Merge pull request #257 from DylanCarbone/pull_requests

Improvements to occDetFunc tests and dependency function tests

.Rbuildignore

@@ -9,3 +9,6 @@ frescalo.exe
 ^docs$
 misc/
 ^appveyor\.yml$
+^\.github$
+^doc$
+^Meta$

.github/.gitignore

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

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,51 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [master, pull_requests]
+  pull_request:
+    branches: [master, pull_requests]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {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@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-build-vignettes", "--no-manual")'
+          args: 'c("--no-vignettes", "--no-manual")'

.gitignore

@@ -1,5 +1,6 @@
-# History files
+# History files and data files
 .Rhistory
+.Rdata
 
 # Example code in package build process
 *-Ex.R
@@ -11,3 +12,5 @@ frescalo.exe
 sparta.Rproj
 
 misc/
+/doc/
+/Meta/

DESCRIPTION

@@ -1,40 +1,57 @@
-Package: sparta
 Type: Package
+Package: sparta
 Title: Trend Analysis for Unstructured Data
 Version: 0.2.19
 Date: 2020-05-26
-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("Colin", "Harrower", role = c("aut")),
-             person("Mark", "Hill", role = c("aut")),
-             person("Jack", "Hatfield", role = c("aut")),
-             person("Francesca", "Mancini", role = c("aut")),
-             person("Nick", "Isaac", role = c("aut")))
-Maintainer: Tom August <[email protected]>
-Description: Methods used to analyse trends in unstructured
-    occurrence datasets such as those collected by volunteer recording
-    schemes.
+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("Nick", "Isaac", role = "aut",
+           comment = c(ORCID = "0000-0002-4869-8052")),
+    person("Francesca", "Mancini", role = "aut",
+           comment = c(ORCID = "0000-0003-4085-4978")),
+    person("Mark", "Hill", role = "aut",
+           comment = c(ORCID = "0000-0002-3323-4458")),
+    person("Colin", "Harrower", role = "aut",
+           comment = c(ORCID = "0000-0001-5070-5293"))
+  )
+Maintainer: Dylan Carbone <[email protected]>
+Description: Methods used to analyse trends in unstructured occurrence
+    datasets such as those collected by volunteer recording schemes.
 License: MIT + file LICENSE
+URL: https://github.com/BiologicalRecordsCentre/sparta
+BugReports: https://github.com/BiologicalRecordsCentre/sparta/issues
 Depends:
-    R (>= 3.1.0),
-    lme4 (>= 1.0)
+    lme4 (>= 1.0),
+    R (>= 3.5.0)
 Imports:
-    plyr,
+    boot,
     dplyr (>= 0.4.1),
-    sp,
-    reshape2,
-    ggplot2,
     gdata,
+    ggplot2,
     LearnBayes,
+    plyr,
+    reshape2,
     rmarkdown,
-    boot
+    sp,
+    xfun (>= 0.4.3)
 Suggests:
-    testthat (>= 0.8.0),
-    roxygen2,
     knitr,
-    R2jags
-VignetteBuilder: knitr
-LazyData: TRUE
-RoxygenNote: 7.1.1
+    R2jags,
+    roxygen2,
+    testthat (>= 0.8.0),
+VignetteBuilder: 
+    knitr
 Encoding: UTF-8
+LazyData: TRUE
+RoxygenNote: 7.2.3
+SystemRequirements: JAGS
+    (https://sourceforge.net/projects/mcmc-jags/files/JAGS/)

R/formatOccData.r

@@ -88,6 +88,9 @@
 #'                                 closure_period = closure_period)
 #'  
 #' # format the unicorns data
+#'
+#' unicorns <- unicorns[complete.cases(unicorns$kmsq), ]
+#'
 #' formatted_data <- formatOccData(taxa = unicorns$CONCEPT,
 #'                                survey = unicorns$Date,
 #'                                site = unicorns$kmsq)
@@ -134,14 +137,17 @@ formatOccData <- function(taxa, site, survey, replicate = NULL, closure_period =
     temp <- group_by(.data = taxa_data, survey, replicate)  
 
     temp <- summarise(temp, ns = length(unique(TP)))
+
     if(any(temp$ns) > 1) {
       # return a warning but assume they know what they're doing
       warning(paste(as.numeric(table(temp$ns >1)[2]), 'survey identities appear in multiple closure periods'))
     }
+
   } else {
     # we need to create the TP from the survey date.
     # survey should be a date if we've got this far, so extract the year
-    taxa_data$TP <- as.numeric(format(taxa_data$survey,'%Y')) # take year from date year 
+    taxa_data$TP <- as.numeric(format(taxa_data$survey, format = '%Y')) # take year from date year 
+
   }
 
   # remove duplicates (in order that List Length is correctly calculated)