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Conduct a copy editing review of text output in final reports

Currently the crawl function within ctcrw_interpolation fills the console with messages. Need to add argument along the lines of quiet = TRUE to suppress output, particularly when running ctcrw_interpolation within a Markdown doc.

Add option to save KBA polygon shapefiles when generating final OPP KBA reports.

Audience of these outputs are operating within the Canadian jurisdiction. For wide ranging species, e.g. storm petrels, including the BC EEZ may be helpful to delineate between international & Canadian waters.

EEZ files can be added via the mregions package.

Add a raw data list of Movebank project ids and write a function that summarises data in each project

Take out BB plots to make maps of other smoothers bigger in diagnostic report.

Add a descriptor column containing metadata about the shapefile data in the KBA template skeleton.

Add legends for purple dots (raw points) vs. cyan dots (interpolated points).

At the moment neither rendering function performs any health checks to ensure all required params are in place to actually render the markdown templates.

When using installed version of package opp_render_report and opp_render_diagnostic cannot find report templates

As the title says.

A potential option for this may be an argument to check whether the data are ARGOS or not, and if they are, to return error classes.

Might be nice to also add a param/argument to the function where you can also supply a list of additional Movebank columns for opp_download_data to add to the output.

The function ud_vol imports spatialEco::raster.vol. This can be replaced with adehabitatHR::getvolumeUD and adehabitatHR::getverticesHR to limit the number of packages being imported.

Reports with a high enough sample size provide the option to save the shapefile output of opp_sites. However, we need to add functionality to save either raw data points/tracks (pending Megan's input) for reports with low sample sizes.

The output for opp_get_trips is a SpatialPointsDataFrame with an associated proj4string, but running sp::is.projected returns FALSE.

Running the same function on the output from ctcrw_interpolation returns TRUE, e.g. sp::is.projected(interp_output$data) and sp::is.projected(interp_output$interp) are both TRUE!

At the moment this is a minor inconvenience as it means opp_kernel cannot calculate kernels on opp_get_trips outputs, only on ctcrw_interpolation outputs.

Request for maps for an annual report:

I can take a look at the tracks and see if a bird has done anything interesting – such as utilizing multiple habitat types, high site fidelity to a landfill, migration, etc.

Map ideas and where we would like to focus, if possible:

•      GWGU tagged on the West Coast of Vancouver Island (Tofino/Ucluelet) in 2022
  

•      Gull(s) heading for breeding grounds in Alaska in 2022
  

•      Fine scale movement map – this could be a gull tagged at a Landfill or natural area
  

•      Gull tagged at a landfill in 2020 or 2021, with interesting track in 2022
  

•      CAGU tagged at the Nanaimo Landfill
  

I can give you more specifics to include once I’ve had a look at the recent Movebank data. However, please feel free to let me know if something exciting pops out at you when you get a chance to look at the data. And as always don’t hesitate to reach out with questions.

The report PDFs are HUGE, let's try a lower DPI to make the file sizes more manageable

add dates from cpf_report_params to the shapefile outputs and reports

Movebank project ID: 696824680

Banding data on Google Drive: https://drive.google.com/drive/u/0/folders/1D3fU8RECZdcXZFctZtJaB_JKF11mIq17

Start with formatting reference data (movebank project data are sparse), then work with Hannah Roodenrijs on location data.

To stay consistent with OPPTools naming convention and move away from the acronym "KBA", the render_kba report function should be renamed. All associated files, e.g. skeleton.Rmd, should be modified accordingly.

Can also potentially delete opp-cpf-report to avoid any further confusion.

Finalize text for methods in diagnostic report.

OPP workflow generates an HTML dependency error when building documentation. Fix this error so documentation can properly compile.

Data for this project have been loaded to Movebank Project: 1912080185

Deployment dates for some don't seem to match GPS location data. LW sent raw field notes to help sort out.

The function change_yaml_matter does not update Rmd params verbatim. For example "TRUE/FALSE" become "yes/no" and strings are pasted in without quotation marks. This means that when a Rmd file is generated using either render_diagnostic or render_kba, the Rmd itself is not knittable until the user manually fixes the params in the YAML header.

All final OPP data products should be in EPSG4326/WGS84 projection. Code for opp_get_trips and opp_sites should either be updated to output 4326 products, or additional lines of code should be written into the KBA skeleton.Rmd file to re-project geospatial products before saving as shapefiles.

Linked to issue #66

When installing and using OPPTools on a new machine, reports are generated wherever the package is installed (e.g. ~Macintosh HD/Library/Frameworks/R. framework/Resources/library/OPPTools/inst/rmarkdown/templates/opp_x_report/ on a Mac). This is an issue with using here::here in the various reporting functions. As this project is currently retired there are no plans to fix this, so this is more of an FYI for anyone who may be using this package in future.

Modify shapefile output to the following:

• Clearer column names indicating % population use vs. number of individuals etc.
  Simplify shapefile bins to: 100% of population using, 75% using, 50% using, and 25% using
  Red KBA polyline output

Need to get breeding population size data for tracked colonies to finalise reports.

Allow user to specify the smoother as a numeric value or 'href' or 'step'. Where selecting href or step uses another function to calcualte those smoothers from the data.