Merge pull request #19 from r-spatialecology/CRAN

Cran
r-spatialecology · Jan 10, 2024 · 4e93abe · 4e93abe
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,32 +1,33 @@
-Type: Package
-Package: onpoint
-Title: Helper Functions for Point Pattern Analysis
-Version: 1.0.4
-Authors@R: 
-  person("Maximilian H.K.", "Hesselbarth", 
-  email = "[email protected]",
-  role = c("aut", "cre"), 
-  comment = c(ORCID = "0000-0003-1125-9918"))
-Maintainer: Maximilian H.K. Hesselbarth <[email protected]>
-Description: 
-  Growing collection of helper functions for point pattern analysis. Most functions
-  are designed to work with the 'spatstat' (<http://spatstat.org>) package. The focus of 
-  most functions are either null models or summary functions for spatial point patterns. 
-  For a detailed description of all null models and summary functions, see 
-  Wiegand and Moloney (2014, ISBN:9781420082548).
-URL: https://r-spatialecology.github.io/onpoint/
-BugReports: https://github.com/r-spatialecology/onpoint/issues
-License: GPL (>= 3)
-Depends: R (>= 3.1)
-Imports:
-  ggplot2,
-  spatstat.explore, 
-  spatstat.geom,
-  spatstat.random,
-  stats
-Suggests: 
-    covr,
-    spatstat (>= 2.0.0),
-    testthat
-Encoding: UTF-8
-RoxygenNote: 7.2.3
+Type: Package
+Package: onpoint
+Title: Helper Functions for Point Pattern Analysis
+Version: 1.0.5
+Authors@R: 
+  person("Maximilian H.K.", "Hesselbarth", 
+  email = "[email protected]",
+  role = c("aut", "cre"), 
+  comment = c(ORCID = "0000-0003-1125-9918"))
+Maintainer: Maximilian H.K. Hesselbarth <[email protected]>
+Description: 
+  Growing collection of helper functions for point pattern analysis. Most functions
+  are designed to work with the 'spatstat' (<http://spatstat.org>) package. The focus of 
+  most functions are either null models or summary functions for spatial point patterns. 
+  For a detailed description of all null models and summary functions, see 
+  Wiegand and Moloney (2014, ISBN:9781420082548).
+URL: https://r-spatialecology.github.io/onpoint/
+BugReports: https://github.com/r-spatialecology/onpoint/issues
+License: GPL (>= 3)
+Depends: R (>= 3.1)
+Imports:
+  ggplot2,
+  spatstat.explore, 
+  spatstat.geom,
+  spatstat.random,
+  stats
+Suggests: 
+    covr,
+    spatstat (>= 2.0.0),
+    testthat (>= 3.0.0)
+Encoding: UTF-8
+RoxygenNote: 7.2.3
+Config/testthat/edition: 3
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+# onpoint 1.0.5
+* Streamlined documentation
+* Updated testthat v3
+* Updated ggplot2 linewidth internally
+* `verbose` does not affect warnings
+
 # onpoint 1.0.4
 * Update some plotting functions
 

diff --git a/R/balance_points.R b/R/balance_points.R
@@ -21,9 +21,6 @@
 #' balance_points(pattern = input, n = 110)
 #' balance_points(pattern = input, n = input_b)
 #'
-#' @aliases balance_points
-#' @rdname balance_points
-#'
 #' @export
 balance_points <- function(pattern, n, verbose = TRUE) {
 
@@ -39,15 +36,16 @@ balance_points <- function(pattern, n, verbose = TRUE) {
     n <- n$n
   }
 
-  if (verbose) {
+  difference_rel <- abs((pattern$n - n)) / pattern$n
 
-    difference_rel <- abs((pattern$n - n)) / pattern$n
+  if (verbose) {
 
     message("> Relative difference between pattern and n: ", round(difference_rel, 2))
 
