diff --git a/.DS_Store b/.DS_Store index 428d21e7..832682c5 100644 Binary files a/.DS_Store and b/.DS_Store differ diff --git a/scripts/.DS_Store b/scripts/.DS_Store index b0ae2913..27ba8cb3 100644 Binary files a/scripts/.DS_Store and b/scripts/.DS_Store differ diff --git a/scripts/occ_model_resultsv3/occ_model_resultsv3.R b/scripts/occ_model_resultsv3/occ_model_resultsv3.R index ca08b2d7..c52b9ee8 100644 --- a/scripts/occ_model_resultsv3/occ_model_resultsv3.R +++ b/scripts/occ_model_resultsv3/occ_model_resultsv3.R @@ -259,14 +259,19 @@ occ_avg<- if(nrow(test_models)<=1){ ##### final_path<- file.path(outputFolder, "final.csv") # Define the file path for the 'val_wkt_path' output write.csv(final, final_path, row.names = T ) # Write the 'val_wkt_path' output - #### Outputing result to JSON #### + + summary_occ_path<- file.path(outputFolder, "summary_occModel.txt") # Define the file path for the 'val_wkt_path' output + sink(summary_occ_path) + print(occ_model) + sink() #### Outputing result to JSON #### output<- list(occprob_raster_export = occprob_raster_path, occse_raster_export = occse_raster_path, occPlotFacet= occPlotFacet_path, - final_export = final_path, VEB_export = FVEB) + final_export = final_path, VEB_export = FVEB, + summary_occ_path= summary_occ_path) diff --git a/scripts/occ_model_resultsv3/occ_model_resultsv3.yml b/scripts/occ_model_resultsv3/occ_model_resultsv3.yml index cef13950..d2a4c56f 100644 --- a/scripts/occ_model_resultsv3/occ_model_resultsv3.yml +++ b/scripts/occ_model_resultsv3/occ_model_resultsv3.yml @@ -11,17 +11,17 @@ inputs: label: site_covs description: "List of site variables (site/landscape characteristics that influence species detection and occupancy). They can be specified by name or through the directory where they are stored in .tif format. Names must match the columns in camptrap_data or will be omitted." type: image/tiff;application=geotiff[] - example: ["scripts/CamTrap_format2/input/stac"] + example: ["bio18_1981_01_01_1982_01_01", "bio4_1981_01_01_1982_01_01" , "bio7_1981_01_01_1982_01_01"] site_covs_Layers: label: site_covs_Layers description: "List of site variables (site/landscape characteristics that influence species detection and occupancy). They can be specified by name or through the directory where they are stored in .tif format. Names must match the columns in camptrap_data or will be omitted." type: image/tiff;application=geotiff[] - example: ["scripts/CamTrap_format2/input/stac"] + example: ["scripts/occ_model_resultsv3/input/"] obs_covs: label: obs_covs description: "List of observation variables (hour, lunar phase, climate) that must match columns in camptrap_data or will be omitted. As they can vary by event, they must be grouped/collapsed for the unmarked object. When they are factors, they are not rounded. Numeric variables are specified as eventTime|1, where 1 is the rounding value. For temporal variables, use eventTime|1|hour. Temporal units from lubridate::round_date are accepted." type: text[] - example: ["eventTime|1|hour"] + example: ["duration_minutes"] nsim: label: nsim description: "The number of bootstrapped samples" @@ -33,6 +33,10 @@ inputs: type: boolean example: false outputs: + summary_occ_path: + label: summary_occ_path + description: "Summary of ocupation model" + type: text/csv occprob_raster_export: label: occprob_raster_export description: "Raster map with occupancy model probability and standar error"