Merge pull request #11 from reginalexavier/quickfix

fix: compatibility with ggplot >= 3.5

.gitignore

@@ -5,4 +5,4 @@ inst/doc
 doc
 Meta
 docs/
-
+*.pdf

DESCRIPTION

@@ -24,7 +24,7 @@ URL: https://reginalexavier.github.io/OpenLand/, https://github.com/reginalexavi
 BugReports: https://github.com/reginalexavier/OpenLand/issues
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.2
+RoxygenNote: 7.3.1
 Depends: 
     R (>= 3.4.0)
 Imports: 

R/OpenLand-package.R

@@ -1,3 +1,4 @@
+"_PACKAGE"
 #' OpenLand: land use and cover (LUC) time series analysis in R.
 #'
 #'
@@ -15,7 +16,7 @@
 #' \code{\link{contingencyTable}},
 #'
 #' @author Reginal Exavier \email{reginalexavier@@rocketmail.com}, Peter Zeilhofer \email{zeilhoferpeter@@gmail.com}
-#' @docType package
+# @docType package
 #' @name OpenLand-package
 #' @aliases OpenLand
 #'

R/demolandscape.R

@@ -1,6 +1,6 @@
 #' Create Raster with Random pixel Value
 #'
-#' This function create a raster serie with some setup like the layer name and
+#' This function creates a raster series with some setup like the layer name and
 #' the sample value for the lulc
 #'
 #' @param year numeric. A vector of year, first and last included.
@@ -13,7 +13,7 @@
 #' @param ymx numeric. y maximum extent.
 #' @param crs character. the coordinate referencing system.
 #' @param category A numeric vector of the raster categories.
-#' @param prob A numreric vector of the probability of occurrence for the
+#' @param prob A numeric vector of the probability of occurrence for the
 #' category list.
 #'
 #'

R/generalfunctions.R

@@ -1,7 +1,7 @@
 
 #' Summary of multiple parameters in a raster directory
 #'
-#' Listing major charateristics of raster inputs. Those characteristics are the
+#' Listing major characteristics of raster inputs. Those characteristics are the
 #' dimensions, the resolution, the extent, the values (min, max) and the
 #' coordinate reference system.
 #'
@@ -24,10 +24,10 @@
 #'
 summary_dir <- function(path) {
 
-  if ((class(path) == "list") &
-      (c(class(path[[1]])) == "RasterLayer")) {
+  if (inherits(path, "list") &
+      inherits(path[[1]], "RasterLayer")) {
     layer_list <- path
-  } else if (class(path) == "character") {
+  } else if (inherits(path, "character")) {
 
     raster_files <-
       list.files(path,
@@ -87,8 +87,8 @@ summary_dir <- function(path) {
 #'
 summary_map <- function(path) {
   rastermap <-
-    if (class(path) != "character") {
-      if (class(path) == "RasterLayer") {
+    if (!inherits(path, "character")) {
+      if (inherits(path, "RasterLayer")) {
         path
       } else {
         path[[1]]

R/otherplots.R

@@ -410,7 +410,7 @@ netgrossplot <-
                    )) +
       scale_fill_manual(values = color) +
       labs(fill = legend_title) +
-      geom_hline(yintercept = 0, size = .3) +
+      geom_hline(yintercept = 0, linewidth = .3) +
       xlab(xlab) +
       ylab(ylab) +
       ggtitle(title) +

