Create script order

Added script order to folder and script names to show order of execution. Updated Readme for final archival and publication.
accs-uaa · Oct 3, 2024 · f4d7286 · f4d7286
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diff --git a/cloudCompute/newInstance_machineLearning.md → ...anagement/01_Cloud_ScikitLearnInstance.md b/cloudCompute/newInstance_machineLearning.md → ...anagement/01_Cloud_ScikitLearnInstance.md
diff --git a/data_StudyAreaBoundary/PrepareStudyArea.py → 01_data_studyarea/PrepareStudyArea.py b/data_StudyAreaBoundary/PrepareStudyArea.py → 01_data_studyarea/PrepareStudyArea.py
diff --git a/..._Topography/PrepareCovariate_Elevation.py → 02_data_topography/01_Covariate_Elevation.py b/..._Topography/PrepareCovariate_Elevation.py → 02_data_topography/01_Covariate_Elevation.py
diff --git a/..._Topography/PrepareCovariate_Roughness.py → 02_data_topography/02_Covariate_Roughness.py b/..._Topography/PrepareCovariate_Roughness.py → 02_data_topography/02_Covariate_Roughness.py
diff --git a/..._Hydrography/PrepareCovariate_LakePond.py → ...ata_hydrography/01_Covariate_Waterbody.py b/..._Hydrography/PrepareCovariate_LakePond.py → ...ata_hydrography/01_Covariate_Waterbody.py
diff --git a/data_Hydrography/PrepareMask_WaterIce.py → 03_data_hydrography/02_Mask_WaterIce.py b/data_Hydrography/PrepareMask_WaterIce.py → 03_data_hydrography/02_Mask_WaterIce.py
diff --git a/...Vegetation/PrepareCovariate_Vegetation.py → ...ata_vegetation/01_Covariate_Vegetation.py b/...Vegetation/PrepareCovariate_Vegetation.py → ...ata_vegetation/01_Covariate_Vegetation.py
diff --git a/data_Vegetation/PrepareCovariate_Barren.py → 04_data_vegetation/02_Covariate_Barren.py b/data_Vegetation/PrepareCovariate_Barren.py → 04_data_vegetation/02_Covariate_Barren.py
diff --git a/...Vegetation/PrepareCovariate_ForestEdge.py → ...ata_vegetation/03_Covariate_ForestEdge.py b/...Vegetation/PrepareCovariate_ForestEdge.py → ...ata_vegetation/03_Covariate_ForestEdge.py
diff --git a/...Vegetation/PrepareCovariate_TundraEdge.py → ...ata_vegetation/04_Covariate_TundraEdge.py b/...Vegetation/PrepareCovariate_TundraEdge.py → ...ata_vegetation/04_Covariate_TundraEdge.py
diff --git a/data_Telemetry/01-createDeployMetadata_GPS.R → ...a_telemetry/01-createDeployMetadata_GPS.R b/data_Telemetry/01-createDeployMetadata_GPS.R → ...a_telemetry/01-createDeployMetadata_GPS.R
diff --git a/..._Telemetry/01-formatParturienceVariable.R → ..._telemetry/01-formatParturienceVariable.R b/..._Telemetry/01-formatParturienceVariable.R → ..._telemetry/01-formatParturienceVariable.R
diff --git a/..._Telemetry/01-importDataSeparateCSV_GPS.R → ..._telemetry/01-importDataSeparateCSV_GPS.R b/..._Telemetry/01-importDataSeparateCSV_GPS.R → ..._telemetry/01-importDataSeparateCSV_GPS.R
diff --git a/data_Telemetry/02-formatData_GPS.R → 05_data_telemetry/02-formatData_GPS.R b/data_Telemetry/02-formatData_GPS.R → 05_data_telemetry/02-formatData_GPS.R
diff --git a/data_Telemetry/03b-cleanLocations_GPS.R → 05_data_telemetry/03b-cleanLocations_GPS.R b/data_Telemetry/03b-cleanLocations_GPS.R → 05_data_telemetry/03b-cleanLocations_GPS.R
diff --git a/data_Telemetry/04-formatForCalvingSeason.R → ...ata_telemetry/04-formatForCalvingSeason.R b/data_Telemetry/04-formatForCalvingSeason.R → ...ata_telemetry/04-formatForCalvingSeason.R
