From 8c2208dd2b677bc8daae02e602ba581877b4c59f Mon Sep 17 00:00:00 2001 From: John Giles Date: Tue, 24 Sep 2024 12:28:38 -0700 Subject: [PATCH] update to est_mobility output, init vignettes --- docs/404.html | 8 +++++++- docs/LICENSE-text.html | 8 +++++++- docs/_pkgdown.yml | 2 +- docs/articles/Project-setup.html | 8 +++++++- docs/articles/Running-MOSAIC.html | 8 +++++++- docs/articles/index.html | 8 +++++++- docs/authors.html | 8 +++++++- docs/index.html | 8 +++++++- docs/pkgdown.yml | 2 +- docs/reference/compile_ENSO_data.html | 8 +++++++- docs/reference/convert_country_to_iso.html | 8 +++++++- docs/reference/convert_iso_codes.html | 8 +++++++- docs/reference/convert_iso_to_country.html | 8 +++++++- docs/reference/download_africa_shapefile.html | 8 +++++++- docs/reference/download_all_country_shapefiles.html | 8 +++++++- docs/reference/download_climate_data.html | 8 +++++++- docs/reference/est_WASH_coverage.html | 8 +++++++- docs/reference/est_immune_decay.html | 8 +++++++- docs/reference/est_mobility.html | 8 +++++++- docs/reference/est_symptomatic_prop.html | 8 +++++++- docs/reference/est_vaccine_effectiveness.html | 8 +++++++- docs/reference/generate_country_grid_dist.html | 8 +++++++- docs/reference/generate_country_grid_n.html | 8 +++++++- docs/reference/get_DMI_forecast.html | 8 +++++++- docs/reference/get_DMI_historical.html | 8 +++++++- docs/reference/get_ENSO_forecast.html | 8 +++++++- docs/reference/get_ENSO_historical.html | 8 +++++++- docs/reference/get_WASH_data.html | 8 +++++++- docs/reference/get_centroid.html | 8 +++++++- docs/reference/get_climate_forecast.html | 8 +++++++- docs/reference/get_climate_future.html | 8 +++++++- docs/reference/get_climate_historical.html | 8 +++++++- docs/reference/get_country_shp.html | 8 +++++++- docs/reference/get_elevation.html | 8 +++++++- docs/reference/get_generation_time_distribution.html | 8 +++++++- docs/reference/get_ggplot_legend.html | 8 +++++++- docs/reference/get_immune_decay_data.html | 8 +++++++- docs/reference/get_paths.html | 8 +++++++- docs/reference/get_suspected_cases.html | 8 +++++++- docs/reference/get_symptomatic_prop_data.html | 8 +++++++- docs/reference/get_vaccine_effectiveness_data.html | 8 +++++++- docs/reference/index.html | 8 +++++++- docs/reference/iso_codes_africa.html | 8 +++++++- docs/reference/iso_codes_africa_central.html | 8 +++++++- docs/reference/iso_codes_africa_east.html | 8 +++++++- docs/reference/iso_codes_africa_north.html | 8 +++++++- docs/reference/iso_codes_africa_south.html | 8 +++++++- docs/reference/iso_codes_africa_west.html | 8 +++++++- docs/reference/iso_codes_mosaic.html | 8 +++++++- docs/reference/iso_codes_ssa.html | 8 +++++++- docs/reference/iso_codes_who_afro.html | 8 +++++++- docs/reference/load_or_install_packages.html | 8 +++++++- docs/reference/make_param_df.html | 8 +++++++- docs/reference/plot_CFR_by_country.html | 8 +++++++- docs/reference/plot_ENSO_data.html | 8 +++++++- docs/reference/plot_africa_map.html | 8 +++++++- docs/reference/plot_generation_time.html | 8 +++++++- docs/reference/plot_mobility.html | 8 +++++++- docs/reference/plot_shedding_rate.html | 8 +++++++- docs/reference/plot_suspected_cases.html | 8 +++++++- docs/reference/plot_vaccine_effectiveness.html | 8 +++++++- docs/reference/process_CFR_data.html | 8 +++++++- docs/reference/process_OAG_data.html | 8 +++++++- docs/reference/process_WHO_annual_data.html | 8 +++++++- docs/reference/process_WHO_weekly_data.html | 8 +++++++- docs/reference/process_demographics_data.html | 8 +++++++- docs/reference/run_WHO_annual_data_app.html | 8 +++++++- docs/reference/set_openmeteo_api_key.html | 8 +++++++- docs/reference/set_root_directory.html | 8 +++++++- pkgdown/_pkgdown.yml | 2 +- 70 files changed, 472 insertions(+), 70 deletions(-) diff --git a/docs/404.html b/docs/404.html index 9d50c37..785c845 100644 --- a/docs/404.html +++ b/docs/404.html @@ -21,7 +21,13 @@ + Skip to contents diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index d280b65..fa816f3 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -2,7 +2,13 @@ License • MOSAIC + Skip to contents diff --git a/docs/_pkgdown.yml b/docs/_pkgdown.yml index 2f9a249..5cf6720 100644 --- a/docs/_pkgdown.yml +++ b/docs/_pkgdown.yml @@ -9,7 +9,7 @@ template: btn-border-radius: 0.25rem danger: "#FF6347" params: - ganalytics: + ganalytics: G-11MTYCTQ7F light-switch: true theme: gruvbox-light theme-dark: gruvbox-dark diff --git a/docs/articles/Project-setup.html b/docs/articles/Project-setup.html index 1e78e76..b707d95 100644 --- a/docs/articles/Project-setup.html +++ b/docs/articles/Project-setup.html @@ -23,7 +23,13 @@ + Skip to contents diff --git a/docs/articles/Running-MOSAIC.html b/docs/articles/Running-MOSAIC.html index 894d555..78f9b60 100644 --- a/docs/articles/Running-MOSAIC.html +++ b/docs/articles/Running-MOSAIC.html @@ -23,7 +23,13 @@ + Skip to contents diff --git a/docs/articles/index.html b/docs/articles/index.html index 4db5b77..28b8d58 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -2,7 +2,13 @@ Articles • MOSAIC + Skip to contents diff --git a/docs/authors.html b/docs/authors.html index 15b30b9..0bc7bc1 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -2,7 +2,13 @@ Authors and Citation • MOSAIC + Skip to contents diff --git a/docs/index.html b/docs/index.html index 2aeffbf..8503bad 100644 --- a/docs/index.html +++ b/docs/index.html @@ -23,7 +23,13 @@ + Skip to contents diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 4c2e10c..876dde3 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -4,7 +4,7 @@ pkgdown_sha: ~ articles: Project-setup: Project-setup.html Running-MOSAIC: Running-MOSAIC.html -last_built: 2024-09-24T19:21Z +last_built: 2024-09-24T19:27Z urls: reference: institutefordiseasemodeling.github.io/MOSAIC-pkg/reference article: institutefordiseasemodeling.github.io/MOSAIC-pkg/articles diff --git a/docs/reference/compile_ENSO_data.html b/docs/reference/compile_ENSO_data.html index e3ff397..4b618d9 100644 --- a/docs/reference/compile_ENSO_data.html +++ b/docs/reference/compile_ENSO_data.html @@ -2,7 +2,13 @@ Compile ENSO and DMI Data (Historical and Forecast) — compile_ENSO_data • MOSAIC + Skip to contents diff --git a/docs/reference/convert_country_to_iso.html b/docs/reference/convert_country_to_iso.html index 814c2cc..8e75a7d 100644 --- a/docs/reference/convert_country_to_iso.html +++ b/docs/reference/convert_country_to_iso.html @@ -2,7 +2,13 @@ Convert Country Names to ISO3 or ISO2 Country Codes — convert_country_to_iso • MOSAIC + Skip to contents diff --git a/docs/reference/convert_iso_codes.html b/docs/reference/convert_iso_codes.html index b0c7fc5..76fc99f 