Merge branch 'update-0.2.1'

R/NLMR.R

@@ -6,12 +6,12 @@
 #' of the \emph{NLMR} package. The vignettes in this package are listed below.
 #'
 #' \describe{
-#' \item{\href{https://marcosci.github.io/NLMR/articles/background.html}{NLM
+#' \item{\href{https://marcosci.github.io/NLMR/articles/background.html/}{NLM
 #' Concepts + Terminology}}{Background information on the concepts and
 #' terminology that underpin the simulation of neutral landscape models.}
-#' \item{\href{https://marcosci.github.io/NLMR/articles/bestiary.html}{NLMR
+#' \item{\href{https://marcosci.github.io/NLMR/articles/bestiary.html/}{NLMR
 #' Bestiary}}{Bestiary of the available neutral landscape models.}
-#' \item{\href{https://marcosci.github.io/NLMR/articles/BasicUsageVignette.html}{
+#' \item{\href{https://marcosci.github.io/NLMR/articles/getstarted.html/}{
 #' Quickstart Guide}}{Short walk-through of the \emph{NLMR} package and how to
 #' handle the simulations.}
 #' }
@@ -21,7 +21,7 @@
 # nolint start
 "_PACKAGE"
 
-globalVariables(c("value", "."))
+globalVariables(c("x", "value", "."))
 
 # nolint end
 # nocov end

R/theme_nlm.R

@@ -36,15 +36,17 @@
 #'                             "viridis - viridis" (= "D",  the default option)
 #'
 #' @details
-#' A focused theme to visualize raster data.
-#' The theme makes use of the Roboto Condensed font (Open Source font from
-#' Google) and sets a lot of defaults for the
+#' A focused theme to visualize raster data that sets a lot of defaults for the
 #' \code{ggplot2::theme}.
+#'
+#' The theme can make use of the Roboto Condensed font (Open Source font from
+#' Google).
 #' If your local font library does not contain Roboto as a font, you can
-#' import it via \code{\link{util_import_roboto_condensed}}.
+#' import it via \code{\link{util_import_roboto_condensed}} (highly recommended).
+#'
 #' The functions are setup in such a way that you can customize your own one by
 #' just wrapping the call and changing the parameters.
-#' The theme itself is heavily influenced by hrbrmstr and his great package
+#' The theme itself is heavily influenced by hrbrmstr and his package
 #' hrbrthemes (\url{https://github.com/hrbrmstr/hrbrthemes/}).
 #'
 #' @seealso \code{\link{util_import_roboto_condensed}}
@@ -53,8 +55,8 @@
 #' # nolint start
 #' \dontrun{
 #' # simulate NLM
-#' x <- NLMR::nlm_random(ncol = 75,
-#'                       nrow = 75)
+#' x <- nlm_random(ncol = 75,
+#'                 nrow = 75)
 #' # classify
 #' y <- c(0.5, 0.15, 0.25)
 #' y <- util_classify(x, y, c("1", "2", "3"))
@@ -109,26 +111,20 @@ NULL
 
 #' @rdname theme_nlm
 #' @export
-theme_nlm <- function(base_family = "Roboto Condensed",
+theme_nlm <- function(base_family = "serif",
                       base_size = 11.5,
-                      plot_title_family = base_family,
+                      plot_title_family = "serif",
                       plot_title_size = 18,
                       plot_title_face = "bold",
                       plot_title_margin = 10,
-                      subtitle_family = if (.Platform$OS.type == "windows")
-                        "Roboto Condensed"
-                      else
-                        "Roboto Condensed Light",
+                      subtitle_family = "serif",
                       subtitle_size = 13,
                       subtitle_face = "plain",
                       subtitle_margin = 15,
                       strip_text_family = base_family,
                       strip_text_size = 12,
                       strip_text_face = "plain",
-                      caption_family = if (.Platform$OS.type == "windows")
-                        "Roboto Condensed"
-                      else
-                        "Roboto Condensed Light",
+                      caption_family = "serif",
                       caption_size = 9,
                       caption_face = "plain",
                       caption_margin = 10,
@@ -143,8 +139,7 @@ theme_nlm <- function(base_family = "Roboto Condensed",
   # extend it
   theme_base <- ret + ggplot2::theme(
     legend.background = ggplot2::element_blank(),
-    legend.text = ggplot2::element_text(size = 8,
-                                        family = "Roboto Condensed Light"),
+    legend.text = ggplot2::element_text(size = 8),
     aspect.ratio = ratio,
     plot.margin = plot_margin,
     strip.text = ggplot2::element_text(
@@ -202,26 +197,20 @@ theme_nlm <- function(base_family = "Roboto Condensed",
 #' @rdname theme_nlm
 #' @export
 theme_nlm_discrete <- function(
-  base_family = "Roboto Condensed",
+  base_family = "serif",
   base_size = 11.5,
   plot_title_family = base_family,
   plot_title_size = 18,
   plot_title_face = "bold",
   plot_title_margin = 10,
-  subtitle_family = if (.Platform$OS.type == "windows")
-   "Roboto Condensed"
-  else
-   "Roboto Condensed Light",
+  subtitle_family = "serif",
   subtitle_size = 13,
   subtitle_face = "plain",
   subtitle_margin = 15,
   strip_text_family = base_family,
   strip_text_size = 12,
   strip_text_face = "plain",
-  caption_family = if (.Platform$OS.type == "windows")
-   "Roboto Condensed"
-  else
-   "Roboto Condensed Light",
+  caption_family = "serif",
   caption_size = 9,
   caption_face = "plain",
   caption_margin = 10,
@@ -237,8 +226,7 @@ theme_nlm_discrete <- function(
   # extend it
   theme_base <- ret + ggplot2::theme(
     legend.background = ggplot2::element_blank(),
-    legend.text = ggplot2::element_text(size = 8,
-                                        family = "Roboto Condensed Light"),
+    legend.text = ggplot2::element_text(size = 8),
     aspect.ratio = ratio,
     plot.margin = plot_margin,
     strip.text = ggplot2::element_text(
@@ -301,26 +289,20 @@ theme_nlm_discrete <- function(
 