-    if (difference_rel > 0.33) {
-      warning("Differences between pattern and n more than 0.33.", call. = FALSE)
-    }
+  }
+
+  if (difference_rel > 0.33) {
+    warning("Differences between pattern and n more than 0.33.", call. = FALSE)
   }
 
   abs((pattern$n - n))

diff --git a/R/calc_area.R b/R/calc_area.R
@@ -16,9 +16,6 @@
 #' calc_area(x = dat)
 #' }
 #'
-#' @aliases calc_area
-#' @rdname calc_area
-#'
 #' @keywords internal
 calc_area <- function(x){
 

diff --git a/R/center_l_function.R b/R/center_l_function.R
@@ -35,9 +35,6 @@
 #' Introduction and methods of edge correction. Journal of Vegetation Science 6, 575–582.
 #' <https://doi.org/10.2307/3236356>
 #'
-#' @aliases center_l_function
-#' @rdname center_l_function
-#'
 #' @export
 center_l_function <- function(x, ...) {
 

diff --git a/R/estimate_o_ring.R b/R/estimate_o_ring.R
@@ -35,9 +35,6 @@
 #' Wiegand, T., Moloney, K.A., 2014. Handbook of spatial point-pattern analysis in
 #' ecology. Chapman and Hall/CRC Press, Boca Raton, USA. <isbn:978-1-4200-8254-8>
 #'
-#' @aliases estimate_o_ring
-#' @rdname estimate_o_ring
-#'
 #' @export
 estimate_o_ring <- function(x, ...) {
 

diff --git a/R/estimate_pcf_fast.R b/R/estimate_pcf_fast.R
@@ -31,9 +31,6 @@
 #' Stoyan, D., Stoyan, H., 1994. Fractals, random shapes and point fields.
 #' John Wiley & Sons, Chichester, UK. <isbn:978-0-471-93757-9>
 #'
-#' @aliases estimate_pcf_fast
-#' @rdname estimate_pcf_fast
-#'
 #' @export
 estimate_pcf_fast <- function(pattern, ...){
 

diff --git a/R/plot.env_summarized.R b/R/plot.env_summarized.R
@@ -29,9 +29,6 @@
 #' x <- summarize_envelope(cluster_env)
 #' plot(x)
 #'
-#' @aliases plot.env_summarized
-#' @rdname plot.env_summarized
-#'
 #' @export
 plot.env_summarized <- function(x, col = c("#97CBDE", "#E1B0B5"),
                                 x_lab = NULL, y_lab = NULL, base_size = 10,

diff --git a/R/plot_quantums.R b/R/plot_quantums.R
@@ -48,9 +48,6 @@
 #' interactions among bacteria and between bacteria and the leaf surface.
 #' FEMS Microbiology Ecology 91, 1–13. <https://doi.org/10.1093/femsec/fiu034>
 #'
-#' @aliases plot_quantums
-#' @rdname plot_quantums
-#'
 #' @export
 plot_quantums <- function(input,
                           labels = NULL, color_scale = NULL,
@@ -142,8 +139,8 @@ plot_quantums <- function(input,
                            ggplot2::aes(xmin = x.min, xmax = x.max, ymin = quantum_position[1], ymax = quantum_position[2],
                                         fill = type, color = type)) +
         ggplot2::geom_ribbon(ggplot2::aes(x = r, ymin = low, ymax = high), fill = "grey") +
-        ggplot2::geom_line(ggplot2::aes(x = r, y = observed, linetype = "Observed"), size = line_size) +
-        ggplot2::geom_line(ggplot2::aes(x = r, y = theoretical, linetype = "Theoretical"), size = line_size) +
+        ggplot2::geom_line(ggplot2::aes(x = r, y = observed, linetype = "Observed"), linewidth = line_size) +
+        ggplot2::geom_line(ggplot2::aes(x = r, y = theoretical, linetype = "Theoretical"), linewidth = line_size) +
         ggplot2::scale_color_manual(name = "", values = color_scale) +
         ggplot2::scale_fill_manual(name = "", values = color_scale) +
         ggplot2::scale_linetype_manual(name = "", values = c(1, 2)) +
@@ -155,8 +152,8 @@ plot_quantums <- function(input,
     else {
       gg_plot <- ggplot2::ggplot(input) +
         ggplot2::geom_ribbon(ggplot2::aes(x = r, ymin = low, ymax = high), fill = "grey") +
-        ggplot2::geom_line(ggplot2::aes(x = r, y = observed, linetype = "Observed"), size = line_size) +
-        ggplot2::geom_line(ggplot2::aes(x = r, y = theoretical, linetype = "Theoretical"), size = line_size) +
+        ggplot2::geom_line(ggplot2::aes(x = r, y = observed, linetype = "Observed"), linewidth = line_size) +
+        ggplot2::geom_line(ggplot2::aes(x = r, y = theoretical, linetype = "Theoretical"), linewidth = line_size) +
         ggplot2::scale_linetype_manual(name = "", values = c(1, 2)) +
         ggplot2::labs(x = xlab, y = ylab, title = title) +
         ggplot2::theme_classic(base_size = base_size) +

