v1.0.6

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: onpoint
 Title: Helper Functions for Point Pattern Analysis
-Version: 1.0.5
+Version: 1.0.6
 Authors@R: 
   person("Maximilian H.K.", "Hesselbarth", 
   email = "[email protected]",
@@ -29,5 +29,5 @@ Suggests:
     spatstat (>= 2.0.0),
     testthat (>= 3.0.0)
 Encoding: UTF-8
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Config/testthat/edition: 3

NEWS.md

@@ -1,55 +1,58 @@
-# 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
-
-# onpoint 1.0.3
-* Small updates to internal code structure
-* Fix DESCRIPTION
-* Update CI actions
-* Update `spatstat` dependency
-
-# onpoint 1.0.2
-* Adapt new `spatstat` package structure
-
-# onpoint 1.0.1
-* Improve documentation for CRAN submission
-* Renamed `summarise_envelope` to `summarize_envelope`
-
-# onpoint 1.0
-* Use GPL3 license
-* Adapt to new `spatstat` structure
-* Prepare CRAN submission
-
-# onpoint 0.6.1
-* Use GitHub actions
-
-# onpoint 0.6
-* `plot_quantums()` uses `geom_linerange()`
-
-# onpoint 0.5
-* add `rlabel_local()` function
-
-# onpoint 0.4
-* Printing method for result of `summarise_envelope()`
-* Plotting method for result of `summarise_envelope()`
-
-# onpoint 0.3
-* New function `summarise_envelope()`
-
-# onpoint 0.2.1
-* Better size arguments for lines and base_size for `plot_quantums()`
-* Generic labels for `plot_quantums()`
-* Use fix_n argument in `simulate_heterogenous_patter()`
-
-# onpoint 0.2.0
-* Added `simulate_antecedent_conditions`.
-* Added `estimate_pcf_fast`
-
-# onpoint 0.1.0
-* Initialised package
-* Added a `NEWS.md` file to track changes to the package.
+# onpoint 1.0.6
+* Order of stable `i` and randomized pattern `j` changed in `simulate_antecedent_conditions`
+
+# 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
+
+# onpoint 1.0.3
+* Small updates to internal code structure
+* Fix DESCRIPTION
+* Update CI actions
+* Update `spatstat` dependency
+
+# onpoint 1.0.2
+* Adapt new `spatstat` package structure
+
+# onpoint 1.0.1
+* Improve documentation for CRAN submission
+* Renamed `summarise_envelope` to `summarize_envelope`
+
+# onpoint 1.0
+* Use GPL3 license
+* Adapt to new `spatstat` structure
+* Prepare CRAN submission
+
+# onpoint 0.6.1
+* Use GitHub actions
+
+# onpoint 0.6
+* `plot_quantums()` uses `geom_linerange()`
+
+# onpoint 0.5
+* add `rlabel_local()` function
+
+# onpoint 0.4
+* Printing method for result of `summarise_envelope()`
+* Plotting method for result of `summarise_envelope()`
+
+# onpoint 0.3
+* New function `summarise_envelope()`
+
+# onpoint 0.2.1
+* Better size arguments for lines and base_size for `plot_quantums()`
+* Generic labels for `plot_quantums()`
+* Use fix_n argument in `simulate_heterogenous_patter()`
+
+# onpoint 0.2.0
+* Added `simulate_antecedent_conditions`.
+* Added `estimate_pcf_fast`
+
+# onpoint 0.1.0
+* Initialised package
+* Added a `NEWS.md` file to track changes to the package.

