readme and citation

.github/.gitignore

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

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

@@ -0,0 +1,49 @@
+# 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: [main, master]
+  pull_request:
+    branches: [main, master]
+
+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@v3
+
+      - 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

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: gbm.auto
 Title: Automated Boosted Regression Tree Modelling and Mapping Suite
-Version: 2023.08.15
+Version: 2023.08.23
 Authors@R: person("Simon", "Dedman", , "simondedman@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-9108-972X"))
 Description: Automates delta log-normal boosted regression tree abundance
     prediction. Loops through parameters provided (LR (learning rate), TC
@@ -23,13 +23,21 @@ Imports:
     dismo (>= 1.3-14),
     dplyr (>= 1.0.9),
     gbm (>= 2.1.1),
+    ggmap (>= 3.0.2),
+    ggplot2 (>= 3.4.3),
+    ggspatial (>= 1.1.9),
     lifecycle,
+    lubridate (>= 1.9.2),
     mapplots (>= 1.5),
     Metrics (>= 0.1.4),
+    readr (>= 2.1.4),
     sf (>= 0.9-7),
-    shapefiles (>= 0.7),
+    stars (>= 0.6-3),
+    starsExtra (>= 0.2.7),
     stats (>= 3.3.1),
-    stringi (>= 1.6.1)
+    stringi (>= 1.6.1),
+    tidyselect (>= 1.2.0),
+    viridis (>= 0.6.4)
 Encoding: UTF-8
 Language: en-GB
 LazyData: true

NEWS.md

@@ -4,6 +4,9 @@ author: "Simon Dedman"
 date: "2023-05-25"
 output: html_document
 ---
+# v2023.08.23
+* citation added, various improvements and cleans, CRAN push
+
 # v2023.08.14
 * gbm.factorplot finished, included in gbm.auto, documented. lifecycle package used for function status.
 

R/data.R

@@ -70,12 +70,9 @@
 #'   \item{Distance_to_Shore}{Metres, decimal}
 #'   \item{F_LPUE}{Commercial fishery LPUE in Kg/Hr}
 #'   \item{Scallop}{Average KwH Scallop effort from logbooks, Marine Institute and MMO combined}
-#'   \item{MI_Av_E_Hr}{Average effort hours, Marine Institute Scallop VMS,
-#'   0.03*0.02 rectangles, all Irish Sea, 2006-14}
-#'   \item{MI_Av_LPUE}{Average scallop CPUE, Marine Institute Scallop VMS,
-#'   0.03*0.02 rectangles, all Irish Sea, 2006-14}
-#'   \item{MI_Sum_Liv}{Sum of live weight. Average scallop CPUE, Marine Institute Scallop VMS,
-#'   0.03*0.02 rectangles, all Irish Sea, 2006-14}
+#'   \item{MI_Av_E_Hr}{Average effort hours, Marine Institute Scallop VMS, 0.03 x 0.02 rectangles, all Irish Sea, 2006-14}
+#'   \item{MI_Av_LPUE}{Average scallop CPUE, Marine Institute Scallop VMS, 0.03 x 0.02 rectangles, all Irish Sea, 2006-14}
+#'   \item{MI_Sum_Liv}{Sum of live weight. Average scallop CPUE, Marine Institute Scallop VMS, 0.03 x 0.02 rectangles, all Irish Sea, 2006-14}
 #'   \item{Whelk}{MMO Whelk LPUE 2009-12, pivot, polygons to points}
 #'   \item{MmoAvScKwh}{MMO Scallop Effort 2009-12, pivot, polygons to points. ICES rectangles}
 #'   \item{Cod_C}{ICES IBTS CPUE of cod caught between 1994 - 2014 large enough to predate upon <= year 1 cuckoo rays}
@@ -134,12 +131,9 @@
 #'   \item{Distance_to_Shore}{Metres, decimal}
 #'   \item{F_LPUE}{Commercial fishery LPUE in Kg/Hr}
 #'   \item{Scallop}{Average KwH Scallop effort from logbooks, Marine Institute and MMO combined}
-#'   \item{MI_Av_E_Hr}{Average effort hours, Marine Institute Scallop VMS,
-#'   0.03*0.02 rectangles, all Irish Sea, 2006-14}
-#'   \item{MI_Av_LPUE}{Average scallop CPUE, Marine Institute Scallop VMS,
-#'   0.03*0.02 rectangles, all Irish Sea, 2006-14}
-#'   \item{MI_Sum_Liv}{Sum of live weight. Average scallop CPUE, Marine Institute Scallop VMS,
-#'   0.03*0.02 rectangles, all Irish Sea, 2006-14}
+#'   \item{MI_Av_E_Hr}{Average effort hours, Marine Institute Scallop VMS, 0.03 x 0.02 rectangles, all Irish Sea, 2006-14}
+#'   \item{MI_Av_LPUE}{Average scallop CPUE, Marine Institute Scallop VMS, 0.03 x 0.02 rectangles, all Irish Sea, 2006-14}
+#'   \item{MI_Sum_Liv}{Sum of live weight. Average scallop CPUE, Marine Institute Scallop VMS, 0.03 x 0.02 rectangles, all Irish Sea, 2006-14}
 #'   \item{Whelk}{MMO Whelk LPUE 2009-12, pivot, polygons to points}
 #'   \item{MmoAvScKwh}{MMO Scallop Effort 2009-12, pivot, polygons to points. ICES rectangles}
 #'   \item{HubDist}{map calc, distance of grid point to nearest datras point representing it (for preds)}

