Merge pull request #85 from DylanCarbone/pull_requests

Pull requests

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/r.yml → .github/workflows/R-CMD-check.yaml

@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [master, pull_requests]
   pull_request:
-    branches: [main, master]
+    branches: [master, pull_requests]
 
 name: R-CMD-check
 
@@ -23,13 +23,13 @@ jobs:
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
           - {os: ubuntu-latest,   r: 'oldrel-1'}
-  
+
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -46,7 +46,6 @@ jobs:
 
       - uses: r-lib/actions/check-r-package@v2
         with:
-          args: 'c("--no-manual", "--no-build-vignettes")'
-          build_args: 'c("--no-build-vignettes", "--no-manual", "--no-resave-data")'
-          error-on: '"error"'
           upload-snapshots: true
+          build_args: 'c("--no-build-vignettes", "--no-manual")'
+          args: 'c("--no-vignettes", "--no-manual")'

.gitignore

@@ -6,4 +6,4 @@ Other_files/
 vignettes/BRCindicators_cache/
 vignettes/BRCindicators_files/
 misc/
-tests/testthat/Rplots.pdf
+tests/testthat/Rplots.pdf

DESCRIPTION

@@ -1,38 +1,57 @@
-Package: BRCindicators
 Type: Package
+Package: BRCindicators
 Title: Creating multispecies biodiversity indicators
 Version: 1.3.7
 Date: 2021-05-24
-Authors@R: c(person("Tom", "August", role = c("aut", "cre"), email = "[email protected]"),
-             person("Gary", "Powney", role = c("aut")),
-             person("Charlie", "Outhwaite", role = c("aut")),
-             person("Jack", "Hatfield", role = c("aut")),
-             person("Mark", "Logie", role = c("aut")),
-             person("Stephen", "Freeman", role = c("aut")),
-             person("Nick", "Isaac", role = c("aut")))
-Maintainer: Tom August <[email protected]>
+Authors@R: c(
+    person("Dylan", "Carbone", email = "[email protected]", role = c("aut", "cre"),
+           comment = c(ORCID = "0009-0003-5290-786X")),
+    person("Tom", "August", email = "[email protected]", role = "aut",
+           comment = c(ORCID = "0000-0003-1116-3385")),
+    person("Gary", "Powney", role = "aut",
+           comment = c(ORCID = "0000-0003-3313-7786")),
+    person("Charlie", "Outhwaite", role = "aut",
+           comment = c(ORCID = "0000-0001-9997-6780")),
+    person("Jack", "Hatfield", role = "aut",
+           comment = c(ORCID = "0000-0002-6361-0629")),
+    person("Mark", "Logie", role = "aut",
+           comment = c(ORCID = "0000-0003-0840-9575")),
+    person("Stephen", "Freeman", role = "aut"),
+    person("Nick", "Isaac", role = "aut",
+           comment = c(ORCID = "0000-0002-4869-8052"))
+  )
+Maintainer: Dylan Carbone <[email protected]>
 Description: This package contains a number of functions used to create
     biodiversity indicators.
+License: GPL-3
+URL: https://github.com/BiologicalRecordsCentre/BRCindicators
+BugReports: 
+    https://github.com/BiologicalRecordsCentre/BRCindicators/issues
 Depends: 
     R (>= 3.5.0)
 Imports: 
-    ggplot2,
-    reshape2,
-    coda,
+    boot,
     car,
-    RColorBrewer,
+    coda,
+    ggplot2,
     mgcv,
-    boot
-VignetteBuilder: knitr
-License: GPL-3
-URL: https://github.com/BiologicalRecordsCentre/BRCindicators
-BugReports: https://github.com/BiologicalRecordsCentre/BRCindicators/issues
-RoxygenNote: 7.1.1
-Encoding: UTF-8
+    mockery,
+    RColorBrewer,
+    reshape2,
+    jagsUI,
+    runjags
 Suggests: 
-    testthat,
     covr,
     knitr,
-    snowfall,
     rmarkdown,
-    jagsUI,
+    snowfall,
+    sparta,
+    testthat (>= 3.0.0)
+VignetteBuilder: 
+    knitr
+Config/testthat/edition: 3
+Encoding: UTF-8
+remotes: BiologicalRecordsCentre/sparta
+RoxygenNote: 7.2.3
+SystemRequirements: JAGS
+    (https://sourceforge.net/projects/mcmc-jags/files/JAGS/)

NAMESPACE

@@ -5,21 +5,17 @@ export(CompositeTrend)
 export(GAM_smoothing)
 export(bma)
 export(bootstrap_indicator)
+export(detect_jags)
 export(get_bmaBUGScode)
 export(lambda_indicator)
 export(msi)
 export(msi_tool)
-export(plot_growthrates)
 export(plot_indicator)
-export(plot_species)
-export(plot_spgrowthrates)
 export(plot_trend_stack)
 export(rescale_posterior)
 export(rescale_species)
-export(simulate_indicator)
 export(summarise_occDet)
 export(trend_assessment)
-export(wrap_plot)
 import(RColorBrewer)
 import(car)
 import(ggplot2)
@@ -30,3 +26,4 @@ importFrom(car,logit)
 importFrom(coda,as.mcmc)
 importFrom(coda,mcmc.list)
 importFrom(reshape2,dcast)
+importFrom(runjags,testjags)