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mhesselbarthmhesselbarth
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Merge pull request #112 from r-spatialecology/main
Update v2.0.2
2 parents 2357706 + e90c84c commit 00da229

23 files changed

+122
-89
lines changed

‎.Rbuildignore

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@@ -3,6 +3,7 @@ codemeta.json
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CODE_OF_CONDUCT.md
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CONTRIBUTING.md
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cran-comments.md
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CRAN-SUBMISSION
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data-raw
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docs
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LICENSE.md
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vignettes/articles
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.github
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_pkgdown.yml
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^.*\.Rproj$
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^\.Rproj\.user$
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^CRAN-SUBMISSION$

‎.github/workflows/Deploy-pkgdown.yaml

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@@ -13,6 +13,10 @@ jobs:
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deploy-pkgdown:
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runs-on: ubuntu-latest
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# Only restrict concurrency for non-PR jobs
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concurrency:
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group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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‎.github/workflows/R-CMD-check.yaml

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# Workflow derived from https://github.com/r-lib/actions/tree/v2-branch/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches: [CRAN, main, development]
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branches: [main, development]
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pull_request:
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branches: [CRAN, main]
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workflow_dispatch:

‎.github/workflows/Render-README.yaml

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# Workflow derived from https://github.com/r-lib/actions/tree/v2-branch/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches: [main, development]
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paths: ["README.Rmd"]
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workflow_dispatch:
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@@ -25,7 +27,7 @@ jobs:
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::rmarkdown, any::spatstat, any::terra
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extra-packages: any::rmarkdown, any::spatstat, any::terra, local::.
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- name: Render README files
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run: Rscript -e 'rmarkdown::render("README.Rmd")'

‎.github/workflows/Test-coverage.yaml

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# Workflow derived from https://github.com/r-lib/actions/tree/v2-branch/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches: [CRAN, main, development]
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branches: [main, development]
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pull_request:
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branches: [CRAN, main]
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workflow_dispatch:

‎.github/workflows/Write-codemeta.yaml

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@@ -2,6 +2,7 @@
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on:
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push:
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branches: [main, development]
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paths: ['DESCRIPTION']
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workflow_dispatch:
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‎.gitignore

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@@ -6,4 +6,4 @@
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inst/doc
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Rplots.pdf
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docs
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^CRAN-SUBMISSION
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CRAN-SUBMISSION

‎DESCRIPTION

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@@ -1,7 +1,7 @@
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Type: Package
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Package: shar
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Title: Species-Habitat Associations
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Version: 2.0.1
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Version: 2.0.2
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Authors@R: c(person("Maximilian H.K.", "Hesselbarth", email = "[email protected]",
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role = c("aut", "cre"), comment = c(ORCID = "0000-0003-1125-9918")),
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person("Marco", "Sciaini", email = "[email protected]",
@@ -27,7 +27,8 @@ Imports:
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graphics,
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grDevices,
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methods,
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spatstat.core,
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spatstat.explore,
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spatstat.model,
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spatstat.geom,
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spatstat.random,
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stats,
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dplyr,
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knitr,
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rmarkdown,
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spatstat (>= 2.0.0),
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testthat (>= 2.1.0)
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Additional_repositories: http://packages.ropensci.org
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spatstat (>= 2.0-0),
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testthat (>= 3.0.0)
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VignetteBuilder: knitr
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Encoding: UTF-8
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LazyData: true

‎NEWS.md

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# shar 2.0.2
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* Various
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* Update `spatstat` dependency
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# shar 2.0.1
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* Improvements
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* Better approach for external repo

‎R/calculate_energy.R

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@@ -82,7 +82,7 @@ calculate_energy <- function(pattern,
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# calculate r sequence
8484
r <- seq(from = 0,
85-
to = spatstat.core::rmax.rule(W = pattern_observed$window,
85+
to = spatstat.explore::rmax.rule(W = pattern_observed$window,
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lambda = spatstat.geom::intensity.ppp(pattern_observed)),
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length.out = 250)
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@@ -117,7 +117,7 @@ calculate_energy <- function(pattern,
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# calculate summary functions for observed pattern
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if (comp_fast) {
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120-
gest_observed <- spatstat.core::Gest(X = pattern_observed, correction = "none",
120+
gest_observed <- spatstat.explore::Gest(X = pattern_observed, correction = "none",
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r = r)
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pcf_observed <- estimate_pcf_fast(pattern = pattern_observed,
@@ -126,10 +126,10 @@ calculate_energy <- function(pattern,
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127127
} else {
128128

129-
gest_observed <- spatstat.core::Gest(X = pattern_observed,
129+
gest_observed <- spatstat.explore::Gest(X = pattern_observed,
130130
correction = "han", r = r)
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132-
pcf_observed <- spatstat.core::pcf(X = pattern_observed,
132+
pcf_observed <- spatstat.explore::pcf(X = pattern_observed,
133133
correction = "best", divisor = "d", r = r)
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135135
}
@@ -140,7 +140,7 @@ calculate_energy <- function(pattern,
140140
# fast computation of summary stats
141141
if (comp_fast) {
142142

