, assign a random value to the four corners
+#'  of the matrix.}
+#'  \item{Square Step:}{For each square in the matrix, assign the average of
 #'  the four corner points plus a random value to the midpoint of that square.}
-#'  \item{Diamond Step: }{ For each diamond in the matrix, assign the average
+#'  \item{Diamond Step:}{For each diamond in the matrix, assign the average
 #'   of the four corner points plus a random value to the midpoint of that
 #'   diamond.}
 #' }
@@ -79,12 +79,12 @@ nlm_mpd <- function(ncol,
   # create the landscape with rcpp_mpd ----
   seed <- sample.int(.Machine$integer.max, 1)
   mpd_raster <- rcpp_mpd(ncol, nrow, rand_dev, roughness, seed, torus)
-  
+
   mpd_raster <- mpd_raster[-1,]
   mpd_raster <- mpd_raster[,-1]
   mpd_raster <- mpd_raster[-nrow(mpd_raster),]
   mpd_raster <- mpd_raster[,-ncol(mpd_raster)]
-  
+
   # Convert matrix to raster ----
   mpd_raster <- raster::raster(mpd_raster)
 

R/nlm_percolation.R

@@ -14,9 +14,9 @@
 #' @details
 #' The simulation of a random percolation map is accomplished in two steps:
 #'
-#' \itemize{
-#'  \item{Initialization: }{ Setup matrix of size (\code{ncol}*\code{nrow})}
-#'  \item{Map generation: }{ For each cell in the matrix a single uniformly
+#' \describe{
+#'  \item{Initialization:}{Setup matrix of size (\code{ncol}*\code{nrow})}
+#'  \item{Map generation:}{For each cell in the matrix a single uniformly
 #'  distributed random number is generated and tested against a probability
 #'  \code{prob}. If the random number is smaller than \code{prob}, the cell is set to
 #'  TRUE - if it is higher the cell is set to FALSE.}

README.Rmd

@@ -19,10 +19,8 @@ knitr::opts_chunk$set(
 
 [![R-CMD-check](https://github.com/ropensci/NLMR/workflows/R-CMD-check/badge.svg)](https://github.com/ropensci/NLMR/actions)
 [![codecov](https://codecov.io/gh/ropensci/NLMR/branch/develop/graph/badge.svg?token=MKCm2fVrDa)](https://codecov.io/gh/ropensci/NLMR)
-[![CRAN\_Status\_Badge](http://www.r-pkg.org/badges/version/NLMR)](https://cran.r-project.org/package=NLMR) 
-[![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing)
-[![](http://cranlogs.r-pkg.org/badges/grand-total/NLMR)](http://cran.rstudio.com/web/packages/NLMR/index.html) 
-[![](https://badges.ropensci.org/188_status.svg)](https://github.com/ropensci/onboarding/issues/188)
+[![Lifecycle](https://img.shields.io/badge/Lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html)
+[![ropensci](https://badges.ropensci.org/188_status.svg)](https://github.com/ropensci/onboarding/issues/188)
 [![DOI:10.1111/2041-210X.13076](https://zenodo.org/badge/DOI/10.1111/2041-210X.13076.svg)](https://doi.org/10.1111/2041-210X.13076)
 
 <!-- badges: end -->

_pkgdown.yml

@@ -1,3 +1,5 @@
+url: https://ropensci.github.io/NLMR/
+
 reference:
   - title: Neutral Landscape Models
     desc: ~

tests/testthat.R

@@ -1,4 +1,12 @@
-library(testthat)
-library(NLMR)
-
-test_check("NLMR")
+# 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(NLMR)
+
+test_check("NLMR")

tests/testthat/setup.R

@@ -0,0 +1,3 @@
+# load additional packages
+
+library(igraph)