[jniedballa]

camtrapR 3.1.0

New function

• simulateCamtrapData(): simulate camera trap data with custom properties (e.g. for testing, examples and teaching)

New features

surveyDashboard

• new welcome screen (modal dialog) on startup
• new data-quality and convergence warning system, flagging potential problems with input data and model fit (modal dialog and sidebar)
• new date range filter for records
• new instructions for CSV uploads, with links to relevant functions
• stricter validation of CSV uploads: a CRS must now be provided (numeric EPSG codes accepted); uploads abort with an informative modal dialog if the loaded table has only one column (wrong delimiter) or if the camera trap table contains duplicate station/camera combinations
• maximum csv file upload size increased to 500 MB (was 10Mb)
• single-species occupancy: new warning UI, improved printing of model summaries and species names, fitted models can now be exported, unmarkedFrame summary shown in a separate tab
• community occupancy: model file name is now printed in the UI
• added GitHub and Google Group links to the header;
• record preview in the filter section is collapsed by default; various label, tooltip and progress-indicator improvements

Occupancy models

• community occupancy models (commOccu) can now be fitted from JAGS model code stored in the new modelText slot, without an external model file
• createCovariates() now accept plain data frames with coordinates (new arguments xcol, ycol, crs; converted to sf internally)
• consistent terminology: "community models" instead of "multi-species models"

Data import

• the Camtrap DP interface was rewritten throughout and now uses the camtrapdp package for reading data packages
• readcamtrapDP renamed to readCamtrapDP (capitalisation in line with official name)
• more tolerant Camtrap DP import: missing vernacularNames are generated from scientific names and observation type; missing placename falls back to the deployment ID (with a warning); informative error if all timestamps fail to parse
• activity estimation with Camtrap DP data now uses only observations of type "event"

Improved displays and summary functions

• recordTable, recordTableIndividual & filterRecordTable now return an object of class "records" with dedicated print, [, summary, and dplyr_reconstruct methods
• cameraOperation now returns an object of class "camOp" with dedicated print, [, summary, and plot methods
• detectionHistory now returns an object of class "detHist" with dedicated print and [ methods
• readCamtrapDP now returns an object of class "cams_dp" with a dedicated print method
• camera tables contained in readCamtrapDP and simulateCamtrapData outputs are now of class "cams" with a dedicated print method
• internal function stripClass to remove added (S3) class and attributes

Other changes

• new vignette 6 introducing the surveyDashboard (with sample data)
• surveyDashboard: documentation expanded (new section on Bayesian priors, more details on model fitting challenges)
• new package dependencies: camtrapdp, checkmate, crayon, tibble (the latter two now direct rather than indirect dependencies)

Bugfixes

• surveyDashboard:
  • fixed several reactivity issues (records not resetting when loading new Camtrap DP data with active filters; number of removed images not updating; broken model selection table)
  • fixed error in export of covariate rasters
  • assert validity of parameter inputs (prevents opening app when e.g. column names specified wrongly)
  • fixed model selection table for ubms 1.2.9
  • ubms models now uses 1 core by default (faster than 3 cores for short runs)
• plot_coef(): fixed colors of plot lines by significance level in community model plots
• fixed wrong color ramp being applied to the original rasters in spatial prediction plots
• more robust aggregation of the camera trap table (all columns checked first, clearer error messages)
• fixed ggplot2 warning by replacing ylab() with labs()