Merge pull request #136 from r-spatialecology/main

Fix doc links
r-spatialecology · Jan 10, 2025 · d13020c · d13020c
2 parents 32c69cd + 9ee8a4d
commit d13020c
Show file tree

Hide file tree

Showing 34 changed files with 43 additions and 43 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -45,7 +45,7 @@ Suggests:
     rmarkdown,
     spatstat (>= 2.0-0),
     testthat (>= 3.0.0)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 VignetteBuilder: knitr
 Encoding: UTF-8
 LazyData: true

diff --git a/R/calculate_energy.R b/R/calculate_energy.R
@@ -15,8 +15,8 @@
 #' nearest neighbour distance function are used to describe the patterns.
 #'
 #' @seealso
-#' \code{\link{plot_energy}} \cr
-#' \code{\link{reconstruct_pattern}} \cr
+#' \code{\link{plot_energy}},
+#' \code{\link{reconstruct_pattern}},
 #' \code{\link{fit_point_process}}
 #'
 #' @return vector

diff --git a/R/classify_habitats.R b/R/classify_habitats.R
@@ -17,7 +17,7 @@
 #' of classes, fixed breaks, etc.).
 #'
 #' @seealso
-#' \code{\link{classIntervals}}
+#' \code{\link[classInt]{classIntervals}}
 #'
 #' @return SpatRaster
 #'

diff --git a/R/get_dist_pairs.R b/R/get_dist_pairs.R
@@ -9,7 +9,7 @@
 #' Returns matrix with point pairs and distances between them.
 #'
 #' @seealso
-#' \code{\link{pcf.ppp}}
+#' \code{\link[spatstat.explore]{pcf.ppp}}
 #'
 #' @return matrix
 #'

diff --git a/R/list_to_randomized.R b/R/list_to_randomized.R
@@ -13,8 +13,8 @@
 #' For more information, please see the "Parallelization" article.
 #'
 #' @seealso
-#' \code{\link{randomize_raster}} \cr
-#' \code{\link{translate_raster}} \cr
+#' \code{\link{randomize_raster}},
+#' \code{\link{translate_raster}},
 #' \code{\link{reconstruct_pattern}}
 #'
 #' @return rd_pat, rd_ras

diff --git a/R/pack_randomized.R b/R/pack_randomized.R
@@ -9,8 +9,8 @@
 #' all raster objects and prepares them for saving first. For further details, see \code{wrap}.
 #'
 #' @seealso
-#' \code{\link{unpack_randomized}}
-#' \code{\link{wrap}}
+#' \code{\link{unpack_randomized}},
+#' \code{\link[terra]{wrap}}
 #'
 #' @return rd_ras
 #'

diff --git a/R/plot.rd_mar.R b/R/plot.rd_mar.R
@@ -23,7 +23,7 @@
 #' will be plotted.
 #'
 #' @seealso
-#' \code{\link{reconstruct_pattern}} \cr
+#' \code{\link{reconstruct_pattern}},
 #' \code{\link{fit_point_process}}
 #'
 #' @return void

diff --git a/R/plot.rd_pat.R b/R/plot.rd_pat.R
@@ -23,7 +23,7 @@
 #' will be plotted.
 #'
 #' @seealso
-#' \code{\link{reconstruct_pattern}} \cr
+#' \code{\link{reconstruct_pattern}},
 #' \code{\link{fit_point_process}}
 #'
 #' @return void

diff --git a/R/plot.rd_ras.R b/R/plot.rd_ras.R
@@ -16,7 +16,7 @@
 #' will be plotted. \code{col, nrow, ncol} are passed to \code{plot}.
 #'
 #' @seealso
-#' \code{\link{randomize_raster}} \cr
+#' \code{\link{randomize_raster}},
 #' \code{\link{translate_raster}}
 #'
 #' @return void

diff --git a/R/plot_energy.R b/R/plot_energy.R
@@ -12,7 +12,7 @@
 #' \code{reconstruct_pattern_*} .
 #'
 #' @seealso
-#' \code{\link{reconstruct_pattern}} \cr
+#' \code{\link{reconstruct_pattern}},
 #' \code{\link{fit_point_process}}
 #'
 #' @return void

diff --git a/R/print.rd_pat.R b/R/print.rd_pat.R
@@ -10,7 +10,7 @@
 #' Printing method for random patterns created with \code{reconstruct_pattern_*}.
 #'
 #' @seealso
-#' \code{\link{reconstruct_pattern}} \cr
+#' \code{\link{reconstruct_pattern}},
 #' \code{\link{fit_point_process}}
 #'
 #' @return void

