Files in vjjan91/eBirdOccupancy
Effect of land cover and climate on bird species occupancy in the sothern Western Ghats using eBird data.
.Rbuildignore
.gitattributes
.gitignore
01_selecting-study-species.Rmd
02_prep-ebird-data.Rmd
03_prep-environmental-predictors.Rmd
04_checklist-calibration-index.Rmd
05_distance-roads-neighbours.ipynb
06_spatial-sampling-bias-distRoads.Rmd
07_temporal-sampling.Rmd
08_final-covar-data.Rmd
09_occupancy-models.Rmd
10_visualize-occu-predictor-effects.Rmd
11_predict-probOfOccupancy.Rmd
DESCRIPTION
LICENSE
NAMESPACE
R/fun_model_estimate_collection.r
R/fun_plot_interaction.r
R/fun_screen_cor.R
R/fun_separate_interactions.r
README.md
_bookdown.yml
_output.yml
appendix/AppendixS1_list-of-species.csv
appendix/AppendixS2_chi-square-goodness-of-fit-tests.csv
appendix/AppendixS3_occupancy-curves-significant-predictors.pdf
appendix/AppendixS4_model-averaged-coefficients-species-traits.csv
bash/get_chelsa.sh
bash/render_books_ebird.sh
common.R
data/chelsa/00_data_exists.txt
data/chelsa/envicloud/placeholder.txt
data/chelsa/envidatS3paths.txt
data/landUseClassification/00_data_exists.txt
data/landUseClassification/landcover_roy_2015_reclassified.tif
data/landUseClassification/lc_01000m.tif
data/landUseClassification/reclassification-matrix-landCover-2015.csv
data/lc_style.qml
data/lc_style2.qml
data/lc_style3.qml
data/lc_style_batlow.qml
data/spatial/00_data_exists.txt
data/spatial/hillsShapefile/Nil_Ana_Pal.cpg
data/spatial/hillsShapefile/Nil_Ana_Pal.dbf
data/spatial/hillsShapefile/Nil_Ana_Pal.prj
data/spatial/hillsShapefile/Nil_Ana_Pal.sbn
data/spatial/hillsShapefile/Nil_Ana_Pal.sbx
data/spatial/hillsShapefile/Nil_Ana_Pal.shp
data/spatial/hillsShapefile/Nil_Ana_Pal.shx
data/spatial/roads_studysite_2019/roads_studysite_2019.cpg
data/spatial/roads_studysite_2019/roads_studysite_2019.dbf
data/spatial/roads_studysite_2019/roads_studysite_2019.prj
data/spatial/roads_studysite_2019/roads_studysite_2019.shp
data/spatial/roads_studysite_2019/roads_studysite_2019.shx
data/species-list.csv
data/species-trait-dat.csv
docs/404.html
docs/adding-covariates-to-checklist-data.html
docs/checking-temporal-sampling-frequency.html
docs/examining-spatial-sampling-bias.html
docs/figs/fig_01.png
docs/figs/fig_02.png
docs/figs/fig_03.png
docs/figs/fig_04.png
docs/figs/fig_05.png
docs/figs/fig_06.png
docs/figs/fig_chk_per_month.png
docs/figs/fig_landcover_resample.png
docs/figs/fig_site_nnb.png
docs/figs/fig_spatial_bias.png
docs/figs/fig_species_prop_checklists_25kmgrids.png
docs/figs/fig_temporal_bias.png
docs/index.html
docs/libs/accessible-code-block-0.0.1/empty-anchor.js
docs/libs/anchor-sections-1.0.1/anchor-sections.css
docs/libs/anchor-sections-1.0.1/anchor-sections.js
docs/libs/gitbook-2.6.7/css/fontawesome/fontawesome-webfont.ttf
docs/libs/gitbook-2.6.7/css/plugin-bookdown.css
docs/libs/gitbook-2.6.7/css/plugin-clipboard.css
docs/libs/gitbook-2.6.7/css/plugin-fontsettings.css
docs/libs/gitbook-2.6.7/css/plugin-highlight.css
docs/libs/gitbook-2.6.7/css/plugin-search.css
docs/libs/gitbook-2.6.7/css/plugin-table.css
docs/libs/gitbook-2.6.7/css/style.css
docs/libs/gitbook-2.6.7/js/app.min.js
docs/libs/gitbook-2.6.7/js/clipboard.min.js
docs/libs/gitbook-2.6.7/js/jquery.highlight.js
docs/libs/gitbook-2.6.7/js/lunr.js
docs/libs/gitbook-2.6.7/js/plugin-bookdown.js
docs/libs/gitbook-2.6.7/js/plugin-clipboard.js
docs/libs/gitbook-2.6.7/js/plugin-fontsettings.js
docs/libs/gitbook-2.6.7/js/plugin-search.js
docs/libs/gitbook-2.6.7/js/plugin-sharing.js
docs/libs/jquery-2.2.3/jquery.min.js
docs/libs/jquery-3.6.0/jquery-3.6.0.min.js
docs/modelling-species-occupancy.html
docs/predicting-species-specific-occupancy-as-a-function-of-significant-predictors.html
docs/prepare-nearest-neighbour-and-road-metrics.html
docs/preparing-checklist-calibration-index.html
docs/preparing-ebird-data.html
docs/preparing-environmental-predictors.html
docs/preparing-observer-expertise-scores.html
docs/reference-keys.txt
docs/references.html
docs/search_index.json
docs/selecting-species-of-interest.html
docs/visualizing-occupancy-predictor-effects.html
eBirdOccupancy.Rproj
ebirdMap.qgz
ebird_occupancy_main_text.log
figs/fig_01.png
figs/fig_02.png
figs/fig_03.png
figs/fig_04.png
figs/fig_05.png
figs/fig_06.png
figs/fig_aic_weight.png
figs/fig_chk_per_month.png
figs/fig_climate_elev.png
figs/fig_landcover_proportion_1km.png
figs/fig_landcover_resample.png
figs/fig_landscape_1km.png
figs/fig_lc_climate.png
figs/fig_lc_elev.png
figs/fig_number_checklists_25km.png
figs/fig_occupancy_predictors.pdf
figs/fig_site_nnb.png
figs/fig_spatial_bias.png
figs/fig_species_prop_checklists_25kmgrids.png
figs/fig_temporal_bias.png
index.Rmd
latex/preamble.tex
references_ebird.bib
results/00_data_exists.txt
results/01_list-of-species-cutoff.csv
results/01_nchk-per-grid.csv
results/01_ngrids-per-spp.csv
results/01_prop-grids-per-spp.csv
results/04_data-covars-perChklist.csv
results/04_data-nspp-per-chk.csv
results/04_data-obsExpertise-score.csv
results/06_distance-roads-sites.csv
results/06_locs-dist-to-road.csv
results/08_data-covars-2.5km.csv.7z
results/09_goodness-of-fit-2.5km.csv
results/09_lc-clim-avg.xlsx
results/09_lc-clim-imp.xlsx
results/09_lc-clim-modelEst.xlsx
results/09_lc-clim.xlsx
results/09_scaled-covars-2.5km.csv.7z
results/10_cumulative-AIC-weights.csv
results/10_data-occupancy-predictors.csv
results/10_data-predictor-direction-nSpecies.csv
results/10_data-predictor-effect.csv
results/10_results-predictors-species-traits.csv
results/modOutput/00_data_exists.txt
results/modOutput/04_model-output-expertise.txt
xx_references.Rmd