143-
gest_reconstruction <- spatstat.core::Gest(X = pattern_randomized[[x]],
143+
gest_reconstruction <- spatstat.explore::Gest(X = pattern_randomized[[x]],
144144
correction = "none",
145145
r = r)
146146

@@ -151,11 +151,11 @@ calculate_energy <- function(pattern,
151151
# normal computation of summary stats
152152
} else {
153153

154-
gest_reconstruction <- spatstat.core::Gest(X = pattern_randomized[[x]],
154+
gest_reconstruction <- spatstat.explore::Gest(X = pattern_randomized[[x]],
155155
correction = "han",
156156
r = r)
157157

158-
pcf_reconstruction <- spatstat.core::pcf(X = pattern_randomized[[x]],
158+
pcf_reconstruction <- spatstat.explore::pcf(X = pattern_randomized[[x]],
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correction = "best",
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divisor = "d",
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r = r)
@@ -193,13 +193,13 @@ calculate_energy <- function(pattern,
193193
} else {
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195195
# calculate summary functions
196-
kmmr_observed <- spatstat.core::markcorr(pattern_observed, correction = "Ripley",
196+
kmmr_observed <- spatstat.explore::markcorr(pattern_observed, correction = "Ripley",
197197
r = r)
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199199
result <- vapply(seq_along(pattern_randomized), function(x) {
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201201
# calculate summary functions
202-
kmmr_reconstruction <- spatstat.core::markcorr(pattern_randomized[[x]],
202+
kmmr_reconstruction <- spatstat.explore::markcorr(pattern_randomized[[x]],
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correction = "Ripley",
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r = r)
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‎R/estimate_pcf_fast.R

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@@ -38,9 +38,9 @@
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#' @export
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estimate_pcf_fast <- function(pattern, ...){
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41-
k_fun <- suppressMessages(spatstat.core::Kest(X = pattern, ...)) # estimate K-fct
41+
k_fun <- suppressMessages(spatstat.explore::Kest(X = pattern, ...)) # estimate K-fct
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43-
result <- spatstat.core::pcf.fv(X = k_fun, ...) # estimate pcf from K-fct
43+
result <- spatstat.explore::pcf.fv(X = k_fun, ...) # estimate pcf from K-fct
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4545
return(result)
4646
}

‎R/fit_point_process.R

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@@ -82,17 +82,17 @@ fit_point_process <- function(pattern,
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} else if (process == "cluster") {
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8484
# fit cluster process
85-
fitted_process <- spatstat.core::kppm(pattern, cluster = "Thomas",
86-
statistic = "pcf",
87-
statargs = list(divisor = "d",
88-
correction = "best"),
89-
method = "mincon", improve.type = "none")
85+
fitted_process <- spatstat.model::kppm(pattern, cluster = "Thomas",
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statistic = "pcf",
87+
statargs = list(divisor = "d",
88+
correction = "best"),
89+
method = "mincon", improve.type = "none")
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9191
result <- lapply(seq_len(n_random), function(x) {
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9393
# simulate clustered pattern
94-
simulated <- spatstat.core::simulate.kppm(fitted_process, window = pattern$window,
95-
nsim = 1, drop = TRUE)
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simulated <- spatstat.model::simulate.kppm(fitted_process, window = pattern$window,
95+
nsim = 1, drop = TRUE)
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# remove points because more points in simulated
9898
if (pattern$n < simulated$n) {

‎R/plot.rd_mar.R

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@@ -84,7 +84,7 @@ plot.rd_mar <- function(x, what = "sf", n = NULL, probs = c(0.025, 0.975), comp_
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name_unit <- spatstat.geom::unitname(x$observed)[[1]] # unit name for labels
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8686
# calculate r
87-
r <- seq(from = 0, to = spatstat.core::rmax.rule(W = x$observed$window,
87+
r <- seq(from = 0, to = spatstat.explore::rmax.rule(W = x$observed$window,
8888
lambda = spatstat.geom::intensity.ppp(x$observed)),
8989
length.out = 250)
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@@ -95,7 +95,7 @@ plot.rd_mar <- function(x, what = "sf", n = NULL, probs = c(0.025, 0.975), comp_
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9696
result <- lapply(seq_along(pattern), function(x) {
9797

98-
mark_corr <- as.data.frame(spatstat.core::markcorr(pattern[[x]],
98+
mark_corr <- as.data.frame(spatstat.explore::markcorr(pattern[[x]],
9999
correction = "Ripley",
100100
r = r))
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‎R/plot.rd_pat.R

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@@ -83,7 +83,7 @@ plot.rd_pat <- function(x, what = "sf", n = NULL, probs = c(0.025, 0.975), comp_
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name_unit <- spatstat.geom::unitname(x$observed)[[1]] # unit name for labels
8484

8585
# calculate r
86-
r <- seq(from = 0, to = spatstat.core::rmax.rule(W = x$observed$window,
86+
r <- seq(from = 0, to = spatstat.explore::rmax.rule(W = x$observed$window,
8787
lambda = spatstat.geom::intensity.ppp(x$observed)),
8888
length.out = 250)
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@@ -98,16 +98,16 @@ plot.rd_pat <- function(x, what = "sf", n = NULL, probs = c(0.025, 0.975), comp_
9898
# calculate summary functions
9999
if (comp_fast) {
100100