R/simulate_antecedent_conditions.R

@@ -3,19 +3,20 @@
 #' @description Simulate heterogenous pattern
 #'
 #' @param x ppp
-#' @param i Mark of points that are randomized.
-#' @param j Mark of points that do not change.
+#' @param i Mark of points that are not not changed.
+#' @param j Mark of points that are randomized.
 #' @param nsim Number of patterns to simulate.
-#' @param heterogenous If TRUE, points with the mark i are randomized using a heterogeneous
+#' @param heterogenous If TRUE, points with the mark j are randomized using a heterogeneous
 #' Poisson process.
 #' @param ... Arguments passed to \code{spatstat.explore::density.ppp()}.
 #'
 #' @details
 #' Simulate point patterns as null model data for \code{spatstat.explore::envelope()} using
-#' antecedent conditions as null model. \code{x} must be marked point pattern.
-#' Antecedent conditions are suitable as a null model if points of type j may influence
-#' points of type i, but not the other way around (Velazquez et al 2016). One example are
-#' the positions of seedlings that may be influenced by the position of mature trees.
+#' antecedent conditions as null model. \code{x} must be a marked point pattern with
+#' two types of marks. Antecedent conditions are suitable as a null model if points
+#' of type i may influence points of type j, but not the other way around (Velazquez et al 2016).
+#' One example are the positions of seedlings that may be influenced by the position
+#' of mature trees.
 #'
 #' Returns a \code{list} with \code{ppp} objects.
 #'
@@ -32,7 +33,7 @@
 #' spatstat.geom::marks(pattern_b) <- "b"
 #' pattern <- spatstat.geom::superimpose(pattern_a, pattern_b)
 #'
-#' null_model <- simulate_antecedent_conditions(x = pattern, i = "b", j = "a", nsim = 19)
+#' null_model <- simulate_antecedent_conditions(x = pattern, i = "a", j = "b", nsim = 19)
 #' spatstat.explore::envelope(Y = pattern, fun = spatstat.explore::pcf,
 #' nsim = 19, simulate = null_model)
 #'
@@ -62,41 +63,32 @@ simulate_antecedent_conditions <- function(x, i, j, nsim, heterogenous = FALSE,
     stop("i and j must be marks of x.", call. = FALSE)
   }
 
-  # only points with mark j
-  pattern_j <- spatstat.geom::subset.ppp(x, marks == j, drop = TRUE)
-
-  # only points with mark i
+  # only points with mark i to keep stable
   pattern_i <- spatstat.geom::subset.ppp(x, marks == i, drop = TRUE)
 
-  if (heterogenous) {
+  # only points with mark j to randomze
+  pattern_j <- spatstat.geom::subset.ppp(x, marks == j, drop = TRUE)
 
-    lambda_xy <- spatstat.explore::density.ppp(pattern_i, ...)
+  if (heterogenous) {
+    lambda_j <- spatstat.explore::density.ppp(pattern_j, ...)
   }
 
   # create nsim patterns
   result <- lapply(seq_len(length.out = nsim), function(current_nsim) {
 
+    # use heterogeneous Poisson
     if (!heterogenous) {
-
-      # random pattern i
-      random_i <- spatstat.random::rpoint(n = pattern_i$n,
-                                        win = pattern_i$window)
-    }
-
-    else {
-
-      # random pattern i
-      random_i <- spatstat.random::rpoint(n = pattern_i$n,
-                                        f = lambda_xy,
-                                        win = x$window)
+      random_j <- spatstat.random::rpoint(n = pattern_j$n, win = pattern_j$window)
+    # use homogenous Poisson
+    } else {
+      random_j <- spatstat.random::rpoint(n = pattern_j$n, f = lambda_j, win = x$window)
     }
 
     # assign same marks again
-    spatstat.geom::marks(random_i) <- spatstat.geom::marks(pattern_i)
+    spatstat.geom::marks(random_j) <- spatstat.geom::marks(pattern_j)
 
     # combine random i with original j
-    pattern_combined <- spatstat.geom::superimpose(j = pattern_j,
-                                                   i = random_i,
+    pattern_combined <- spatstat.geom::superimpose(i = pattern_i, j = random_j,
                                                    W = pattern_j$window)
 