 #' @rdname theme_nlm
 #' @export
-theme_nlm_grey <- function(base_family = "Roboto Condensed",
+theme_nlm_grey <- function(base_family = "serif",
                            base_size = 11.5,
                            plot_title_family = base_family,
                            plot_title_size = 18,
                            plot_title_face = "bold",
                            plot_title_margin = 10,
-                           subtitle_family = if (.Platform$OS.type == "windows")
-                             "Roboto Condensed"
-                           else
-                             "Roboto Condensed Light",
+                           subtitle_family = "serif",
                            subtitle_size = 13,
                            subtitle_face = "plain",
                            subtitle_margin = 15,
                            strip_text_family = base_family,
                            strip_text_size = 12,
                            strip_text_face = "plain",
-                           caption_family = if (.Platform$OS.type == "windows")
-                             "Roboto Condensed"
-                           else
-                             "Roboto Condensed Light",
+                           caption_family = "serif",
                            caption_size = 9,
                            caption_face = "plain",
                            caption_margin = 10,
@@ -335,8 +317,7 @@ theme_nlm_grey <- function(base_family = "Roboto Condensed",
   # extend it
   theme_base <- ret + ggplot2::theme(
     legend.background = ggplot2::element_blank(),
-    legend.text = ggplot2::element_text(size = 8,
-                                        family = "Roboto Condensed Light"),
+    legend.text = ggplot2::element_text(size = 8),
     aspect.ratio = ratio,
     plot.margin = plot_margin,
     strip.text = ggplot2::element_text(
@@ -394,26 +375,20 @@ theme_nlm_grey <- function(base_family = "Roboto Condensed",
 #' @rdname theme_nlm
 #' @export
 theme_nlm_grey_discrete <-
-  function(base_family = "Roboto Condensed",
+  function(base_family = "serif",
            base_size = 11.5,
            plot_title_family = base_family,
            plot_title_size = 18,
            plot_title_face = "bold",
            plot_title_margin = 10,
-           subtitle_family = if (.Platform$OS.type == "windows")
-             "Roboto Condensed"
-           else
-             "Roboto Condensed Light",
+           subtitle_family = "serif",
            subtitle_size = 13,
            subtitle_face = "plain",
            subtitle_margin = 15,
            strip_text_family = base_family,
            strip_text_size = 12,
            strip_text_face = "plain",
-           caption_family = if (.Platform$OS.type == "windows")
-             "Roboto Condensed"
-           else
-             "Roboto Condensed Light",
+           caption_family = "serif",
            caption_size = 9,
            caption_face = "plain",
            caption_margin = 10,
@@ -429,8 +404,7 @@ theme_nlm_grey_discrete <-
     # extend it
     theme_base <- ret + ggplot2::theme(
       legend.background = ggplot2::element_blank(),
-      legend.text = ggplot2::element_text(size = 8,
-                                          family = "Roboto Condensed Light"),
+      legend.text = ggplot2::element_text(size = 8),
       aspect.ratio = ratio,
       plot.margin = plot_margin,
       strip.text = ggplot2::element_text(

