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README.html
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<!-- README.md is generated from README.Rmd. Please edit that file -->
<h1 id="an-open-source-framework-for-rift-valley-fever-forecasting">An
open-source framework for Rift Valley Fever forecasting</h1>
<!-- badges: start -->
<p><a href="https://www.repostatus.org/#wip"><svg id="svg_a056ad2c8a8eeefa3116" role="img" aria-label="Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public." alt="Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public." width="106" height="20" viewBox="0 0 106 20"><title>repo status: WIP</title><linearGradient id="svg_a056ad2c8a8eeefa3116_s" x2="0" y2="100%"><stop offset="0" stop-color="#bbb" stop-opacity=".1"></stop><stop offset="1" stop-opacity=".1"></stop></linearGradient><clipPath id="svg_a056ad2c8a8eeefa3116_r"><rect width="106" height="20" rx="3" fill="#fff" /></clipPath><g clip-path="url(#svg_a056ad2c8a8eeefa3116_r)"><rect width="73" height="20" fill="#555" /><rect x="73" width="33" height="20" fill="#dfb317" /><rect width="106" height="20" fill="url(#svg_a056ad2c8a8eeefa3116_s)" /></g><g fill="#fff" text-anchor="middle" font-family="Verdana,Geneva,DejaVu Sans,sans-serif" text-rendering="geometricPrecision" font-size="110"><text aria-hidden="true" x="375" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="630">repo status</text><text x="375" y="140" transform="scale(.1)" fill="#fff" textLength="630">repo status</text><text aria-hidden="true" x="885" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="230">WIP</text><text x="885" y="140" transform="scale(.1)" fill="#fff" textLength="230">WIP</text></g></svg></a>
<a href="https://lifecycle.r-lib.org/articles/stages.html#experimental"><img role="img" aria-label="Lifecycle: experimental" src="data:image/svg+xml;charset=utf-8;base64,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" alt="Lifecycle: experimental" /></a> <a href="https://opensource.org/licenses/MIT"><img role="img" aria-label="License (for code): MIT" 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alt="License: CC-BY-4.0" /></a></p>
<!-- badges: end -->
<h3 id="openrvfcast">OpenRVFcast</h3>
<p>EcoHealth Alliance’s ongoing OpenRVFcast project is developing a
generalizable, open-source modeling framework for predicting Rift Valley
Fever (RVF) outbreaks in Africa, funded by the Wellcome Trust’s
climate-sensitive infectious disease <a href="https://wellcome.org/news/digital-tools-climate-sensitive-infectious-disease">modeling
initiative</a>. We aim to integrate open data sets of climatic and
vegetation data with internationally-reported outbreak data to build an
modeling pipeline that can be adapted to varying local conditions in
RVF-prone regions across the continent.</p>
<h3 id="repository-structure-and-reproducibility">Repository Structure
and Reproducibility</h3>
<ul>
<li><code>data/</code> contains downloaded and transformed data sources.
These data are .gitignored and non-EHA users will need to download the
data.</li>
<li><code>R/</code> contains functions used in this analysis.</li>
<li><code>reports/</code> contains literate code for R Markdown reports
generated in the analysis</li>
<li><code>outputs/</code> contains compiled reports and figures.</li>
<li>This project uses the <a href="https://rstudio.github.io/renv/">{renv}</a> framework to record R
package dependencies and versions. Packages and versions used are
recorded in <code>renv.lock</code> and code used to manage dependencies
is in <code>renv/</code> and other files in the root project directory.
On starting an R session in the working directory, run
<code>renv::restore()</code> to install R package dependencies.</li>
<li>This project uses the <a href="https://wlandau.github.io/targets-manual/">{targets}</a> framework
to organize build steps for analysis pipeline. The schematic figure
below summarizes the steps. (The figure is generated using
<code>mermaid.js</code> syntax and should display as a graph on GitHub.
