Merge pull request #65 from EOGrady21/develop

CRAN update v0.4

.Rbuildignore

@@ -15,3 +15,4 @@ CODE_OF_CONDUCT.md
 CONTRIBUTING.md
 SECURITY.md
 ^CRAN-SUBMISSION$
+^Meta$

.github/workflows/pkgdown.yaml

@@ -11,6 +11,8 @@ on:
 
 name: pkgdown
 
+permissions: read-all
+
 jobs:
   pkgdown:
     runs-on: ubuntu-latest
@@ -22,7 +24,7 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -41,7 +43,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
           clean: false
           branch: gh-pages

.gitignore

@@ -9,3 +9,5 @@ Meta
 
 doc
 docs
+/doc/
+/Meta/

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: vprr
 Type: Package
 Title: Processing and Visualization of Video Plankton Recorder Data
-Version: 0.2.3
-Authors@R: c(person("Emily O'Grady",  role = c("aut", "cre","cph"), email = "[email protected]"), person("Kevin Sorochan", role = "aut", "dev"), person("Catherine Johnson", role = "aut"))
+Version: 0.3.0
+Authors@R: c(person("Emily O'Grady",  role = c("aut", "cre"), email = "[email protected]"), person("Kevin Sorochan", role = "aut"), person("Catherine Johnson", role = "aut"))
 Maintainer: Emily O'Grady <[email protected]>
 Description: An oceanographic data processing package for analyzing and visualizing Video 
     Plankton Recorder data.  This package was developed at 'Bedford Institute of Oceanography'.
@@ -11,7 +11,7 @@ Description: An oceanographic data processing package for analyzing and visualiz
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Depends: R (>= 2.10)
 Imports: ggplot2,
     oce,
@@ -26,7 +26,10 @@ Imports: ggplot2,
     lubridate,
     cmocean,
     withr,
-    usethis
+    usethis,
+    data.table,
+    fs,
+    rjson
 Suggests: 
     knitr,
     rmarkdown,

NAMESPACE

@@ -5,11 +5,8 @@ export(bin_cast)
 export(concentration_category)
 export(ctd_cast)
 export(ctd_df_cols)
-export(getRoiMeasurements)
-export(isopycnal_calculate)
 export(px_to_mm)
-export(vp_plot_matrix)
-export(vp_plot_unkn)
+export(read_aid_cnn)
 export(vpr_autoid_check)
 export(vpr_autoid_copy)
 export(vpr_autoid_create)
@@ -20,44 +17,36 @@ export(vpr_ctd_files)
 export(vpr_ctd_read)
 export(vpr_ctd_ymd)
 export(vpr_ctdroi_merge)
-export(vpr_ctdroisize_merge)
 export(vpr_day)
 export(vpr_dayhour)
+export(vpr_export)
 export(vpr_hour)
-export(vpr_img_category)
-export(vpr_img_check)
-export(vpr_img_copy)
-export(vpr_img_depth)
-export(vpr_img_reclassified)
 export(vpr_manual_classification)
 export(vpr_oce_create)
-export(vpr_plot_TS)
-export(vpr_plot_TScat)
-export(vpr_plot_contour)
-export(vpr_plot_histsize)
-export(vpr_plot_profile)
-export(vpr_plot_sizefreq)
 export(vpr_pred_read)
 export(vpr_roi)
 export(vpr_roi_concentration)
 export(vpr_save)
-export(vpr_size_bin)
-export(vpr_summary)
-export(vpr_trrois_size)
 import(dplyr)
 import(ggplot2)
 import(gridExtra, except = combine)
 import(metR, except = coriolis)
 
 import(oce)
+importFrom(data.table,rbindlist)
+importFrom(fs,dir_create)
+importFrom(fs,file_copy)
 importFrom(graphics,hist)
 importFrom(graphics,par)
 importFrom(graphics,plot.new)
+importFrom(rjson,toJSON)
 importFrom(stats,aggregate)
 importFrom(stats,median)
 importFrom(stats,quantile)
+importFrom(tools,file_ext)
 importFrom(usethis,use_data)
 importFrom(utils,menu)
 importFrom(utils,read.csv)
 importFrom(utils,read.table)
+importFrom(utils,write.csv)
 importFrom(utils,write.table)

NEWS.md

@@ -1,11 +1,43 @@
+# vprr 0.3.0
+## BUG FIXES AND ENHANCEMENTS
+* [ENHANCEMENT] Generalize vpr_category to better handle duplicate category names
+* [BUG FIX] Check for missing category values can accept a list
+* [ENHANCEMENT] Update vpr_autoid_check() to reflect better data checks and not touch original files
+* [BUG FIX] Major bug fixed in vpr_autoid_create(), ROIs are now correctly pulled from misclassified & reclassified files and inserted into new aid files
+* [ENHANCEMENT] vpr_autoid_copy() now has functionality for automated output from CNNs and option to limit copying by a CNN probability threshold (to only copy low confidence images for manual reclassification). Also updates copying method to improve speed. 
+* [ENHANCEMENT] Update vpr_manual_classification() to include CNN automated classification functionality and print automated classification confidence and ROI numbers on images 
+* [ENHANCEMENT] add organization structure options to vpr_autoid_copy()
+* [BUG FIX] fix example in vpr_autoid_create()
+* [ENHANCEMENT] Update CTD column naming flexibility and defaults, and include input validation for column names
+* [ENHANCEMENT] Update required metadata in vpr_save() to specify start & stop latitude and longitude to match start & end time values
+* [ENHANCEMENT] Lintr clean up of formatting
+* [ENHANCEMENT] add input validation to all functions
+
+## CHANGES
+* taxa replaced with category in all objects & instances
+* update to v2 of pkgdown workflow in GH actions
+* Remove unnecessary hard coding of variables to be added to oce-ctd object in vpr_oce_create()
+* added data.table dependency for quicker handling of large tables
+* add read_aid_cnn() function to smooth reading of automated classification output
+* Removed references to Visual Plankton, no longer relevant
+* implement tidy paths
+* update processing vignette to simplify example workflow, run with data contained in package, and improve flowchart figures.
+* removed deprecated function (getROIMeasurments)
+* compressed extdata files to avoid NOTE on R CMD CHECK
+
+## NEW CONTENT
+* New function vpr_export() for saving standardized data products (csv & json)
+* New vignette about data sharing
+* Update README to include badges and HEX sticker
+
 # vprr 0.2.0
-### BUG FIXES AND ENHANCEMENTS
+## BUG FIXES AND ENHANCEMENTS
 * [ENHANCEMENT] CodeFactor suggested updates to style
 * [BUG FIX] export vpr_manual_classification (Issue #23)
 * [ENHANCEMENT] update processing method to be flexible enough to run prediction output from non-vp automated classification system
 * [BUG FIX] consistency in variable naming for plotting depth/pressure (Issue #22)
 
-### CHANGES
+## CHANGES
 * Removed all reference to akima package (due to licensing issue brought to attention by CRAN)
 * Migrate from Travis CI to GH Actions
 * clarify directory structure and contain any file output to organized folders