100644 --- a/docs/reference/convert_iso_codes.html +++ b/docs/reference/convert_iso_codes.html @@ -2,7 +2,13 @@ Convert ISO3 to ISO2 or ISO2 to ISO3 Country Codes — convert_iso_codes • MOSAIC + Skip to contents diff --git a/docs/reference/convert_iso_to_country.html b/docs/reference/convert_iso_to_country.html index d0121a5..ab58389 100644 --- a/docs/reference/convert_iso_to_country.html +++ b/docs/reference/convert_iso_to_country.html @@ -2,7 +2,13 @@ Convert ISO2 or ISO3 Country Codes to Country Names — convert_iso_to_country • MOSAIC + Skip to contents diff --git a/docs/reference/download_africa_shapefile.html b/docs/reference/download_africa_shapefile.html index b1c300f..8c43012 100644 --- a/docs/reference/download_africa_shapefile.html +++ b/docs/reference/download_africa_shapefile.html @@ -2,7 +2,13 @@ Download and Save Africa Shapefile — download_africa_shapefile • MOSAIC + Skip to contents diff --git a/docs/reference/download_all_country_shapefiles.html b/docs/reference/download_all_country_shapefiles.html index d3509d6..4320b72 100644 --- a/docs/reference/download_all_country_shapefiles.html +++ b/docs/reference/download_all_country_shapefiles.html @@ -4,7 +4,13 @@ The function iterates through ISO3 country codes for Africa (from the MOSAIC framework) and saves each country's shapefile individually."> + Skip to contents diff --git a/docs/reference/download_climate_data.html b/docs/reference/download_climate_data.html index 5cb0d59..f4447cb 100644 --- a/docs/reference/download_climate_data.html +++ b/docs/reference/download_climate_data.html @@ -2,7 +2,13 @@ Download and Save Climate Data for Multiple Countries (Parquet Format) — download_climate_data • MOSAIC + Skip to contents diff --git a/docs/reference/est_WASH_coverage.html b/docs/reference/est_WASH_coverage.html index 5615956..18598e0 100644 --- a/docs/reference/est_WASH_coverage.html +++ b/docs/reference/est_WASH_coverage.html @@ -2,7 +2,13 @@ Estimate and Visualize WASH Coverage and Correlation with Cholera Incidence — est_WASH_coverage • MOSAIC + Skip to contents diff --git a/docs/reference/est_immune_decay.html b/docs/reference/est_immune_decay.html index 441a578..a927089 100644 --- a/docs/reference/est_immune_decay.html +++ b/docs/reference/est_immune_decay.html @@ -6,7 +6,13 @@ for predicted immune durability and decay rate distributions."> + Skip to contents diff --git a/docs/reference/est_mobility.html b/docs/reference/est_mobility.html index 1d662ee..cae2f3d 100644 --- a/docs/reference/est_mobility.html +++ b/docs/reference/est_mobility.html @@ -2,7 +2,13 @@ Fit Mobility Model Using Flight Data and Distance Matrices — est_mobility • MOSAIC + Skip to contents diff --git a/docs/reference/est_symptomatic_prop.html b/docs/reference/est_symptomatic_prop.html index 0882465..361c340 100644 --- a/docs/reference/est_symptomatic_prop.html +++ b/docs/reference/est_symptomatic_prop.html @@ -2,7 +2,13 @@ Estimate and Visualize Symptomatic Proportion Data — est_symptomatic_prop • MOSAIC + Skip to contents diff --git a/docs/reference/est_vaccine_effectiveness.html b/docs/reference/est_vaccine_effectiveness.html index a19a36b..77bfcb2 100644 --- a/docs/reference/est_vaccine_effectiveness.html +++ b/docs/reference/est_vaccine_effectiveness.html @@ -2,7 +2,13 @@ Estimate Vaccine Effectiveness Decay