It can also be viewed by pasting the code into <a href="https://mermaid.live">https://mermaid.live</a>.)</li>
</ul>
<p>Warning messages: 1: package ‘rmarkdown’ was built under R version
4.3.3 2: package ‘paws’ was built under R version 4.3.3 3: package
‘terra’ was built under R version 4.3.3</p>
<pre class="mermaid"><code>graph LR
subgraph Project Workflow
subgraph Graph
direction LR
x5130788afbe32544["modis_ndvi_transformed"]:::queued --> xddb5620937cdbc01(["nasa_weather_transformed_AWS_upload"]):::queued
xdc843e2504e22144(["modis_ndvi_transformed_directory"]):::skipped --> xddb5620937cdbc01(["nasa_weather_transformed_AWS_upload"]):::queued
xba6244832b5285ba(["continent_raster_template"]):::queued --> x3b5d33025a7856bb["ecmwf_forecasts_transformed"]:::queued
x73599238bfebd1c5(["ecmwf_forecasts_api_parameters"]):::queued --> x3b5d33025a7856bb["ecmwf_forecasts_transformed"]:::queued
x16ce463b7b647c1e(["ecmwf_forecasts_transformed_directory"]):::skipped --> x3b5d33025a7856bb["ecmwf_forecasts_transformed"]:::queued
x32725338020380f8(["get_ecmwf_forecasts_AWS"]):::queued --> x3b5d33025a7856bb["ecmwf_forecasts_transformed"]:::queued
x0381132b9136146c(["elevation_directory"]):::skipped --> xd9f5e6274aef515b(["elevation_preprocessed_AWS_upload"]):::queued
x0dffb1605751d1b1(["elevation_preprocessed"]):::queued --> xd9f5e6274aef515b(["elevation_preprocessed_AWS_upload"]):::queued
x24983cd244fff5db(["modis_ndvi_bundle_request_file"]):::queued --> xcfc776190ac6b73c(["modis_ndvi_bundle_request"]):::queued
xa5bc51cd67d5e6c0(["modis_ndvi_task_id_continent"]):::queued --> xcfc776190ac6b73c(["modis_ndvi_bundle_request"]):::queued
x3f3ba2f9e89a9591(["modis_ndvi_token"]):::completed --> xcfc776190ac6b73c(["modis_ndvi_bundle_request"]):::queued
xe3c4533ec81ef618(["continent_polygon"]):::skipped --> x39ef63e4c3553f78(["wahis_raster_template"]):::queued
xb06c08f4a8f21445(["lag_intervals"]):::skipped --> x8d58a79e9d066b5d(["ndvi_anomalies_AWS"]):::queued
xc61c34839fb8c873(["model_dates_selected"]):::queued --> x8d58a79e9d066b5d(["ndvi_anomalies_AWS"]):::queued
xe2329877730e44b5(["ndvi_anomalies_directory"]):::skipped --> x8d58a79e9d066b5d(["ndvi_anomalies_AWS"]):::queued
x92b237aaa434cba4(["ndvi_date_lookup"]):::queued --> x8d58a79e9d066b5d(["ndvi_anomalies_AWS"]):::queued
x44345ceb9b3d4a81["ndvi_historical_means"]:::queued --> x8d58a79e9d066b5d(["ndvi_anomalies_AWS"]):::queued
xba6244832b5285ba(["continent_raster_template"]):::queued --> x4110b36142c7dd5b(["soil_AWS"]):::queued
x9c14f0532ee1f83c(["soil_directory"]):::skipped --> x4110b36142c7dd5b(["soil_AWS"]):::queued
x3b5d33025a7856bb["ecmwf_forecasts_transformed"]:::queued --> x680f7450837c9229["forecasts_anomalies"]:::queued
x16ce463b7b647c1e(["ecmwf_forecasts_transformed_directory"]):::skipped --> x680f7450837c9229["forecasts_anomalies"]:::queued
