Files in ecohealthalliance/sars_cov_risk
What the Package Does (One Line, Title Case)
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
R/GDALresample.R
R/calcCounts.R
R/convertHabitatTypesLong.R
R/estimateSpillover.R
R/getAOH.R
R/getIUCNshapes.R
R/getMapColors.R
R/getRedlistData.R
R/libraries.R
R/modifyFacets.R
R/prepRastersCategorical.R
R/prepSEAfiles.R
R/setDistributions.R
R/validateAOH.R
README.md
data-raw/41597_2020_599_MOESM2_ESM.csv
data-raw/IgGtimeseries.csv
data-raw/SARSrCoVhosts/Latinne_TableS1_betaCoV_hosts.csv
data-raw/SARSrCoVhosts/Olival_Table_S1_data_release_beta-CoVs_bats.csv
data-raw/SARSrCoVhosts/additional_hosts.csv
data-raw/bat_contact_data.csv
data-raw/detection_data.csv
data-raw/karst_wgs.zip
data-raw/ne_50m_land.zip
data-raw/searchterms.csv
data/AOH/Aselliscus stoliczkanus.tif
data/AOH/Aselliscus stoliczkanus_binary.tif
data/AOH/Chaerephon plicatus.tif
data/AOH/Chaerephon plicatus_binary.tif
data/AOH/Hipposideros armiger.tif
data/AOH/Hipposideros armiger_binary.tif
data/AOH/Hipposideros galeritus.tif
data/AOH/Hipposideros galeritus_binary.tif
data/AOH/Hipposideros gentilis.tif
data/AOH/Hipposideros gentilis_binary.tif
data/AOH/Hipposideros larvatus.tif
data/AOH/Hipposideros larvatus_binary.tif
data/AOH/Hipposideros pratti.tif
data/AOH/Hipposideros pratti_binary.tif
data/AOH/Nyctalus leisleri.tif
data/AOH/Nyctalus leisleri_binary.tif
data/AOH/Rhinolophus acuminatus.tif
data/AOH/Rhinolophus acuminatus_binary.tif
data/AOH/Rhinolophus affinis.tif
data/AOH/Rhinolophus affinis_binary.tif
data/AOH/Rhinolophus creaghi.tif
data/AOH/Rhinolophus creaghi_binary.tif
data/AOH/Rhinolophus ferrumequinum.tif
data/AOH/Rhinolophus ferrumequinum_binary.tif
data/AOH/Rhinolophus hipposideros.tif
data/AOH/Rhinolophus hipposideros_binary.tif
data/AOH/Rhinolophus luctus.tif
data/AOH/Rhinolophus luctus_binary.tif
data/AOH/Rhinolophus macrotis.tif
data/AOH/Rhinolophus macrotis_binary.tif
data/AOH/Rhinolophus malayanus.tif
data/AOH/Rhinolophus malayanus_binary.tif
data/AOH/Rhinolophus marshalli.tif
data/AOH/Rhinolophus marshalli_binary.tif
data/AOH/Rhinolophus pearsonii.tif
data/AOH/Rhinolophus pearsonii_binary.tif
data/AOH/Rhinolophus pusillus.tif
data/AOH/Rhinolophus pusillus_binary.tif
data/AOH/Rhinolophus rex.tif
data/AOH/Rhinolophus rex_binary.tif
data/AOH/Rhinolophus shameli.tif
data/AOH/Rhinolophus shameli_binary.tif
data/AOH/Rhinolophus siamensis.tif
data/AOH/Rhinolophus siamensis_binary.tif
data/AOH/Rhinolophus sinicus.tif
data/AOH/Rhinolophus sinicus_binary.tif
data/AOH/Rhinolophus stheno.tif
data/AOH/Rhinolophus stheno_binary.tif
data/AOH/Rhinolophus thomasi.tif
data/AOH/Rhinolophus thomasi_binary.tif
data/AOH/Tadarida teniotis.tif
data/AOH/Tadarida teniotis_binary.tif
data/AOH_heatmap.tif
data/IUCNareas.rda
data/PubMedCoVByCountry.rda
data/SARSrCoVhostShapefiles.dbf
data/SARSrCoVhostShapefiles.prj
data/SARSrCoVhostShapefiles.shp
data/SARSrCoVhostShapefiles.shx
data/SEA.dbf
data/SEA.prj
data/SEA.shp
data/SEA.shx
data/SEAelevation.tif
data/SEAhabitat.tif
data/SEAhabitatKarst.tif
data/countsHT.rda
data/countsOverall.rda
data/hostHabElev.rda
data/lhs_adjContact.rda
data/lhs_adjContactDetect.rda
data/lhs_adjDetect.rda
data/lhsdata.rda
data/mapColors.rda
data/sars_cov_hosts.rda
data/sobolIndices.rda
data/valResults.rda
data/wpop_resampled.tif
figures/Fig1.png
figures/Fig2.png
figures/FigS1.png
figures/FigS2.png
figures/FigS3.png
figures/FigS4.png
figures/fig3.png
sars_cov_risk.Rproj
scripts/01_data_download.R
scripts/02_sars_cov_hosts.R
scripts/03_get_gbif_data.R
scripts/04_aoh_bat_spatial_data.R
scripts/05_host_habitat_elevation_download.R
scripts/06_other_preprocessing.R
scripts/07_estimate_bats_aoh.R
scripts/08_aoh_validation.R
scripts/09_explore_AOH_results.R
scripts/10_spillover_and_sensitivity.R
scripts/11_make_Fig1.R
scripts/12_make_Fig2.R
scripts/13_make_Fig3.R
scripts/14_make_FigS1.R
scripts/15_make_FigS2.R
scripts/16_make_FigS3.R
scripts/17_make_FigS4.R