diff --git a/data_Telemetry/explore-animatePaths.R → 05_data_telemetry/explore-animatePaths.R b/data_Telemetry/explore-animatePaths.R → 05_data_telemetry/explore-animatePaths.R
diff --git a/data_Telemetry/explore-interpolateData_GPS.R → ...a_telemetry/explore-interpolateData_GPS.R b/data_Telemetry/explore-interpolateData_GPS.R → ...a_telemetry/explore-interpolateData_GPS.R
diff --git a/data_Paths/01-generateDistributions.R → 06_data_paths/01-generateDistributions.R b/data_Paths/01-generateDistributions.R → 06_data_paths/01-generateDistributions.R
diff --git a/data_Paths/02-generateConvexHulls.py → 06_data_paths/02-generateConvexHulls.py b/data_Paths/02-generateConvexHulls.py → 06_data_paths/02-generateConvexHulls.py
diff --git a/data_Paths/03-createRandomStartPoints.py → 06_data_paths/03-createRandomStartPoints.py b/data_Paths/03-createRandomStartPoints.py → 06_data_paths/03-createRandomStartPoints.py
diff --git a/data_Paths/04-createRandomPaths.R → 06_data_paths/04-createRandomPaths.R b/data_Paths/04-createRandomPaths.R → 06_data_paths/04-createRandomPaths.R
diff --git a/data_Paths/05-convertToShapefile.py → 06_data_paths/05-convertToShapefile.py b/data_Paths/05-convertToShapefile.py → 06_data_paths/05-convertToShapefile.py
diff --git a/data_Paths/06-extractCovariates.R → 06_data_paths/06-extractCovariates.R b/data_Paths/06-extractCovariates.R → 06_data_paths/06-extractCovariates.R
diff --git a/data_Paths/07-summarizeByPath.R → 06_data_paths/07-summarizeByPath.R b/data_Paths/07-summarizeByPath.R → 06_data_paths/07-summarizeByPath.R
diff --git a/data_Paths/08-extractSelection.R → 06_data_paths/08-extractSelection.R b/data_Paths/08-extractSelection.R → 06_data_paths/08-extractSelection.R
diff --git a/data_Paths/09-removeConfidentialInfo.R → 06_data_paths/09-removeConfidentialInfo.R b/data_Paths/09-removeConfidentialInfo.R → 06_data_paths/09-removeConfidentialInfo.R
diff --git a/data_Paths/explore-amtPackage.R → 06_data_paths/explore-amtPackage.R b/data_Paths/explore-amtPackage.R → 06_data_paths/explore-amtPackage.R
diff --git a/data_Validation/01-formatData_VHF.R → 07_data_validation/01-formatData_VHF.R b/data_Validation/01-formatData_VHF.R → 07_data_validation/01-formatData_VHF.R
diff --git a/data_Validation/01-formatData_VHF_Togiak.R → ...ata_validation/01-formatData_VHF_Togiak.R b/data_Validation/01-formatData_VHF_Togiak.R → ...ata_validation/01-formatData_VHF_Togiak.R
diff --git a/geospatial_AnalyticGrids/DataExtract_Grids.R → 08_data_grids/01_Extract_Grids.R b/geospatial_AnalyticGrids/DataExtract_Grids.R → 08_data_grids/01_Extract_Grids.R
diff --git a/statistics_PathSelection/01-dataPrep.R → 09_statistics_selection/01_Prepare_Data.R b/statistics_PathSelection/01-dataPrep.R → 09_statistics_selection/01_Prepare_Data.R
diff --git a/statistics_PathSelection/HabitatTrainTest.py → ...stics_selection/02_Selection_TrainTest.py b/statistics_PathSelection/HabitatTrainTest.py → ...stics_selection/02_Selection_TrainTest.py
diff --git a/...ics_PathSelection/HabitatPredict_Grids.py → ...tistics_selection/03_Selection_Predict.py b/...ics_PathSelection/HabitatPredict_Grids.py → ...tistics_selection/03_Selection_Predict.py
diff --git a/...ection/summaryStatistics_Calf_VS_NoCalf.R → ...istics_selection/04a_Summary_Statistics.R b/...ection/summaryStatistics_Calf_VS_NoCalf.R → ...istics_selection/04a_Summary_Statistics.R