R/plotMethods.R

@@ -79,8 +79,8 @@ methods::setMethod(
       ) +
       geom_hline(aes(yintercept = dataset[[4]], color = "U"),
                  linetype = 5,
-                 size = .5) +
-      geom_hline(aes(yintercept = 0), size = .01) +
+                 linewidth = .5) +
+      geom_hline(aes(yintercept = 0), linewidth = .01) +
       scale_fill_manual(values = c(color_bar[[1]], color_bar[[2]])) +
       ylab(NULL) +
       scale_color_manual(values = "black") +
@@ -97,7 +97,7 @@ methods::setMethod(
           xend = (length(unique(dataset[[1]])) / 2) + leg_curv[[2]],
           yend = dataset[[4]] + leg_curv[[1]]
         ),
-        size = .6,
+        linewidth = .6,
         curvature = .1,
         arrow = arrow(length = unit(2, "mm"), ends = "first")
       ) +
@@ -140,7 +140,7 @@ methods::setMethod(
       coord_flip() +
       xlab(expression(paste("Periodo de tempo [ ", Y[t], ",", Y[t + 1], "]"))) +
       ylab(NULL) +
-      geom_hline(aes(yintercept = 0), size = .01) +
+      geom_hline(aes(yintercept = 0), linewidth = .01) +
       scale_y_reverse(expand = expansion(mult = c(0.01, 0))) +
       scale_x_discrete(position = "top", expand = expansion(mult = c(0.06, 0.06))) +
       theme(
@@ -231,10 +231,10 @@ methods::setMethod(
                                                                   levels(dataset[[2]])))]])) +
       xlab(NULL) +
       ylab(NULL) +
-      geom_hline(aes(yintercept = 0), size = .3) +
+      geom_hline(aes(yintercept = 0), linewidth = .3) +
       geom_hline(aes(yintercept = dataset[[6]], color = names(dataset)[[6]]),
                  linetype = 5,
-                 size = .3) +
+                 linewidth = .3) +
       scale_color_manual(values = "black") +
       coord_flip() +
       labs(fill = labs[[1]], colour = labs[[2]]) +
@@ -290,7 +290,7 @@ methods::setMethod(
                                                                  levels(dataset[[2]])))]])) +
       xlab(NULL) +
       ylab(NULL) +
-      geom_hline(aes(yintercept = 0), size = .3) +
+      geom_hline(aes(yintercept = 0), linewidth = .3) +
       coord_flip() +
       labs(fill = "Categories") +
       scale_y_reverse(expand = expansion(mult = c(0.01, 0))) +
@@ -390,10 +390,10 @@ methods::setMethod(
                                                                  levels(dataset[[2]])))]])) +
       xlab(NULL) +
       ylab(NULL) +
-      geom_hline(aes(yintercept = 0), size = .3) +
+      geom_hline(aes(yintercept = 0), linewidth = .3) +
       geom_hline(aes(yintercept = dataset[[7]], color = names(dataset)[[7]]),
                  linetype = 5,
-                 size = .3) +
+                 linewidth = .3) +
       scale_color_manual(values = "black") +
       coord_flip() +
       labs(fill = labs[[1]], colour = labs[[2]]) +
@@ -448,7 +448,7 @@ methods::setMethod(
                                                                  levels(dataset[[2]])))]])) +
       xlab(NULL) +
       ylab(NULL) +
-      geom_hline(aes(yintercept = 0), size = .3) +
+      geom_hline(aes(yintercept = 0), linewidth = .3) +
       coord_flip() +
       labs(fill = "Categories") +
       scale_y_reverse(expand = expansion(mult = c(0.01, 0))) +

tests/testthat/test_generalfunctions.R

@@ -24,19 +24,25 @@ test_that("Behavior of acc_changes", {
 })
 
 
-# testFolder <- tempdir()
-#
-# lapply(.demo_landscape(year = 2000:2004), function(x)
-#   raster::writeRaster(x,
-#                       filename = file.path(testFolder, paste0(names(x), ".tif")),
-#                       datatype = 'INT1U',
-#                       overwrite = TRUE
-#   ))
+if (FALSE){
+  testFolder <- tempdir()
+
+  lapply(.demo_landscape(year = 2000:2004), function(x)
+    raster::writeRaster(x,
+                        filename = file.path(testFolder, paste0(names(x), ".tif")),
+                        datatype = 'INT1U',
+                        overwrite = TRUE
+    ))
+
+  expect_silent(summary_dir(testFolder))
+  expect_equal(nrow(summary_dir(testFolder)), 5)
+
+}
+
 
 test_that("Behavior of summary_dir", {
 
-  # expect_silent(summary_dir(testFolder))
-  # expect_equal(nrow(summary_dir(testFolder)), 5)
+
   expect_silent(summary_dir(demo_raster))
   expect_visible(summary_dir(demo_raster))
   expect_error(summary_dir(raster::stack(demo_raster)))

tests/testthat/test_plots.R

@@ -53,11 +53,14 @@ test_that("Behavior of the other plots", {
   expect_visible(sankeyLand(demo_cont$lulc_Multistep, demo_cont$tb_legend))
 
 
+  expect_output(str(barplotLand(demo_cont$lulc_Multistep, demo_cont$tb_legend)), "List of 11")
+  expect_output(str(netgrossplot(demo_cont$lulc_Multistep, demo_cont$tb_legend)), "List of 11")
   expect_s3_class(barplotLand(demo_cont$lulc_Multistep, demo_cont$tb_legend), "ggplot")
-  #expect_null(str(chordDiagramLand(demo_cont$lulc_Onestep, demo_cont$tb_legend)))
+  # expect_type(str(chordDiagramLand(demo_cont$lulc_Onestep, demo_cont$tb_legend)), "NULL")
   expect_s3_class(netgrossplot(demo_cont$lulc_Multistep, demo_cont$tb_legend), "ggplot")
   expect_output(str(sankeyLand(demo_cont$lulc_Onestep, demo_cont$tb_legend)), "List of 8")
   expect_output(str(sankeyLand(demo_cont$lulc_Multistep, demo_cont$tb_legend)), "List of 8")
 
 
 })
+

vignettes/openland_vignette.Rmd

@@ -3,7 +3,7 @@ title: "Quick introduction to the OpenLand package"
 output: rmarkdown::html_vignette
 bibliography: papers_OpenLand.bib
 vignette: >
-  %\VignetteIndexEntry{Quick Intro for OpenLand Package}
+  %\VignetteIndexEntry{Quick introduction to the OpenLand package}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
@@ -90,7 +90,7 @@ For our study area, `contingenceTable(input_raster = SaoLourencoBasin, pixelreso
 
 ```{r}
 
-# SL_2002_2014 <- contingenceTable(input_raster = SaoLourencoBasin, pixelresolution = 30)
+# SL_2002_2014 <- contingencyTable(input_raster = SaoLourencoBasin, pixelresolution = 30)
 
 SL_2002_2014