x259885b5bdbd7dfc(["forecasts_anomalies_AWS"]):::queued --> x680f7450837c9229["forecasts_anomalies"]:::queued
x8ff15aa322c64802(["forecasts_anomalies_directory"]):::skipped --> x680f7450837c9229["forecasts_anomalies"]:::queued
x021b0407fd88c849(["lead_intervals"]):::skipped --> x680f7450837c9229["forecasts_anomalies"]:::queued
xc61c34839fb8c873(["model_dates_selected"]):::queued --> x680f7450837c9229["forecasts_anomalies"]:::queued
xbd6b5d8fe3154d5a["weather_historical_means"]:::queued --> x680f7450837c9229["forecasts_anomalies"]:::queued
x1f222a4448edddc4(["days_of_year"]):::skipped --> xbd6b5d8fe3154d5a["weather_historical_means"]:::queued
xb06c08f4a8f21445(["lag_intervals"]):::skipped --> xbd6b5d8fe3154d5a["weather_historical_means"]:::queued
x021b0407fd88c849(["lead_intervals"]):::skipped --> xbd6b5d8fe3154d5a["weather_historical_means"]:::queued
x0548e231345702f7["nasa_weather_transformed"]:::queued --> xbd6b5d8fe3154d5a["weather_historical_means"]:::queued
x711dc87df29f0a9c(["nasa_weather_transformed_directory"]):::skipped --> xbd6b5d8fe3154d5a["weather_historical_means"]:::queued
xce069f3121e32dfb(["weather_historical_means_AWS"]):::queued --> xbd6b5d8fe3154d5a["weather_historical_means"]:::queued
x4407a62768444c3e(["weather_historical_means_directory"]):::skipped --> xbd6b5d8fe3154d5a["weather_historical_means"]:::queued
x049b29595ee19108(["aspect_AWS"]):::queued --> x155e2f0b29a20e05(["aspect_preprocessed"]):::queued
x42a5375a64b48216(["aspect_directory"]):::skipped --> x155e2f0b29a20e05(["aspect_preprocessed"]):::queued
x213d1d2657d00cd0(["aspect_urls"]):::skipped --> x155e2f0b29a20e05(["aspect_preprocessed"]):::queued
xba6244832b5285ba(["continent_raster_template"]):::queued --> x155e2f0b29a20e05(["aspect_preprocessed"]):::queued
x1f222a4448edddc4(["days_of_year"]):::skipped --> x44345ceb9b3d4a81["ndvi_historical_means"]:::queued
xb06c08f4a8f21445(["lag_intervals"]):::skipped --> x44345ceb9b3d4a81["ndvi_historical_means"]:::queued
x92b237aaa434cba4(["ndvi_date_lookup"]):::queued --> x44345ceb9b3d4a81["ndvi_historical_means"]:::queued
x42d785b9e0106385(["ndvi_historical_means_AWS"]):::queued --> x44345ceb9b3d4a81["ndvi_historical_means"]:::queued
x7fef416d6ce259f3(["ndvi_historical_means_directory"]):::skipped --> x44345ceb9b3d4a81["ndvi_historical_means"]:::queued
xe8b8ca5535fe5f2a(["bioclim_directory"]):::skipped --> xe2930fde1049416f(["bioclim_AWS"]):::queued
xba6244832b5285ba(["continent_raster_template"]):::queued --> xe2930fde1049416f(["bioclim_AWS"]):::queued
xa33032ce29b67c7f(["wahis_distance_matrix"]):::queued --> x200daf9f58e96ac5(["wahis_outbreak_history_AWS"]):::queued
x50043477563454fd(["wahis_outbreak_dates"]):::queued --> x200daf9f58e96ac5(["wahis_outbreak_history_AWS"]):::queued
xcc02e30ec90a7edd(["wahis_outbreak_history_directory"]):::skipped --> x200daf9f58e96ac5(["wahis_outbreak_history_AWS"]):::queued