R/util_facetplot.R

@@ -18,15 +18,16 @@
 #' \dontrun{
 #' l1 <- nlm_fBm(64, 64)
 #' l2 <- nlm_planargradient(64, 64)
-#' l3 <- nlm_mosaicfield(42, 42)
+#' l3 <- nlm_randomrectangularcluster(ncol = 60, nrow = 60, minl = 5, maxl = 10)
+#' l4 <- nlm_random(64, 64)
 #'
 #' bri1 <- raster::brick(l1, l2)
 #' util_facetplot(bri1)
 #'
-#' lst1 <- list(lay1 = l1,
-#'              lay2 = l2,
-#'              lay3 = l3,
-#'              lay4 = nlm_random(70, 70))
+#' lst1 <- list(layer1 = l1,
+#'              layer2 = l2,
+#'              layer3 = l3,
+#'              layer4 = l4)
 #' util_facetplot(lst1)
 #' }
 #'

R/zzz.R

@@ -8,14 +8,17 @@
   # https://github.com/hrbrmstr/hrbrthemes
 
   if (.Platform$OS.type == "windows")  {
-    if (interactive()) packageStartupMessage("Registering Windows fonts with R")
+    if (interactive()) packageStartupMessage(
+      "Registering Windows fonts with R for advanced plotting options"
+      )
     # work around for https://github.com/wch/extrafont/issues/44
     windowsFonts <- grDevices::windowsFonts
     extrafont::loadfonts("win", quiet = TRUE)
   }
 
-  if (interactive()) packageStartupMessage("Registering PDF &
-                                           PostScript fonts with R")
+  if (interactive()) packageStartupMessage(
+      "Registering PDF & PostScript fonts with R for advanced plotting options"
+      )
   #work around for https://github.com/wch/extrafont/issues/44
   pdfFonts <- grDevices::pdfFonts
   extrafont::loadfonts("pdf", quiet = TRUE)

README.md

@@ -30,11 +30,27 @@ Here we will provide a simple example on using `NLMR`:
 
 ``` r
 library(NLMR)
-#> Registering PDF &
-#>                                            PostScript fonts with R
 library(magrittr)
+#> 
+#> Attaching package: 'magrittr'
+#> The following object is masked from 'package:raster':
+#> 
+#>     extract
+#> The following objects are masked from 'package:testthat':
+#> 
+#>     equals, is_less_than, not
 library(ggplot2)  # to extend the plot functionality of NLMR 
+#> 
+#> Attaching package: 'ggplot2'
+#> The following object is masked from 'package:raster':
+#> 
+#>     calc
 library(SDMTools) # to calculate basic landscape metrics
+#> 
+#> Attaching package: 'SDMTools'
+#> The following object is masked from 'package:raster':
+#> 
+#>     distance
 
 # Simulate 50x50 rectangular cluster raster
 nlm_raster <- nlm_randomrectangularcluster(50,50, resolution = 1, minl = 3, maxl = 7)
@@ -71,9 +87,9 @@ raster::as.matrix(nlm_raster) %>%
 
 |  patchID|  n.cell|  n.core.cell|  n.edges.perimeter|  n.edges.internal|  area|  core.area|  perimeter|  perim.area.ratio|  shape.index|  frac.dim.index|  core.area.index|
 |--------:|-------:|------------:|------------------:|-----------------:|-----:|----------:|----------:|-----------------:|------------:|---------------:|----------------:|
-|        0|    1245|          559|                832|              4148|  1245|        559|        832|         0.6682731|     5.859155|        1.497859|        0.4489960|
-|        1|     608|          196|                580|              1852|   608|        196|        580|         0.9539474|     5.800000|        1.552761|        0.3223684|
-|        2|     647|          163|                654|              1934|   647|        163|        654|         1.0108192|     6.411765|        1.574951|        0.2519320|
+|        0|    1221|          622|                682|              4202|  1221|        622|        682|         0.5585586|     4.871429|        1.446019|        0.5094185|
+|        1|     641|          197|                628|              1936|   641|        197|        628|         0.9797192|     6.156863|        1.564667|        0.3073323|
+|        2|     638|          178|                602|              1950|   638|        178|        602|         0.9435737|     5.901961|        1.552710|        0.2789969|
 
 Citation
 --------
@@ -90,7 +106,7 @@ Citation
       @Misc{,
         title = {{NLMR}: Simulating neutral landscape models.},
         author = {Marco Sciaini and Matthias Fritsch and Craig E. Simpkins},
-        note = {R package version 0.2},
+        note = {R package version 0.2.1},
         url = {https://CRAN.R-project.org/package=NLMR},
       }
 

cran-comments.md

@@ -1,7 +1,6 @@
 ## Updated package
 
-This update adds more functionality to the package and provides some additional
-bug fixes.
+This update fixes an error on CRAN and has small updates.
 
 ## Test environments
 

docs/articles/getstarted_cache/html/__packages

@@ -1,3 +1,4 @@
 base
 sp
 raster
+NLMR