Model — est_vaccine_effectiveness • MOSAIC + Skip to contents diff --git a/docs/reference/generate_country_grid_dist.html b/docs/reference/generate_country_grid_dist.html index c10b1f8..dfd2bb9 100644 --- a/docs/reference/generate_country_grid_dist.html +++ b/docs/reference/generate_country_grid_dist.html @@ -2,7 +2,13 @@ Generate a Grid of Points Within a Country's Shapefile Based on Distance — generate_country_grid_dist • MOSAIC + Skip to contents diff --git a/docs/reference/generate_country_grid_n.html b/docs/reference/generate_country_grid_n.html index 265b932..40cf9c0 100644 --- a/docs/reference/generate_country_grid_n.html +++ b/docs/reference/generate_country_grid_n.html @@ -2,7 +2,13 @@ Generate a Grid of Points Within a Country's Shapefile Based on Number of Points — generate_country_grid_n • MOSAIC + Skip to contents diff --git a/docs/reference/get_DMI_forecast.html b/docs/reference/get_DMI_forecast.html index 6331fdb..5f1dc14 100644 --- a/docs/reference/get_DMI_forecast.html +++ b/docs/reference/get_DMI_forecast.html @@ -2,7 +2,13 @@ Get DMI (Dipole Mode Index) Forecast Data — get_DMI_forecast • MOSAIC + Skip to contents diff --git a/docs/reference/get_DMI_historical.html b/docs/reference/get_DMI_historical.html index 391fb25..8efde15 100644 --- a/docs/reference/get_DMI_historical.html +++ b/docs/reference/get_DMI_historical.html @@ -2,7 +2,13 @@ Download and Process Historical DMI Data — get_DMI_historical • MOSAIC + Skip to contents diff --git a/docs/reference/get_ENSO_forecast.html b/docs/reference/get_ENSO_forecast.html index 5963005..10ceb88 100644 --- a/docs/reference/get_ENSO_forecast.html +++ b/docs/reference/get_ENSO_forecast.html @@ -2,7 +2,13 @@ Get ENSO (Niño3, Niño3.4, and Niño4) Forecast Data — get_ENSO_forecast • MOSAIC + Skip to contents diff --git a/docs/reference/get_ENSO_historical.html b/docs/reference/get_ENSO_historical.html index 3170f80..0ca68e4 100644 --- a/docs/reference/get_ENSO_historical.html +++ b/docs/reference/get_ENSO_historical.html @@ -2,7 +2,13 @@ Download and Process Historical ENSO Data (Niño3, Niño3.4, Niño4) — get_ENSO_historical • MOSAIC + Skip to contents diff --git a/docs/reference/get_WASH_data.html b/docs/reference/get_WASH_data.html index 6bef208..c4d3716 100644 --- a/docs/reference/get_WASH_data.html +++ b/docs/reference/get_WASH_data.html @@ -2,7 +2,13 @@ Download, Process, and Save WASH Coverage Data — get_WASH_data • MOSAIC + Skip to contents diff --git a/docs/reference/get_centroid.html b/docs/reference/get_centroid.html index 6cb2d26..8269d43 100644 --- a/docs/reference/get_centroid.html +++ b/docs/reference/get_centroid.html @@ -2,7 +2,13 @@ Calculate the Centroid of a Country from its Shapefile — get_centroid • MOSAIC + Skip to contents diff --git a/docs/reference/get_climate_forecast.html b/docs/reference/get_climate_forecast.html index 3efdd04..3dffd84 100644 --- a/docs/reference/get_climate_forecast.html +++ b/docs/reference/get_climate_forecast.html @@ -2,7 +2,13 @@ Get Climate Forecast Data (Daily) — get_climate_forecast • MOSAIC + Skip to contents diff --git a/docs/reference/get_climate_future.html b/docs/reference/get_climate_future.html index 9dc316a..3d3037f 100644 --- a/docs/reference/get_climate_future.html +++ b/docs/reference/get_climate_future.html @@ -2,7 +2,13 @@ Download Future