diff --git a/...lection/summaryStatistics_Obs_VS_Random.R → ...ics_selection/04b_Summary_Obs_vs_Random.R b/...lection/summaryStatistics_Obs_VS_Random.R → ...ics_selection/04b_Summary_Obs_vs_Random.R
diff --git a/...ction/summaryStatistics_PlotCorrelation.R → ...tatistics_selection/05_Plot_Correlation.R b/...ction/summaryStatistics_PlotCorrelation.R → ...tatistics_selection/05_Plot_Correlation.R
diff --git a/...maryStatistics_PlotCovariateImportances.R → ..._selection/06_Plot_CovariateImportances.R b/...maryStatistics_PlotCovariateImportances.R → ..._selection/06_Plot_CovariateImportances.R
diff --git a/...ion/summaryStatistics_VegetationHeights.R → ...stics_selection/07_Plot_HeightDiversity.R b/...ion/summaryStatistics_VegetationHeights.R → ...stics_selection/07_Plot_HeightDiversity.R
diff --git a/...offIndex/HabitatPredict_ObservedPoints.py → ...difference/01_Selection_Predict_Points.py b/...offIndex/HabitatPredict_ObservedPoints.py → ...difference/01_Selection_Predict_Points.py
diff --git a/...ndex/MaternalTradeoff_CalculateTradeoff.R → ...difference/02_Index_CalculateDifference.R b/...ndex/MaternalTradeoff_CalculateTradeoff.R → ...difference/02_Index_CalculateDifference.R
diff --git a/...ndex/MaternalTradeoff_SummarizeTradeoff.R → ...difference/03_Index_SummarizeDifference.R b/...ndex/MaternalTradeoff_SummarizeTradeoff.R → ...difference/03_Index_SummarizeDifference.R
diff --git a/...Index/MaternalTradeoff_PlotDistribution.R → ...tics_difference/04_Plot_DifferenceIndex.R b/...Index/MaternalTradeoff_PlotDistribution.R → ...tics_difference/04_Plot_DifferenceIndex.R
diff --git a/...bitat/HabitatPrediction_ConvertToRaster.R → 11_postprocess_rasters/01_Convert_Rasters.R b/...bitat/HabitatPrediction_ConvertToRaster.R → 11_postprocess_rasters/01_Convert_Rasters.R
diff --git a/..._Habitat/HabitatPrediction_MergeRasters.R → 11_postprocess_rasters/02_Merge_Rasters.R b/..._Habitat/HabitatPrediction_MergeRasters.R → 11_postprocess_rasters/02_Merge_Rasters.R
diff --git a/...ss_Habitat/HabitatPrediction_ApplyMask.py → 11_postprocess_rasters/03_Apply_Mask.py b/...ss_Habitat/HabitatPrediction_ApplyMask.py → 11_postprocess_rasters/03_Apply_Mask.py
diff --git a/...tPrediction_CalculateEuclideanDistance.py → ...rocess_rasters/04_Distance_To_Selected.py b/...tPrediction_CalculateEuclideanDistance.py → ...rocess_rasters/04_Distance_To_Selected.py
diff --git a/...HabitatPrediction_PrepareVHFValidation.py → ...tprocess_rasters/05_Prepare_Validation.py b/...HabitatPrediction_PrepareVHFValidation.py → ...tprocess_rasters/05_Prepare_Validation.py
diff --git a/...summaryStatistics_IndependentValidation.R → ...s_rasters/06_Selection_ProximalAccuracy.R b/...summaryStatistics_IndependentValidation.R → ...s_rasters/06_Selection_ProximalAccuracy.R
@@ -1,9 +1,9 @@
 # ---------------------------------------------------------------------------
-# Calculate Independent Validation
+# Calculate proximal accuracy
 # Author: Timm Nawrocki, Alaska Center for Conservation Science
 # Last Updated: 2021-10-06
 # Usage: Script should be executed in R 4.1.0+.
-# Description: "Calculate Independent Validation" calculates the proximity accuracy of independent VHF validation data relative to landscape mean distance to habitat.
+# Description: "Calculate proximal accuracy" calculates the proximity accuracy of independent VHF validation data relative to landscape mean distance to habitat.
 # ---------------------------------------------------------------------------
 
