Created pest_host_table_list_creator helper function #195
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Will address lintr issues, and create a new pull request. |
R/error_messages.R
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| @@ -10,7 +10,6 @@ detailed_file_exists_error <- function(file_name) { | |||
| frequency_error <- | |||
| "Output frequency must be either 'week', 'month', 'day', 'year', 'time_step', or 'every_n_steps'" | |||
| raster_type_error <- | |||
| "file is not one of '.grd', '.tif', '.img', or '.vrt'" | |||
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this shouldn't have been removed
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removed in latest commit
R/RcppExports.R
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this file shouldn't have changed.
src/RcppExports.cpp
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This file also shouldn't have changed.
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I can't see the changes here online. did anything change in the data?
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This is how it changed: 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.
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This is how it changed: 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.
R/checks.R
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| @@ -383,7 +396,7 @@ multihost_checks <- | |||
| names(outs) <- failed_check_list | |||
| return(outs) | |||
| } | |||
| } | |||
| } | |||
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this looks like it is misalligned shouldn't have the tab there.
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removed in latest commit
Codecov ReportAttention:
Additional details and impacted files@@ Coverage Diff @@
## main #195 +/- ##
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+ Coverage 84.27% 84.63% +0.35%
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Files 59 59
Lines 6170 6209 +39
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+ Hits 5200 5255 +55
+ Misses 970 954 -16 ☔ View full report in Codecov by Sentry. |
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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.