Climate Data for Multiple Locations — get_climate_future • MOSAIC + Skip to contents diff --git a/docs/reference/get_climate_historical.html b/docs/reference/get_climate_historical.html index db212a6..8413534 100644 --- a/docs/reference/get_climate_historical.html +++ b/docs/reference/get_climate_historical.html @@ -2,7 +2,13 @@ Get Historical Climate Data — get_climate_historical • MOSAIC + Skip to contents diff --git a/docs/reference/get_country_shp.html b/docs/reference/get_country_shp.html index 99630f5..ba20303 100644 --- a/docs/reference/get_country_shp.html +++ b/docs/reference/get_country_shp.html @@ -2,7 +2,13 @@ Get a country shapefile from GeoBoundaries API — get_country_shp • MOSAIC + Skip to contents diff --git a/docs/reference/get_elevation.html b/docs/reference/get_elevation.html index 37030ae..9d330af 100644 --- a/docs/reference/get_elevation.html +++ b/docs/reference/get_elevation.html @@ -2,7 +2,13 @@ Get Median Elevation Data for Multiple Countries Using Shapefiles — get_elevation • MOSAIC + Skip to contents diff --git a/docs/reference/get_generation_time_distribution.html b/docs/reference/get_generation_time_distribution.html index 3897265..b34a494 100644 --- a/docs/reference/get_generation_time_distribution.html +++ b/docs/reference/get_generation_time_distribution.html @@ -2,7 +2,13 @@ Estimate the Generation Time Distribution for Days and Weeks — get_generation_time_distribution • MOSAIC + Skip to contents diff --git a/docs/reference/get_ggplot_legend.html b/docs/reference/get_ggplot_legend.html index fa99dc0..06093ec 100644 --- a/docs/reference/get_ggplot_legend.html +++ b/docs/reference/get_ggplot_legend.html @@ -4,7 +4,13 @@ The extracted legend can then be used independently, for instance, to combine the legend with other plots."> + Skip to contents diff --git a/docs/reference/get_immune_decay_data.html b/docs/reference/get_immune_decay_data.html index 2834ebf..def8531 100644 --- a/docs/reference/get_immune_decay_data.html +++ b/docs/reference/get_immune_decay_data.html @@ -4,7 +4,13 @@ The data includes time (in days), effectiveness, and confidence intervals from studies."> + Skip to contents diff --git a/docs/reference/get_paths.html b/docs/reference/get_paths.html index f8c9a0c..e2db992 100644 --- a/docs/reference/get_paths.html +++ b/docs/reference/get_paths.html @@ -2,7 +2,13 @@ Generate Directory Paths for the MOSAIC Project — get_paths • MOSAIC + Skip to contents diff --git a/docs/reference/get_suspected_cases.html b/docs/reference/get_suspected_cases.html index 206eb44..abaa9dc 100644 --- a/docs/reference/get_suspected_cases.html +++ b/docs/reference/get_suspected_cases.html @@ -2,7 +2,13 @@ Get Proportion of Suspected Cholera Cases and Save Parameter Data Frame — get_suspected_cases • MOSAIC + Skip to contents diff --git a/docs/reference/get_symptomatic_prop_data.html b/docs/reference/get_symptomatic_prop_data.html index e65b05d..df7dc18 100644 --- a/docs/reference/get_symptomatic_prop_data.html +++ b/docs/reference/get_symptomatic_prop_data.html @@ -2,7 +2,13 @@ Get Symptomatic Proportion Data — get_symptomatic_prop_data • MOSAIC + Skip to contents diff --git a/docs/reference/get_vaccine_effectiveness_data.html b/docs/reference/get_vaccine_effectiveness_data.html index f123003..0dfc2f6 100644 --- a/docs/reference/get_vaccine_effectiveness_data.html +++ b/docs/reference/get_vaccine_effectiveness_data.html @@ -2,7 +2,13 @@ Get Vaccine Effectiveness Data — get_vaccine_effectiveness_data • MOSAIC + Skip to contents diff --git a/docs/reference/index.html b/docs/reference/index.html index 3515425..669d9cd 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -2,7 +2,13 @@ Function reference • MOSAIC + Skip to contents diff --git a/docs/reference/iso_codes_africa.html b/docs/reference/iso_codes_africa.html index 1cc8e87..37e641b 100644 --- a/docs/reference/iso_codes_africa.html +++ b/docs/reference/iso_codes_africa.html @@ -2,7 +2,13 @@ ISO3 Country Codes for All African Countries — iso_codes_africa • MOSAIC + Skip to contents diff --git a/docs/reference/iso_codes_africa_central.html b/docs/reference/iso_codes_africa_central.html index 7eff4ba..e21b41d 100644 --- a/docs/reference/iso_codes_africa_central.html +++ b/docs/reference/iso_codes_africa_central.html @@ -2,7 +2,13 @@ ISO3 Country Codes for Central African Countries — iso_codes_africa_central • MOSAIC + Skip to contents diff --git a/docs/reference/iso_codes_africa_east.html b/docs/reference/iso_codes_africa_east.html index 850ac31..5ae4606 100644 --- a/docs/reference/iso_codes_africa_east.html +++ b/docs/reference/iso_codes_africa_east.html @@ -2,7 +2,13 @@ ISO3 Country Codes for East African Countries — iso_codes_africa_east • MOSAIC + Skip to contents diff --git a/docs/reference/iso_codes_africa_north.html b/docs/reference/iso_codes_africa_north.html index a6c171d..6ee5c17 100644 --- a/docs/reference/iso_codes_africa_north.html +++ b/docs/reference/iso_codes_africa_north.html @@ -2,7 +2,13 @@ ISO3 Country Codes for North African Countries — iso_codes_africa_north • MOSAIC + Skip to contents diff --git a/docs/reference/iso_codes_africa_south.html b/docs/reference/iso_codes_africa_south.html index 58faae5..a42e331 100644 --- a/docs/reference/iso_codes_africa_south.html +++ b/docs/reference/iso_codes_africa_south.html @@ -2,7 +2,13 @@ ISO3 Country Codes for Southern African Countries — iso_codes_africa_south • MOSAIC + Skip to contents diff --git a/docs/reference/iso_codes_africa_west.html b/docs/reference/iso_codes_africa_west.html index aa0d173..a075eec 100644 --- a/docs/reference/iso_codes_africa_west.html +++ b/docs/reference/iso_codes_africa_west.html @@ -2,7 +2,13 @@ ISO3 Country Codes for West African Countries — iso_codes_africa_west • MOSAIC + Skip to contents diff --git a/docs/reference/iso_codes_mosaic.html b/docs/reference/iso_codes_mosaic.html index 4074c34..208cd28 100644 --- a/docs/reference/iso_codes_mosaic.html +++ b/docs/reference/iso_codes_mosaic.html @@ -2,7 +2,13 @@ ISO3 Country Codes for MOSAIC Modeling Framework — iso_codes_mosaic • MOSAIC + Skip to contents diff --git a/docs/reference/iso_codes_ssa.html b/docs/reference/iso_codes_ssa.html index 96e686e..03a8ead 100644 --- a/docs/reference/iso_codes_ssa.html +++ b/docs/reference/iso_codes_ssa.html @@ -2,7 +2,13 @@ ISO3 Country Codes for Sub-Saharan African Countries — iso_codes_ssa • MOSAIC + Skip to contents diff --git a/docs/reference/iso_codes_who_afro.html b/docs/reference/iso_codes_who_afro.html index b38a6e9..4a9d665 100644 --- a/docs/reference/iso_codes_who_afro.html +++ b/docs/reference/iso_codes_who_afro.html @@ -2,7 +2,13 @@ ISO3 Country Codes for