 # Define version

diff --git a/README.md b/README.md
@@ -1,14 +1,18 @@
-# Calving Season Habitat Preferences of Moose in Southwest Alaska
-Scripts for processing GPS telemetry data and analyzing properties of movement and space use of migratory and resident moose. 
-
-This project is a collaboration between the Alaska Center for Conservation Science and the Alaska Department of Fish and Game.
+# Calving Season Habitat Selection of Moose in Southwest Alaska
+Calving habitat selection for maternal and non-maternal females and comparison of among individual variation
 
 *Authors*:
 Amanda Droghini, Timm W. Nawrocki, Alaska Center for Conservation Science, University of Alaska Anchorage
 
-*Last updated*: 2021-04-29
+*Last updated*: 2024-10-02
+
+*Description*: This repository includes scripts for processing GPS telemetry data, preparing geospatial covariates, analyzing selection patterns among female moose in maternal and non-maternal group, and plotting variation among individuals between both groups along a relative unitless scale. Folders and scripts are numbered in order of execution, except those that contain functions (folders starting with "package_"). This project is a collaboration between the Alaska Center for Conservation Science and the Alaska Department of Fish and Game.
+
+## Getting Started
+
+The installation of R, ArcGIS Pro bundled with Python, and an independent Python with the dependencies listed below is required to execute the full suite of scripts included in this repository. The header of each script indicates in what system the script should be executed.
 
-# Prerequisites
+### Prerequisites
 1. ArcGIS Pro 2.5.2+
    1. Python 3.6.9+
 2. R 4.0.0+
@@ -25,22 +29,25 @@ Amanda Droghini, Timm W. Nawrocki, Alaska Center for Conservation Science, Unive
    11. tlocoh 1.40.7+
    12. zoo 1.8.8+
 3. R Studio 1.3.9+
+4. Python 3.8.8+ (Anaconda 2021.05 or later distribution)
+   1. scikit-learn 0.24.2+
 
-# Credits
 
-## Authors
+## Credits
+
+### Authors
 * **Amanda Droghini** - *Alaska Center for Conservation Science, University of Alaska Anchorage*
 * **Timm W. Nawrocki** - *Alaska Center for Conservation Science, University of Alaska Anchorage*
 
-## Usage Requirements
+### Usage Requirements
 Use of the scripts included in this repository should be cited as follows:
 
-Droghini, A., and T.W. Nawrocki. 2021. Space Use and Movement Patterns of Moose in Southwest Alaska. Git Repository. Available: https://github.com/accs-uaa/southwest-alaska-moose
+Droghini, A., T.W. Nawrocki, J.B. Stetz, P.A. Schuette, A.R. Aderman, and K.E. Colson. 2024. Variation in habitat selection among individuals differs by maternal status for moose in a region with low calf survival. Ecosphere [volume:identifier].
 
-## Citations
-Evans J.S., J. Oakleaf, S. A. Cushman. 2014. An ArcGIS Toolbox for Surface Gradient and Geomorphometric Modeling, version 2.0-0. Available: https://github.com/jeffreyevans/GradientMetrics
+### Citations
+We referenced the following for the scripts that calculate topographic indices:
 
-Nawrocki, T.W. 2020. Beringian Vegetation. Git Repository. Available: https://github.com/accs-uaa/beringian-vegetation
+Evans J.S., J. Oakleaf, S. A. Cushman. 2014. An ArcGIS Toolbox for Surface Gradient and Geomorphometric Modeling, version 2.0-0. Available: https://github.com/jeffreyevans/GradientMetrics
 
 ### License
 

diff --git a/geospatial_AnalyticGrids/archive/DataExtract_Grids_Tundra.R b/geospatial_AnalyticGrids/archive/DataExtract_Grids_Tundra.R
diff --git a/geospatial_AnalyticGrids/archive/DataExtract_MergeGrids.R b/geospatial_AnalyticGrids/archive/DataExtract_MergeGrids.R
diff --git a/postprocess_Habitat/HabitatPrediction_CompareConfidenceIntervals.R b/postprocess_Habitat/HabitatPrediction_CompareConfidenceIntervals.R
diff --git a/statistics_PathSelection/02a-exploratory-CollinearityVIF.py b/statistics_PathSelection/02a-exploratory-CollinearityVIF.py