diff --git a/R/print.env_summarized.R b/R/print.env_summarized.R
@@ -25,9 +25,6 @@
 #' x <- summarize_envelope(cluster_env)
 #' print(x)
 #'
-#' @aliases print.env_summarized
-#' @rdname print.env_summarized
-#'
 #' @export
 print.env_summarized <- function(x, return_area = FALSE, digits = 2, ...) {
 

diff --git a/R/rlabel_local.R b/R/rlabel_local.R
@@ -7,7 +7,6 @@
 #' @param nsim Number of patterns to simulate.
 #' @param drop If nsim = 1 and drop = TRUE , the result will be a point pattern,
 #' rather than a list containing a point pattern.
-#' @param verbose If TRUE warning messages are printed.
 #'
 #' @details
 #' Local random labelling function, i.e. marks will be shuffeld only across points
@@ -38,12 +37,9 @@
 #' Wiegand, T., Moloney, K.A., 2014. Handbook of spatial point-pattern analysis in
 #' ecology. Chapman and Hall/CRC Press, Boca Raton, USA. <isbn:978-1-4200-8254-8>
 #'
-#' @aliases rlabel_local
-#' @rdname rlabel_local
-#'
 #' @export
 rlabel_local <- function(X, distance, nsim = 19,
-                         drop = TRUE, verbose = TRUE) {
+                         drop = TRUE) {
 
   # check if pattern is marked
   if (!spatstat.geom::is.marked(X) |
@@ -108,9 +104,8 @@ rlabel_local <- function(X, distance, nsim = 19,
     # still return list if nsim > 1 but throw warning
     if (nsim != 1) {
 
-      if (verbose) {
-        warning("drop = TRUE only possible for nsim = 1.", call. = FALSE)
-      }
+      warning("drop = TRUE only possible for nsim = 1.", call. = FALSE)
+
     }
 
     # return only ppp

diff --git a/R/simulate_antecedent_conditions.R b/R/simulate_antecedent_conditions.R
@@ -44,9 +44,6 @@
 #' Wiegand, T., Moloney, K.A., 2014. Handbook of spatial point-pattern analysis in
 #' ecology. Chapman and Hall/CRC Press, Boca Raton, USA. <isbn:978-1-4200-8254-8>
 #'
-#' @aliases simulate_antecedent_conditions
-#' @rdname simulate_antecedent_conditions
-#'
 #' @export
 simulate_antecedent_conditions <- function(x, i, j, nsim, heterogenous = FALSE, ...) {
 

diff --git a/R/simulate_heterogenous_pattern.R b/R/simulate_heterogenous_pattern.R
@@ -34,9 +34,6 @@
 #' Wiegand, T., Moloney, K.A., 2014. Handbook of spatial point-pattern analysis in
 #' ecology. Chapman and Hall/CRC Press, Boca Raton, USA. <isbn:978-1-4200-8254-8>
 #'
-#' @aliases simulate_heterogenous_pattern
-#' @rdname simulate_heterogenous_pattern
-#'
 #' @export
 simulate_heterogenous_pattern <- function(x, nsim, fix_n = FALSE, ...) {
 

diff --git a/R/split_at.R b/R/split_at.R
@@ -18,9 +18,6 @@
 #' split_at(x = x, pos = 3)
 #' }
 #'
-#' @aliases split_at
-#' @rdname split_at
-#'
 #' @keywords internal
 split_at <- function(x, pos) {
 

diff --git a/R/summarize_envelope.R b/R/summarize_envelope.R
@@ -32,9 +32,6 @@
 #'
 #' summarize_envelope(cluster_env)
 #'
-#' @aliases summarize_envelope
-#' @rdname summarize_envelope
-#'
 #' @export
 summarize_envelope <- function(x, plot_result = FALSE) {
 

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,3 +1,6 @@
+# onpoint 1.0.5
+* Minor cosmetic updates
+
 # onpoint 1.0.4
 * Some small function updates
 

diff --git a/tests/testthat.R b/tests/testthat.R
@@ -1,6 +1,12 @@
+# 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(spatstat.explore)
-library(spatstat.geom)
 library(onpoint)
 
 test_check("onpoint")
diff --git a/tests/testthat/test-balance_points.R b/tests/testthat/test-balance_points.R
@@ -1,10 +1,10 @@
-context("test-balance_points")
+# context("test-balance_points")
 
 test_that("balance_points works for integer n", {
 
   input <- spatstat.random::rpoispp(lambda = 100)
 