WHO AFRO Region Countries — iso_codes_who_afro • MOSAIC + Skip to contents diff --git a/docs/reference/load_or_install_packages.html b/docs/reference/load_or_install_packages.html index 0d1c397..fcce13a 100644 --- a/docs/reference/load_or_install_packages.html +++ b/docs/reference/load_or_install_packages.html @@ -2,7 +2,13 @@ Load or Install Required Packages (with GitHub handling for mobility, propvacc, and MOSAIC) — load_or_install_packages • MOSAIC + Skip to contents diff --git a/docs/reference/make_param_df.html b/docs/reference/make_param_df.html index 89eb2e0..601578f 100644 --- a/docs/reference/make_param_df.html +++ b/docs/reference/make_param_df.html @@ -2,7 +2,13 @@ Get Template for Parameter Values — make_param_df • MOSAIC + Skip to contents diff --git a/docs/reference/plot_CFR_by_country.html b/docs/reference/plot_CFR_by_country.html index 7ccb945..d510a8c 100644 --- a/docs/reference/plot_CFR_by_country.html +++ b/docs/reference/plot_CFR_by_country.html @@ -2,7 +2,13 @@ Plot Case Fatality Ratios, Total Cases, and Beta Distributions by Country — plot_CFR_by_country • MOSAIC + Skip to contents diff --git a/docs/reference/plot_ENSO_data.html b/docs/reference/plot_ENSO_data.html index 6b7b5f8..f309dce 100644 --- a/docs/reference/plot_ENSO_data.html +++ b/docs/reference/plot_ENSO_data.html @@ -2,7 +2,13 @@ Plot ENSO and DMI Data — plot_ENSO_data • MOSAIC + Skip to contents diff --git a/docs/reference/plot_africa_map.html b/docs/reference/plot_africa_map.html index db4215a..40dadc7 100644 --- a/docs/reference/plot_africa_map.html +++ b/docs/reference/plot_africa_map.html @@ -2,7 +2,13 @@ Plot Africa Map with Cholera Outbreak Countries — plot_africa_map • MOSAIC + Skip to contents diff --git a/docs/reference/plot_generation_time.html b/docs/reference/plot_generation_time.html index 1927171..9bfab01 100644 --- a/docs/reference/plot_generation_time.html +++ b/docs/reference/plot_generation_time.html @@ -2,7 +2,13 @@ Plot Generation Time as Gamma Distribution for Days and Weeks — plot_generation_time • MOSAIC + Skip to contents diff --git a/docs/reference/plot_mobility.html b/docs/reference/plot_mobility.html index 6cb9799..365903b 100644 --- a/docs/reference/plot_mobility.html +++ b/docs/reference/plot_mobility.html @@ -2,7 +2,13 @@ Plot Mobility Data, Mobility Network, and Results — plot_mobility • MOSAIC + Skip to contents diff --git a/docs/reference/plot_shedding_rate.html b/docs/reference/plot_shedding_rate.html index 9383b02..4e7adc2 100644 --- a/docs/reference/plot_shedding_rate.html +++ b/docs/reference/plot_shedding_rate.html @@ -10,7 +10,13 @@ The plot is saved as a PNG file in the directory specified by PATHS$DOCS_FIGURES."> + Skip to contents diff --git a/docs/reference/plot_suspected_cases.html b/docs/reference/plot_suspected_cases.html index ec90fd8..d410a15 100644 --- a/docs/reference/plot_suspected_cases.html +++ b/docs/reference/plot_suspected_cases.html @@ -2,7 +2,13 @@ Plot Proportion of Suspected Cholera Cases — plot_suspected_cases • MOSAIC + Skip to contents diff --git a/docs/reference/plot_vaccine_effectiveness.html b/docs/reference/plot_vaccine_effectiveness.html index 7a3923e..8649edf 100644 --- a/docs/reference/plot_vaccine_effectiveness.html +++ b/docs/reference/plot_vaccine_effectiveness.html @@ -2,7 +2,13 @@ Plot Vaccine