x659aa62eded9787b(["wahis_outbreaks"]):::queued --> x200daf9f58e96ac5(["wahis_outbreak_history_AWS"]):::queued
x39ef63e4c3553f78(["wahis_raster_template"]):::queued --> x200daf9f58e96ac5(["wahis_outbreak_history_AWS"]):::queued
xba6244832b5285ba(["continent_raster_template"]):::queued --> x955e49f3e0c22510(["landcover_AWS"]):::queued
x8894af119fe2eaa1(["landcover_directory"]):::skipped --> x955e49f3e0c22510(["landcover_AWS"]):::queued
x42a5375a64b48216(["aspect_directory"]):::skipped --> x7039ba6fde7353f3(["soil_preprocessed_AWS_upload"]):::queued
xd70b16641fa1b4ef(["soil_preprocessed"]):::queued --> x7039ba6fde7353f3(["soil_preprocessed_AWS_upload"]):::queued
xba6244832b5285ba(["continent_raster_template"]):::queued --> xa4eb23442420052a["sentinel_ndvi_transformed"]:::queued
xa9eddcdb0d1f1d02(["get_sentinel_ndvi_AWS"]):::queued --> xa4eb23442420052a["sentinel_ndvi_transformed"]:::queued
x6e1924e349d8e6e8(["sentinel_ndvi_api_parameters"]):::skipped --> xa4eb23442420052a["sentinel_ndvi_transformed"]:::queued
x3ea733d22e9c32e7(["sentinel_ndvi_transformed_directory"]):::skipped --> xa4eb23442420052a["sentinel_ndvi_transformed"]:::queued
xe3c4533ec81ef618(["continent_polygon"]):::skipped --> xba6244832b5285ba(["continent_raster_template"]):::queued
x97fc33c6215703a3(["rsa_polygon"]):::skipped --> x8367f94bdb991b08(["rsa_polygon_spatial_weights"]):::queued
x4847fdb918188b25(["country_polygons"]):::skipped --> x53c4b2fb80542353(["country_bounding_boxes"]):::queued
xb06c08f4a8f21445(["lag_intervals"]):::skipped --> xf9b79e824823a870["ndvi_anomalies"]:::queued
xc61c34839fb8c873(["model_dates_selected"]):::queued --> xf9b79e824823a870["ndvi_anomalies"]:::queued
x8d58a79e9d066b5d(["ndvi_anomalies_AWS"]):::queued --> xf9b79e824823a870["ndvi_anomalies"]:::queued
xe2329877730e44b5(["ndvi_anomalies_directory"]):::skipped --> xf9b79e824823a870["ndvi_anomalies"]:::queued
x92b237aaa434cba4(["ndvi_date_lookup"]):::queued --> xf9b79e824823a870["ndvi_anomalies"]:::queued
x44345ceb9b3d4a81["ndvi_historical_means"]:::queued --> xf9b79e824823a870["ndvi_anomalies"]:::queued
x3ea733d22e9c32e7(["sentinel_ndvi_transformed_directory"]):::skipped --> xa9eddcdb0d1f1d02(["get_sentinel_ndvi_AWS"]):::queued
x53c4b2fb80542353(["country_bounding_boxes"]):::queued --> xc54ffbea58c4afd9(["nasa_weather_coordinates"]):::queued
xa72a356ab8b0f2e4["forecasts_anomalies_validate"]:::queued --> x705cc9e765652376(["forecasts_anomalies_validate_AWS_upload"]):::queued
x309ea01959a83a5a(["forecasts_validate_directory"]):::skipped --> x705cc9e765652376(["forecasts_anomalies_validate_AWS_upload"]):::queued
xba6244832b5285ba(["continent_raster_template"]):::queued --> x5130788afbe32544["modis_ndvi_transformed"]:::queued
xcfc776190ac6b73c(["modis_ndvi_bundle_request"]):::queued --> x5130788afbe32544["modis_ndvi_transformed"]:::queued
