ncsu-landscape-dynamics / rpops

PoPS (Pest or Pathogen Spread) R Package
https://ncsu-landscape-dynamics.github.io/rpops/
GNU General Public License v3.0
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Created pest_host_table_list_creator helper function #195

Closed cyborginhas closed 5 months ago

cyborginhas commented 5 months ago

Updated associated extdata pest host tables to have additional columns: susceptiblity_mean, susceptibility_sd, mortality_rate_mean, mortality_rate_sd

Updated pest_host_table_wrong_columns check & error message & list scripts to include additional information needed to confirm that the pest_host_table includes the correct columns: hosts, susceptiblity_mean, susceptibility_sd, mortality_rate_mean, mortality_rate_sd, mortality_time_lag

Added competency_table_wrong_columns check (and associated code to error messages and lists scripts)

Added config$pest_host_table_list to calibrate, validate, pops_multirun, pops, and validate scripts.

Fixed competency typo in competency_table_list_creator function and associated extdata competency tables.

Updated all instances called pest_host_table$mortality_rate to pest_host_table$mortality_rate_mean

Note: Changed one value (from 2 to 1) in the infected file 2x2 test layers that were throwing an error for "Using multiple hosts with uncertainty works as expected" infected_tanoak.tif and infected_tanoak_wsd.tif. One of the expect_gte() tests consistently failed because previously mentioned rasters had a value of 2, but data$host_pools[[2]]$infected[[1]][[1]] predicted 1.

cyborginhas commented 5 months ago

Will address lintr issues, and create a new pull request.

codecov[bot] commented 5 months ago

Codecov Report

Attention: 10 lines in your changes are missing coverage. Please review.

Comparison is base (b70235a) 84.27% compared to head (897f8d7) 84.63%.

:exclamation: Current head 897f8d7 differs from pull request most recent head 4bdcd5c. Consider uploading reports for the commit 4bdcd5c to get more accurate results

Files Patch % Lines
R/checks.R 70.83% 7 Missing :warning:
R/helpers.R 88.46% 3 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #195 +/- ## ========================================== + Coverage 84.27% 84.63% +0.35% ========================================== Files 59 59 Lines 6170 6209 +39 ========================================== + Hits 5200 5255 +55 + Misses 970 954 -16 ```

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