R/gbm.mapsf.R

@@ -41,6 +41,7 @@
 #' Default 9.
 #' @param shape If mapsource is "gbm.basemap", enter the full path to gbm.basemaps downloaded map,
 #' typically Crop_Map.shp, including the .shp. Default NULL.
+#' @param expandfactor Extents expansion factor for basemap. default 0.
 #' @param colourscale Scale fill colour scheme to use, default "viridis", other option is
 #' "gradient".
 #' @param colorscale Scale fill colour scheme to use, default NULL, populating this will overwrite

README.Rmd

@@ -16,7 +16,7 @@ knitr::opts_chunk$set(
 # gbm.auto
 
 <!-- badges: start -->
-[![R-CMD-check](https://github.com/SimonDedman/gbm.auto/workflows/R-CMD-check--as-cran/badge.svg)](https://github.com/SimonDedman/gbm.auto/actions)
+[![R-CMD-check](https://github.com/SimonDedman/gbm.auto/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/SimonDedman/gbm.auto/actions/workflows/R-CMD-check.yaml)
 [![CRAN\_Status\_Badge](https://www.r-pkg.org/badges/version/gbm.auto)](https://cran.r-project.org/package=gbm.auto)
 [![CRAN RStudio mirror downloads](https://cranlogs.r-pkg.org/badges/gbm.auto)](https://cran.r-project.org/package=gbm.auto)
 <!-- badges: end -->

README.md

@@ -5,7 +5,7 @@
 
 <!-- badges: start -->
 
-[![R-CMD-check](https://github.com/SimonDedman/gbm.auto/workflows/R-CMD-check--as-cran/badge.svg)](https://github.com/SimonDedman/gbm.auto/actions)
+[![R-CMD-check](https://github.com/SimonDedman/gbm.auto/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/SimonDedman/gbm.auto/actions/workflows/R-CMD-check.yaml)
 [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/gbm.auto)](https://cran.r-project.org/package=gbm.auto)
 [![CRAN RStudio mirror
 downloads](https://cranlogs.r-pkg.org/badges/gbm.auto)](https://cran.r-project.org/package=gbm.auto)

inst/CITATION

@@ -0,0 +1,12 @@
+bibentry(
+  bibtype  = "Article",
+  title    = "Gbm.auto: A software tool to simplify spatial modelling and Marine Protected Area planning",
+  author   = "Dedman, Simon and Officer, Rick and Clarke, Maurice and Reid, David G and Brophy, Deirdre",
+  journal  = "PloS ONE",
+  year     = "2017",
+  volume   = "12",
+  number   = "12",
+  pages    = "e0188955",
+  doi      = "https://doi.org/10.1371/journal.pone.0188955",
+  url      = "https://github.com/SimonDedman/gbm.auto"
+)