Effectiveness and Beta Distribution — plot_vaccine_effectiveness • MOSAIC + Skip to contents diff --git a/docs/reference/process_CFR_data.html b/docs/reference/process_CFR_data.html index c3da840..193412d 100644 --- a/docs/reference/process_CFR_data.html +++ b/docs/reference/process_CFR_data.html @@ -2,7 +2,13 @@ Process Cholera Data to Calculate Aggregated Case Fatality Ratios and Fit Beta Distributions (2014-2024) — process_CFR_data • MOSAIC + Skip to contents diff --git a/docs/reference/process_OAG_data.html b/docs/reference/process_OAG_data.html index 0db55ad..53fb70d 100644 --- a/docs/reference/process_OAG_data.html +++ b/docs/reference/process_OAG_data.html @@ -6,7 +6,13 @@ all African countries and a subset of countries used in the MOSAIC modeling framework."> + Skip to contents diff --git a/docs/reference/process_WHO_annual_data.html b/docs/reference/process_WHO_annual_data.html index 62b2e0c..ba777d5 100644 --- a/docs/reference/process_WHO_annual_data.html +++ b/docs/reference/process_WHO_annual_data.html @@ -2,7 +2,13 @@ Download, Process, and Save Historical Annual WHO Cholera Data for Africa — process_WHO_annual_data • MOSAIC + Skip to contents diff --git a/docs/reference/process_WHO_weekly_data.html b/docs/reference/process_WHO_weekly_data.html index e02d4e9..24c3549 100644 --- a/docs/reference/process_WHO_weekly_data.html +++ b/docs/reference/process_WHO_weekly_data.html @@ -2,7 +2,13 @@ Process Weekly Cholera Data: Convert Country Names to ISO3 and Filter by AFRO Countries — process_WHO_weekly_data • MOSAIC + Skip to contents diff --git a/docs/reference/process_demographics_data.html b/docs/reference/process_demographics_data.html index 7ddafc3..e4945ee 100644 --- a/docs/reference/process_demographics_data.html +++ b/docs/reference/process_demographics_data.html @@ -2,7 +2,13 @@ Process UN World Prospects Data for African Countries — process_demographics_data • MOSAIC + Skip to contents diff --git a/docs/reference/run_WHO_annual_data_app.html b/docs/reference/run_WHO_annual_data_app.html index 87ffcb1..727cf6a 100644 --- a/docs/reference/run_WHO_annual_data_app.html +++ b/docs/reference/run_WHO_annual_data_app.html @@ -2,7 +2,13 @@ Run Shiny Application for Visualizing WHO Annual Cholera Data in AFRO Countries — run_WHO_annual_data_app • MOSAIC + Skip to contents diff --git a/docs/reference/set_openmeteo_api_key.html b/docs/reference/set_openmeteo_api_key.html index f306a31..83b883f 100644 --- a/docs/reference/set_openmeteo_api_key.html +++ b/docs/reference/set_openmeteo_api_key.html @@ -4,7 +4,13 @@ If an API key is provided as an argument, it will be used. If not, the function will prompt for the key interactively."> + Skip to contents diff --git a/docs/reference/set_root_directory.html b/docs/reference/set_root_directory.html index fa846be..0d12973 100644 --- a/docs/reference/set_root_directory.html +++ b/docs/reference/set_root_directory.html @@ -2,7 +2,13 @@ Set Root Directory — set_root_directory • MOSAIC + Skip to contents diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml index 2f9a249..5cf6720 100644 --- a/pkgdown/_pkgdown.yml +++ b/pkgdown/_pkgdown.yml @@ -9,7 +9,7 @@ template: btn-border-radius: 0.25rem danger: "#FF6347" params: - ganalytics: + ganalytics: G-11MTYCTQ7F light-switch: true theme: gruvbox-light theme-dark: gruvbox-dark