-  result <- balance_points(pattern = input, n = 110)
+  result <- balance_points(pattern = input, n = 110, verbose = FALSE)
 
   expect_equal(object = result$n, expected = 110)
 })
@@ -14,7 +14,7 @@ test_that("balance_points works for ppp n", {
   input <- spatstat.random::rpoispp(lambda = 100)
   input_b <- spatstat.random::rpoispp(lambda = 100)
 
-  result <- balance_points(pattern = input, n = input_b)
+  result <- balance_points(pattern = input, n = input_b, verbose = FALSE)
 
   expect_equal(object = result$n, expected = input_b$n)
 })
@@ -23,7 +23,7 @@ test_that("balance_points returns error", {
 
   input <- spatstat.random::rpoispp(lambda = 100)
 
-  expect_error(object = balance_points(pattern = input, n = 50.5),
+  expect_error(object = balance_points(pattern = input, n = 50.5, verbose = FALSE),
                regexp = "n must be either integer or ppp.")
 })
 

diff --git a/tests/testthat/test-center_l_function.R b/tests/testthat/test-center_l_function.R
@@ -1,4 +1,4 @@
-context("test-center_l_function")
+# context("test-center_l_function")
 
 test_that("center_l_function works for point pattern", {
 

diff --git a/tests/testthat/test-estimate_o_ring.R b/tests/testthat/test-estimate_o_ring.R
@@ -1,4 +1,4 @@
-context("test-estimate_o_ring")
+# context("test-estimate_o_ring")
 
 test_that("estimate_o_ring returns fv", {
 

diff --git a/tests/testthat/test-estimate_pcf_fast.R b/tests/testthat/test-estimate_pcf_fast.R
@@ -1,10 +1,10 @@
-testthat::context("test-estimate_pcf_fast")
+# testthat::context("test-estimate_pcf_fast")
 
 testthat::test_that("estimate_pcf returns spatstat.fv object", {
 
   pattern <- spatstat.random::runifpoint(n = 100)
 
   pcf_est <- estimate_pcf_fast(pattern)
 
-  testthat::expect_is(pcf_est, "fv")
+  testthat::expect_s3_class(pcf_est, "fv")
 })
diff --git a/tests/testthat/test-plot.R b/tests/testthat/test-plot.R
@@ -1,4 +1,4 @@
-context("test-plot")
+# context("test-plot")
 
 set.seed(42)
 csr_pattern <- spatstat.random::runifpoint(n = 100)

diff --git a/tests/testthat/test-plot_quantums.R b/tests/testthat/test-plot_quantums.R
@@ -1,4 +1,4 @@
-context("test-plot_quantums")
+# context("test-plot_quantums")
 
 test_that("plot_quantums returns ggplot", {
 
@@ -12,7 +12,7 @@ test_that("plot_quantums returns ggplot", {
 
   plot <- plot_quantums(csr_envelope, ylab = "g(r)")
 
-  expect_is(plot, "ggplot")
+  expect_s3_class(plot, "ggplot")
   expect_true(plot$labels$y == "g(r)")
   expect_length(plot$layers, n = 4)
 })
@@ -29,7 +29,7 @@ test_that("plot_quantums returns ggplot (only quantum)", {
 
   plot <- plot_quantums(csr_envelope, ylab = "g(r)", full_fun = FALSE)
 
-  expect_is(plot, "ggplot")
+  expect_s3_class(plot, "ggplot")
   expect_length(plot$layers, n = 1)
 })
 
@@ -45,7 +45,7 @@ test_that("plot_quantums returns ggplot only function", {
 
   plot <- plot_quantums(csr_envelope, ylab = "g(r)", quantum = FALSE)
 
-  expect_is(plot, "ggplot")
+  expect_s3_class(plot, "ggplot")
   expect_length(plot$layers, n = 3)
 })
 

diff --git a/tests/testthat/test-print.R b/tests/testthat/test-print.R
@@ -1,4 +1,4 @@
-context("test-print")
+# context("test-print")
 
 set.seed(42)
 csr_pattern <- spatstat.random::runifpoint(n = 100)