Files in mrajeev08/MadaAccess
MadaAccess Research Compendium
.Rbuildignore
.gitignore
.nojekyll
DESCRIPTION
LICENSE.md
MadaAccess.Rproj
NAMESPACE
R/batch_functions.R
R/bezier.R
R/data.R
R/data_functions.R
R/estimate_pars.R
R/geom_raincloud.R
R/get_d3_data.R
R/match_names.R
R/match_pop.R
R/predict_functions.R
R/split_render.R
R/summarize_samps.R
R/ttime_functions.R
R/utils.R
_pkgdown.yml
analysis/figs/main/M2_ttimes.jpeg
analysis/figs/main/M2_ttimes.tiff
analysis/figs/main/M3_bitemaps.jpeg
analysis/figs/main/M3_bitemaps.tiff
analysis/figs/main/M4_mods.jpeg
analysis/figs/main/M4_mods.tiff
analysis/figs/main/M5_burden_base.jpeg
analysis/figs/main/M5_burden_base.tiff
analysis/figs/main/M6_addARMC.jpeg
analysis/figs/main/M6_addARMC.tiff
analysis/figs/striking_img.tiff
analysis/figs/supplementary/S1.1_inputs.jpeg
analysis/figs/supplementary/S1.2_raw.jpeg
analysis/figs/supplementary/S1.3_modes.jpeg
analysis/figs/supplementary/S1.4_lms.jpeg
analysis/figs/supplementary/S1.5_outputs.jpeg
analysis/figs/supplementary/S2.1_catchments.jpeg
analysis/figs/supplementary/S2.2_vialcomps.jpeg
analysis/figs/supplementary/S3.1_corrs.jpeg
analysis/figs/supplementary/S3.2_fitted.jpeg
analysis/figs/supplementary/S3.3_outfit.jpeg
analysis/figs/supplementary/S3.4_posts_all.jpeg
analysis/figs/supplementary/S3.5_preds_OD.jpeg
analysis/figs/supplementary/S3.6_posts_intercepts.jpeg
analysis/figs/supplementary/S3.7_preds_ODcomp.jpeg
analysis/figs/supplementary/S3.8_posts_rep_se.jpeg
analysis/figs/supplementary/S3.9_preds_rep_se.jpeg
analysis/figs/supplementary/S4.1_exprange.jpeg
analysis/figs/supplementary/S4.2_scaling_rels.jpeg
analysis/figs/supplementary/S5.1_tests.jpeg
analysis/figs/supplementary/S5.2_ARMCadded.jpeg
analysis/figs/supplementary/S5.3_map_shifts.jpeg
analysis/figs/supplementary/S5.3_map_shifts.tiff
analysis/figs/supplementary/S5.4_ttimes_bites.jpeg
analysis/figs/supplementary/S5.5_reporting_shifts.jpeg
analysis/figs/supplementary/S5.6_clinic_shifts.jpeg
analysis/figs/supplementary/S5.7_comm_map.jpeg
analysis/figs/supplementary/S5.8_dist_map.jpeg
analysis/figs/supplementary/S6.1_base_se.jpeg
analysis/figs/supplementary/S6.2_addARMC_se.jpeg
analysis/figs/supplementary/S6.3_vial_se.jpeg
analysis/figs/supplementary/S6.4_scaling_se.jpeg
analysis/paper/bib/refs_all.bib
analysis/paper/bib/refs_pkgs.bib
analysis/paper/bib/refs_supextra.bib
analysis/paper/format/abbreviations.json
analysis/paper/format/author-info-blocks.lua
analysis/paper/format/chicago-author-date.csl
analysis/paper/format/main.yaml
analysis/paper/format/multiple-bibliographies.lua
analysis/paper/format/mytemplate.tex
analysis/paper/format/pagebreak.lua
analysis/paper/format/plos-neglected-tropical-diseases.csl
analysis/paper/format/scholarly-metadata.lua
analysis/paper/format/supplement.yaml
analysis/paper/log.md
analysis/paper/make_paper.R
analysis/paper/manuscript.Rmd
analysis/paper/minor_revision_1/manuscript_supplement_tracked.pdf
analysis/paper/minor_revision_1/response_reviewers.Rmd
analysis/paper/minor_revision_1/response_reviewers.pdf
analysis/paper/minor_revision_1/supplement.pdf
analysis/paper/minor_revision_1/word2pdf.sh
analysis/paper/subfiles/cover_letter.Rmd
analysis/paper/subfiles/cover_letter.pdf
analysis/paper/subfiles/man.pdf
analysis/paper/subfiles/supplement.pdf
analysis/paper/subfiles/word2pdf.sh
analysis/src/00_install.R
analysis/src/01_ttimes/01_baseline.R
analysis/src/01_ttimes/02_groundtruth.R
analysis/src/02_bitedata/01_bite_incidence.R
analysis/src/02_bitedata/02_bite_incidence_se.R
analysis/src/03_bitemodels/01_run_bitemods.R
analysis/src/03_bitemodels/02_get_modpreds.R
analysis/src/03_bitemodels/03_model_se.R
analysis/src/04_addclinics/01_ttimes_candidates.R
analysis/src/04_addclinics/02_test_metrics.R