     # select only original marks

README.Rmd

@@ -25,7 +25,7 @@ README Last updated: `r Sys.Date()`
 [![Project Status](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
 [![lifecycle](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://www.tidyverse.org/lifecycle/#stable)
 [![CRAN status](https://www.r-pkg.org/badges/version/onpoint)](https://CRAN.R-project.org/package=onpoint)
-[![CRAN logs](http://cranlogs.r-pkg.org/badges/grand-total/onpoint)](http://cran.rstudio.com/web/packages/onpoint/index.html)
+[![CRAN logs](https://cranlogs.r-pkg.org/badges/grand-total/onpoint)](http://cran.rstudio.com/web/packages/onpoint/index.html)
 [![License](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 
 <!-- badges: end -->

README.md

@@ -5,7 +5,7 @@
 
 <!-- badges: start -->
 
-README Last updated: 2023-03-08
+README Last updated: 2024-07-29
 
 [![R-CMD-check](https://github.com/r-spatialecology/onpoint/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/r-spatialecology/onpoint/actions/workflows/R-CMD-check.yaml)
 [![codecov](https://codecov.io/gh/r-spatialecology/onpoint/branch/main/graph/badge.svg?token=RkgCfHnPyf)](https://codecov.io/gh/r-spatialecology/onpoint)
@@ -15,7 +15,7 @@ Status](https://www.repostatus.org/badges/latest/active.svg)](https://www.repost
 [![CRAN
 status](https://www.r-pkg.org/badges/version/onpoint)](https://CRAN.R-project.org/package=onpoint)
 [![CRAN
-logs](http://cranlogs.r-pkg.org/badges/grand-total/onpoint)](http://cran.rstudio.com/web/packages/onpoint/index.html)
+logs](https://cranlogs.r-pkg.org/badges/grand-total/onpoint)](http://cran.rstudio.com/web/packages/onpoint/index.html)
 [![License](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 
 <!-- badges: end -->

cran-comments.md

@@ -1,36 +1,39 @@
-# onpoint 1.0.5
-* Minor cosmetic updates
-
-# onpoint 1.0.4
-* Some small function updates
-
-# onpoint 1.0.3
-* Small DESCRIPTION fixes
-
-# onpoint 1.0.2
-* Adapt new `spatstat` package structure
-
-# onpoint 1.0.1
-Please add some more details about the package functionality and implemented methods in your Description text.
-
-* Done as suggested
-
-Please add \value to .Rd files regarding exported methods and explain the functions results in the documentation. [...]
-
-* Done as suggested
-
-# onpoint 1.0
-* First submission to CRAN
-
-## Test environments
-* local R installation, R 4.1.1
-* GitHub Actions
-  * {os: windows-latest, r: 'release'}
-  * {os: macOS-latest, r: 'release'}
-  * {os: ubuntu-20.04, r: 'release'}
-
-## R CMD check results
-
-0 errors ✓ | 0 warnings ✓ | 0 notes ✓
-
-* This is a new release.
+# onpoint 1.0.6
+* Minor methodological improvements
+
+# onpoint 1.0.5
+* Minor cosmetic updates
+
+# onpoint 1.0.4
+* Some small function updates
+
+# onpoint 1.0.3
+* Small DESCRIPTION fixes
+
+# onpoint 1.0.2
+* Adapt new `spatstat` package structure
+
+# onpoint 1.0.1
+Please add some more details about the package functionality and implemented methods in your Description text.
+
+* Done as suggested
+
+Please add \value to .Rd files regarding exported methods and explain the functions results in the documentation. [...]
+
+* Done as suggested
+
+# onpoint 1.0
+* First submission to CRAN
+
+## Test environments
+* local R installation, R 4.1.1
+* GitHub Actions
+  * {os: windows-latest, r: 'release'}
+  * {os: macOS-latest, r: 'release'}
+  * {os: ubuntu-20.04, r: 'release'}
+
+## R CMD check results
+
+0 errors ✓ | 0 warnings ✓ | 0 notes ✓
+
+* This is a new release.