x3f3ba2f9e89a9591(["modis_ndvi_token"]):::completed --> x5130788afbe32544["modis_ndvi_transformed"]:::queued
xf36f13d6d1345340(["modis_ndvi_transformed_AWS"]):::queued --> x5130788afbe32544["modis_ndvi_transformed"]:::queued
xdc843e2504e22144(["modis_ndvi_transformed_directory"]):::skipped --> x5130788afbe32544["modis_ndvi_transformed"]:::queued
x44345ceb9b3d4a81["ndvi_historical_means"]:::queued --> x1be60916d37ebe0f(["ndvi_historical_means_AWS_upload"]):::queued
x7fef416d6ce259f3(["ndvi_historical_means_directory"]):::skipped --> x1be60916d37ebe0f(["ndvi_historical_means_AWS_upload"]):::queued
xba6244832b5285ba(["continent_raster_template"]):::queued --> xdecc37cc7e708cec(["landcover_preprocessed"]):::queued
x955e49f3e0c22510(["landcover_AWS"]):::queued --> xdecc37cc7e708cec(["landcover_preprocessed"]):::queued
x8894af119fe2eaa1(["landcover_directory"]):::skipped --> xdecc37cc7e708cec(["landcover_preprocessed"]):::queued
x684d7fe78b0e841d(["landcover_types"]):::skipped --> xdecc37cc7e708cec(["landcover_preprocessed"]):::queued
xba6244832b5285ba(["continent_raster_template"]):::queued --> x32725338020380f8(["get_ecmwf_forecasts_AWS"]):::queued
x73599238bfebd1c5(["ecmwf_forecasts_api_parameters"]):::queued --> x32725338020380f8(["get_ecmwf_forecasts_AWS"]):::queued
x16ce463b7b647c1e(["ecmwf_forecasts_transformed_directory"]):::skipped --> x32725338020380f8(["get_ecmwf_forecasts_AWS"]):::queued
xba6244832b5285ba(["continent_raster_template"]):::queued --> x0dffb1605751d1b1(["elevation_preprocessed"]):::queued
x98b1351d966647f6(["elevation_AWS"]):::queued --> x0dffb1605751d1b1(["elevation_preprocessed"]):::queued
x0381132b9136146c(["elevation_directory"]):::skipped --> x0dffb1605751d1b1(["elevation_preprocessed"]):::queued
x5130788afbe32544["modis_ndvi_transformed"]:::queued --> xe90a7836ba709288(["modis_ndvi_transformed_AWS_upload"]):::queued
xdc843e2504e22144(["modis_ndvi_transformed_directory"]):::skipped --> xe90a7836ba709288(["modis_ndvi_transformed_AWS_upload"]):::queued
xb06c08f4a8f21445(["lag_intervals"]):::skipped --> x01b9e03cb52b7b05["weather_anomalies"]:::queued
xc61c34839fb8c873(["model_dates_selected"]):::queued --> x01b9e03cb52b7b05["weather_anomalies"]:::queued
x0548e231345702f7["nasa_weather_transformed"]:::queued --> x01b9e03cb52b7b05["weather_anomalies"]:::queued
x711dc87df29f0a9c(["nasa_weather_transformed_directory"]):::skipped --> x01b9e03cb52b7b05["weather_anomalies"]:::queued
x0df1395319c2f010(["weather_anomalies_AWS"]):::queued --> x01b9e03cb52b7b05["weather_anomalies"]:::queued
xf94f7486eed9869c(["weather_anomalies_directory"]):::skipped --> x01b9e03cb52b7b05["weather_anomalies"]:::queued
xbd6b5d8fe3154d5a["weather_historical_means"]:::queued --> x01b9e03cb52b7b05["weather_anomalies"]:::queued
xe8b8ca5535fe5f2a(["bioclim_directory"]):::skipped --> xe4be5b46895c0f8c(["bioclim_preprocessed_AWS_upload"]):::queued