101-
gest_result <- spatstat.core::Gest(pattern[[x]], correction = "none", r = r)
101+
gest_result <- spatstat.explore::Gest(pattern[[x]], correction = "none", r = r)
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103103
pcf_result <- estimate_pcf_fast(pattern[[x]], correction = "none",
104104
method = "c", spar = 0.5, r = r)
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106106
} else {
107107

108-
gest_result <- spatstat.core::Gest(pattern[[x]], correction = "han", r = r)
108+
gest_result <- spatstat.explore::Gest(pattern[[x]], correction = "han", r = r)
109109

110-
pcf_result <- spatstat.core::pcf(pattern[[x]], divisor = "d",
110+
pcf_result <- spatstat.explore::pcf(pattern[[x]], divisor = "d",
111111
correction = "best", r = r)
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113113
}

‎R/reconstruct_pattern_cluster.R

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122122
# calculate r
123123
r <- seq(from = 0,
124-
to = spatstat.core::rmax.rule(W = pattern$window,
124+
to = spatstat.explore::rmax.rule(W = pattern$window,
125125
lambda = spatstat.geom::intensity.ppp(pattern)),
126126
length.out = r_length)
127127

128128
# start with fitted pattern
129129
# fit Thomas process
130-
fitted_process <- spatstat.core::kppm.ppp(pattern, cluster = "Thomas",
131-
statistic = "pcf",
132-
statargs = list(divisor = "d",
133-
correction = "best"),
134-
improve.type = "none")
130+
fitted_process <- spatstat.model::kppm.ppp(pattern, cluster = "Thomas",
131+
statistic = "pcf",
132+
statargs = list(divisor = "d",
133+
correction = "best"),
134+
improve.type = "none")
135135

136136
# simulte clustered pattern
137-
simulated <- spatstat.core::simulate.kppm(fitted_process, nsim = 1, drop = TRUE,
138-
window = pattern$window, verbose = FALSE)
137+
simulated <- spatstat.model::simulate.kppm(fitted_process, nsim = 1, drop = TRUE,
138+
window = pattern$window, verbose = FALSE)
139139

140140
# remove points because more points in simulated
141141
if (pattern$n < simulated$n) {
@@ -167,9 +167,9 @@ reconstruct_pattern_cluster <- function(pattern,
167167
# fast computation of summary functions
168168
if (comp_fast) {
169169

170-
gest_observed <- spatstat.core::Gest(pattern, correction = "none", r = r)
170+
gest_observed <- spatstat.explore::Gest(pattern, correction = "none", r = r)
171171

172-
gest_simulated <- spatstat.core::Gest(simulated, correction = "none", r = r)
172+
gest_simulated <- spatstat.explore::Gest(simulated, correction = "none", r = r)
173173

174174
pcf_observed <- estimate_pcf_fast(pattern, correction = "none",
175175
method = "c", spar = 0.5, r = r)
@@ -180,14 +180,14 @@ reconstruct_pattern_cluster <- function(pattern,
180180
# normal computation of summary functions
181181
} else {
182182

183-
gest_observed <- spatstat.core::Gest(X = pattern, correction = "han", r = r)
183+
gest_observed <- spatstat.explore::Gest(X = pattern, correction = "han", r = r)
184184

185-
gest_simulated <- spatstat.core::Gest(X = simulated, correction = "han", r = r)
185+
gest_simulated <- spatstat.explore::Gest(X = simulated, correction = "han", r = r)
186186

187-
pcf_observed <- spatstat.core::pcf.ppp(X = pattern, correction = "best",
187+
pcf_observed <- spatstat.explore::pcf.ppp(X = pattern, correction = "best",
188188
divisor = "d", r = r)
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190-
pcf_simulated <- spatstat.core::pcf.ppp(X = simulated, correction = "best",
190+
pcf_simulated <- spatstat.explore::pcf.ppp(X = simulated, correction = "best",
191191
divisor = "d", r = r)
192192

193193
}
@@ -247,16 +247,16 @@ reconstruct_pattern_cluster <- function(pattern,
247247
# calculate summary functions after relocation
248248
if (comp_fast) {
249249

250-
gest_relocated <- spatstat.core::Gest(relocated, correction = "none", r = r)
250+
gest_relocated <- spatstat.explore::Gest(relocated, correction = "none", r = r)
251251

252252
pcf_relocated <- estimate_pcf_fast(relocated, correction = "none",
253253
method = "c", spar = 0.5, r = r)
254254

255255
} else {
256256

257-
gest_relocated <- spatstat.core::Gest(X = relocated, correction = "han", r = r)
257+
gest_relocated <- spatstat.explore::Gest(X = relocated, correction = "han", r = r)
258258

259-
pcf_relocated <- spatstat.core::pcf.ppp(X = relocated, correction = "best",
259+
pcf_relocated <- spatstat.explore::pcf.ppp(X = relocated, correction = "best",
260260
divisor = "d", r = r)
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262262
}

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