diff --git a/R/print.rd_ras.R b/R/print.rd_ras.R
@@ -10,7 +10,7 @@
 #' \code{\link{translate_raster}}.
 #'
 #' @seealso
-#' \code{\link{randomize_raster}} \cr
+#' \code{\link{randomize_raster}},
 #' \code{\link{translate_raster}}
 #'
 #' @return void

diff --git a/R/reconstruct_pattern.R b/R/reconstruct_pattern.R
@@ -59,7 +59,7 @@
 #' }
 #'
 #' @seealso
-#' \code{\link{calculate_energy}} \cr
+#' \code{\link{calculate_energy}},
 #' \code{\link{reconstruct_pattern_marks}}
 #'
 #' @return rd_pat

diff --git a/R/reconstruct_pattern_marks.R b/R/reconstruct_pattern_marks.R
@@ -35,7 +35,7 @@
 #' the computational time while increasing the "bumpiness" of the summary function.
 #'
 #' @seealso
-#' \code{\link{fit_point_process}} \cr
+#' \code{\link{fit_point_process}},
 #' \code{\link{reconstruct_pattern}}
 #'
 #' @return rd_mar

diff --git a/R/reconstruct_pattern_multi.R b/R/reconstruct_pattern_multi.R
@@ -66,8 +66,8 @@
 #' A comprehensive description of the method can be found in Wudel et al. (2023).
 #'
 #' @seealso
-#' \code{\link{fit_point_process}} \cr
-#' \code{\link{reconstruct_pattern}} \cr
+#' \code{\link{fit_point_process}},
+#' \code{\link{reconstruct_pattern}},
 #' \code{\link{reconstruct_pattern_marks}}
 #'
 #' @return rd_multi

diff --git a/R/results_habitat_association.R b/R/results_habitat_association.R
@@ -26,7 +26,7 @@
 #' the breaks will be included as well.
 #'
 #' @seealso
-#' \code{\link{reconstruct_pattern}} \cr
+#' \code{\link{reconstruct_pattern}},
 #' \code{\link{fit_point_process}}
 #'
 #' @return data.frame

diff --git a/R/unpack_randomized.R b/R/unpack_randomized.R
@@ -11,7 +11,7 @@
 #'
 #' @seealso
 #' \code{\link{pack_randomized}}
-#' \code{\link{wrap}}
+#' \code{\link[terra]{wrap}}
 #'
 #' @return rd_ras
 #'

diff --git a/codemeta.json b/codemeta.json
@@ -13,7 +13,7 @@
     "name": "R",
     "url": "https://r-project.org"
   },
-  "runtimePlatform": "R version 4.3.3 (2024-02-29)",
+  "runtimePlatform": "R version 4.4.2 (2024-10-31)",
   "provider": {
     "@id": "https://cran.r-project.org",
     "@type": "Organization",
@@ -257,7 +257,7 @@
     },
     "SystemRequirements": null
   },
-  "fileSize": "1074.197KB",
+  "fileSize": "1074.193KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",

diff --git a/man/calculate_energy.Rd b/man/calculate_energy.Rd
diff --git a/man/classify_habitats.Rd b/man/classify_habitats.Rd
diff --git a/man/get_dist_pairs.Rd b/man/get_dist_pairs.Rd
diff --git a/man/list_to_randomized.Rd b/man/list_to_randomized.Rd
diff --git a/man/pack_randomized.Rd b/man/pack_randomized.Rd
diff --git a/man/plot.rd_mar.Rd b/man/plot.rd_mar.Rd
diff --git a/man/plot.rd_pat.Rd b/man/plot.rd_pat.Rd
diff --git a/man/plot.rd_ras.Rd b/man/plot.rd_ras.Rd
diff --git a/man/plot_energy.Rd b/man/plot_energy.Rd
diff --git a/man/print.rd_pat.Rd b/man/print.rd_pat.Rd
diff --git a/man/print.rd_ras.Rd b/man/print.rd_ras.Rd
diff --git a/man/reconstruct_pattern.Rd b/man/reconstruct_pattern.Rd
diff --git a/man/reconstruct_pattern_marks.Rd b/man/reconstruct_pattern_marks.Rd
diff --git a/man/reconstruct_pattern_multi.Rd b/man/reconstruct_pattern_multi.Rd
diff --git a/man/results_habitat_association.Rd b/man/results_habitat_association.Rd
diff --git a/man/unpack_randomized.Rd b/man/unpack_randomized.Rd