x1c7b6e6a1c101e59(["bioclim_preprocessed"]):::queued --> xe4be5b46895c0f8c(["bioclim_preprocessed_AWS_upload"]):::queued
x680f7450837c9229["forecasts_anomalies"]:::queued --> xa72a356ab8b0f2e4["forecasts_anomalies_validate"]:::queued
xcc18535b953bde28(["forecasts_anomalies_validate_AWS"]):::queued --> xa72a356ab8b0f2e4["forecasts_anomalies_validate"]:::queued
x309ea01959a83a5a(["forecasts_validate_directory"]):::skipped --> xa72a356ab8b0f2e4["forecasts_anomalies_validate"]:::queued
x021b0407fd88c849(["lead_intervals"]):::skipped --> xa72a356ab8b0f2e4["forecasts_anomalies_validate"]:::queued
xc61c34839fb8c873(["model_dates_selected"]):::queued --> xa72a356ab8b0f2e4["forecasts_anomalies_validate"]:::queued
x0548e231345702f7["nasa_weather_transformed"]:::queued --> xa72a356ab8b0f2e4["forecasts_anomalies_validate"]:::queued
xbd6b5d8fe3154d5a["weather_historical_means"]:::queued --> xa72a356ab8b0f2e4["forecasts_anomalies_validate"]:::queued
x3b5d33025a7856bb["ecmwf_forecasts_transformed"]:::queued --> x259885b5bdbd7dfc(["forecasts_anomalies_AWS"]):::queued
x8ff15aa322c64802(["forecasts_anomalies_directory"]):::skipped --> x259885b5bdbd7dfc(["forecasts_anomalies_AWS"]):::queued
x021b0407fd88c849(["lead_intervals"]):::skipped --> x259885b5bdbd7dfc(["forecasts_anomalies_AWS"]):::queued
xc61c34839fb8c873(["model_dates_selected"]):::queued --> x259885b5bdbd7dfc(["forecasts_anomalies_AWS"]):::queued
xbd6b5d8fe3154d5a["weather_historical_means"]:::queued --> x259885b5bdbd7dfc(["forecasts_anomalies_AWS"]):::queued
x1f222a4448edddc4(["days_of_year"]):::skipped --> xce069f3121e32dfb(["weather_historical_means_AWS"]):::queued
xb06c08f4a8f21445(["lag_intervals"]):::skipped --> xce069f3121e32dfb(["weather_historical_means_AWS"]):::queued
x021b0407fd88c849(["lead_intervals"]):::skipped --> xce069f3121e32dfb(["weather_historical_means_AWS"]):::queued
x0548e231345702f7["nasa_weather_transformed"]:::queued --> xce069f3121e32dfb(["weather_historical_means_AWS"]):::queued
x4407a62768444c3e(["weather_historical_means_directory"]):::skipped --> xce069f3121e32dfb(["weather_historical_means_AWS"]):::queued
x6bae1f342f811d0b(["wahis_rvf_controls_raw"]):::skipped --> x2668bdb7843be979(["wahis_rvf_controls_preprocessed"]):::queued
x165085d61327782d(["slope_directory"]):::skipped --> x5aa9efa15ecd03d0(["slope_preprocessed_AWS_upload"]):::queued
x680370f9b58b9f6d(["slope_preprocessed"]):::queued --> x5aa9efa15ecd03d0(["slope_preprocessed_AWS_upload"]):::queued
xdc843e2504e22144(["modis_ndvi_transformed_directory"]):::skipped --> x24983cd244fff5db(["modis_ndvi_bundle_request_file"]):::queued
xb49d77ffc5b097ae(["continent_bounding_box"]):::queued --> x73599238bfebd1c5(["ecmwf_forecasts_api_parameters"]):::queued
x680f7450837c9229["forecasts_anomalies"]:::queued --> x72d065c3b2ed1267(["forecasts_anomalies_AWS_upload"]):::queued
