In robgf/nwasc:

Guiding Principles

• Simple
• Reproducible results
• Well documented

R-Package Solution

• Organized code
• Documentation standards
  • The Comprehensive R Archive Network (CRAN) https://cran.r-project.org
  • RStudio https://rstudio.com
  • Tidyverse https://www.tidyverse.org
• Testable style requirements
• Facilitates unit testing
• Works well with GitHub https://www.github.com

Package Location and Installing

• https://github.com/robgf/nwasc
• Install:

devtools::install_github("robgf/nwasc")

Organized Code

• Keeping it simple ~883 files in 326 folders
• Four (4) exported functions
  • All with prefix "nwasc_"
  • Two Segmentation Functions
    • CTS data: nwasc_segmentCTS()
    • DTS data: nwasc_segmentDTS()
  • Two function for finalizing results into one file
• Example of clean data (circa Summer 2017) included in package (35MB)

Documentation

• R/Tidyverse has two documentation forms, short and long
• Short form
  • Technical internal documentation
  • Allows for standard R help:

?nwasc
?nwasc_SegmentCTS

• Long form vignette
  • Full example of running code

Running code

• Requirements for catalog query in documentation

  • Webpage
  • Vignette
  • Function documentation

• Due to the size of the NWASC this takes a while

library(nwasc)
seg.dat.phase2 = nwasc_segmentCTS(nwasc.ph2.obs.pre,
                            nwasc.ph2.shp.pre,
                            nwasc.ph2.cts.dat,

seg.dat.phase1.cts = nwasc_segmentCTS(nwasc.ph1.obs.pre,
                                nwasc.ph1.shp.pre,
                                nwasc.ph1.cts.dat,

seg.dat.phase1.dts = nwasc_segmentDTS(nwasc.ph1.dts.obs.dat,
                                nwasc.ph1.dts.dat)

segmented_seabird_catalogs <- nwasc_bind_phases(seg.dat.phase2, seg.dat.phase1.cts, seg.dat.phase1.dts)
nwasc_write_segmented_csv(segmented_seabird_catalogs)
zip("segmented_results", file = "segmented_seabird_catalog-2018-09-27-combined_transects_3 .csv")

Testing

• Testing inputs
  • Occurs with QA/QC of Catalog
• Testing functions
  • unit tests of functions
  • presently at 89% coverage
    • .onLoad can't be tested externally
    • Legacy code has unused options
    • Writing final output produces >200MB file and shouldn't be tested on third party server

Passed Standards

• External Continuous Integration Services

  • Travis CI
  • AppVeyor

• Test Coverage Reviews

  • Codecov
  • Coveralls

Viewing Results (ongoing work)

• Leaflet Map of tracks with observations
• Overlay of segments
• Example:
  • Different discretization for subset of NWASC
  • Winter seaducks FWS flights 'segments' common bins over years

• Next Steps:

  • Implement shiny version of maps for catalog
  • Similar to ARCGIS/QGIS maps, but without software or knowledge prerequisite.

• Move copy of repository to FWS GitHub account

robgf/nwasc documentation built on Oct. 29, 2021, 8:13 p.m.