analysis/src/04_addclinics/03_ttimes_added.R
analysis/src/04_addclinics/04_postprocess.R
analysis/src/05_predictions/01_preds_incremental.R
analysis/src/05_predictions/02_se_pars.R
analysis/src/05_predictions/03_preds_se.R
analysis/src/05_predictions/04_scaling_se.R
analysis/src/figures/M2_ttimes.R
analysis/src/figures/M3_bitemaps.R
analysis/src/figures/M4_modpreds.R
analysis/src/figures/M5_burden.R
analysis/src/figures/M6_incremental.R
analysis/src/figures/SM1_ttimes.R
analysis/src/figures/SM2_bitedata.R
analysis/src/figures/SM3_bitemods.R
analysis/src/figures/SM4_exprange.R
analysis/src/figures/SM5_shifts.R
analysis/src/figures/SM6_burden_se.R
analysis/src/figures/SM6_scaling_se.R
analysis/src/process_session.R
bin/clean.sh
bin/compile.sh
bin/subrsync.sh
bin/word2pdf.sh
bin/zenodo.sh
data-raw/misc/aa_exposures.csv
data-raw/misc/figM1/M1_dtree.R
data-raw/misc/figM1/decision_tree.key
data-raw/misc/figM1/figM1_final.tiff
data-raw/misc/figM1/sankey_nolabs.jpeg
data-raw/misc/matched/ipm_dist_matched.csv
data-raw/misc/matched/moramanga_dist_matched.csv
data-raw/misc/moramanga_exposures.csv
data-raw/misc/ttimes_IPM.csv
data-raw/out/bitedata/moramanga.csv
data-raw/out/bitedata/moramanga_ttimes.csv
data-raw/out/bitedata/national.csv
data-raw/out/clinics/clinic_per_comm.csv
data-raw/out/clinics/clinic_per_dist.csv
data-raw/out/clinics/csb2.csv
data-raw/out/clinics/ctar_metadata.csv
data-raw/out/match_names/ipm_comm_matches.csv
data-raw/out/match_names/ipm_dist_matches.csv
data-raw/out/match_names/moramanga_comm_matches.csv
data-raw/out/match_names/moramanga_dist_matches.csv
data-raw/out/match_names/peripheral_comm_matches.csv
data-raw/out/rasters/friction_mada_masked.tif
data-raw/out/rasters/trans_gc_masked.rds
data-raw/out/rasters/wp_2015_1x1.tif
data-raw/out/shapefiles/mada_communes.dbf
data-raw/out/shapefiles/mada_communes.prj
data-raw/out/shapefiles/mada_communes.shp
data-raw/out/shapefiles/mada_communes.shx
data-raw/out/shapefiles/mada_districts.dbf
data-raw/out/shapefiles/mada_districts.prj
data-raw/out/shapefiles/mada_districts.shp
data-raw/out/shapefiles/mada_districts.shx
data-raw/raw/ctar_metadata.csv
data-raw/raw/moramanga/CTAR_%28V3%29_20190918150219.csv
data-raw/raw/moramanga/ctar_data_dictionary.csv
data-raw/raw/shapefiles/communes/mdg_admbnda_adm3_BNGRC_OCHA_20181031.cpg
data-raw/raw/shapefiles/communes/mdg_admbnda_adm3_BNGRC_OCHA_20181031.dbf
data-raw/raw/shapefiles/communes/mdg_admbnda_adm3_BNGRC_OCHA_20181031.prj
data-raw/raw/shapefiles/communes/mdg_admbnda_adm3_BNGRC_OCHA_20181031.sbn
data-raw/raw/shapefiles/communes/mdg_admbnda_adm3_BNGRC_OCHA_20181031.sbx
data-raw/raw/shapefiles/communes/mdg_admbnda_adm3_BNGRC_OCHA_20181031.shp
data-raw/raw/shapefiles/communes/mdg_admbnda_adm3_BNGRC_OCHA_20181031.shp.xml
data-raw/raw/shapefiles/communes/mdg_admbnda_adm3_BNGRC_OCHA_20181031.shx
data-raw/raw/shapefiles/districts/mdg_admbnda_adm2_BNGRC_OCHA_20181031.cpg
data-raw/raw/shapefiles/districts/mdg_admbnda_adm2_BNGRC_OCHA_20181031.dbf
data-raw/raw/shapefiles/districts/mdg_admbnda_adm2_BNGRC_OCHA_20181031.prj
data-raw/raw/shapefiles/districts/mdg_admbnda_adm2_BNGRC_OCHA_20181031.sbn
data-raw/raw/shapefiles/districts/mdg_admbnda_adm2_BNGRC_OCHA_20181031.sbx
data-raw/raw/shapefiles/districts/mdg_admbnda_adm2_BNGRC_OCHA_20181031.shp
data-raw/raw/shapefiles/districts/mdg_admbnda_adm2_BNGRC_OCHA_20181031.shp.xml
data-raw/raw/shapefiles/districts/mdg_admbnda_adm2_BNGRC_OCHA_20181031.shx
data-raw/readme.md
data-raw/src/01_rasters.R
data-raw/src/02_shapefiles.R
data-raw/src/03_clinics.R
data-raw/src/04_match_names.R
data-raw/src/05_bitedata.R
data-raw/src/06_doc_data.R
docs/index.html
logs/log_last_ran.csv
logs/pkgs_used.csv
readme.md
renv.lock
renv/.gitignore
renv/activate.R
renv/settings.dcf
runit.sh