x8ff15aa322c64802(["forecasts_anomalies_directory"]):::skipped --> x72d065c3b2ed1267(["forecasts_anomalies_AWS_upload"]):::queued
xa4eb23442420052a["sentinel_ndvi_transformed"]:::queued --> x6db823df8cb78984(["sentinel_ndvi_transformed_AWS_upload"]):::queued
x3ea733d22e9c32e7(["sentinel_ndvi_transformed_directory"]):::skipped --> x6db823df8cb78984(["sentinel_ndvi_transformed_AWS_upload"]):::queued
xba6244832b5285ba(["continent_raster_template"]):::queued --> xd70b16641fa1b4ef(["soil_preprocessed"]):::queued
x4110b36142c7dd5b(["soil_AWS"]):::queued --> xd70b16641fa1b4ef(["soil_preprocessed"]):::queued
x9c14f0532ee1f83c(["soil_directory"]):::skipped --> xd70b16641fa1b4ef(["soil_preprocessed"]):::queued
xe8b8ca5535fe5f2a(["bioclim_directory"]):::skipped --> x1c7b6e6a1c101e59(["bioclim_preprocessed"]):::queued
xba6244832b5285ba(["continent_raster_template"]):::queued --> x1c7b6e6a1c101e59(["bioclim_preprocessed"]):::queued
xba6244832b5285ba(["continent_raster_template"]):::queued --> x71c93c84792ad529(["glw_AWS"]):::queued
x5448b80c3909d641(["glw_directory"]):::skipped --> x71c93c84792ad529(["glw_AWS"]):::queued
x42a5375a64b48216(["aspect_directory"]):::skipped --> x890a8fc59a28f6b2(["slope_AWS"]):::queued
xba6244832b5285ba(["continent_raster_template"]):::queued --> x890a8fc59a28f6b2(["slope_AWS"]):::queued
xba6244832b5285ba(["continent_raster_template"]):::queued --> x680370f9b58b9f6d(["slope_preprocessed"]):::queued
x890a8fc59a28f6b2(["slope_AWS"]):::queued --> x680370f9b58b9f6d(["slope_preprocessed"]):::queued
x165085d61327782d(["slope_directory"]):::skipped --> x680370f9b58b9f6d(["slope_preprocessed"]):::queued
x1ef0d1881ff89dbd(["slope_urls"]):::skipped --> x680370f9b58b9f6d(["slope_preprocessed"]):::queued
xba6244832b5285ba(["continent_raster_template"]):::queued --> xf36f13d6d1345340(["modis_ndvi_transformed_AWS"]):::queued
xcfc776190ac6b73c(["modis_ndvi_bundle_request"]):::queued --> xf36f13d6d1345340(["modis_ndvi_transformed_AWS"]):::queued
x3f3ba2f9e89a9591(["modis_ndvi_token"]):::completed --> xf36f13d6d1345340(["modis_ndvi_transformed_AWS"]):::queued
xdc843e2504e22144(["modis_ndvi_transformed_directory"]):::skipped --> xf36f13d6d1345340(["modis_ndvi_transformed_AWS"]):::queued
x2b83f10567783884(["wahis_rvf_outbreaks_preprocessed"]):::queued --> x50043477563454fd(["wahis_outbreak_dates"]):::queued
xa33032ce29b67c7f(["wahis_distance_matrix"]):::queued --> x27dbf0f2484063f3["wahis_outbreak_history"]:::queued
x50043477563454fd(["wahis_outbreak_dates"]):::queued --> x27dbf0f2484063f3["wahis_outbreak_history"]:::queued
x200daf9f58e96ac5(["wahis_outbreak_history_AWS"]):::queued --> x27dbf0f2484063f3["wahis_outbreak_history"]:::queued
xcc02e30ec90a7edd(["wahis_outbreak_history_directory"]):::skipped --> x27dbf0f2484063f3["wahis_outbreak_history"]:::queued
x659aa62eded9787b(["wahis_outbreaks"]):::queued --> x27dbf0f2484063f3["wahis_outbreak_history"]:::queued
x39ef63e4c3553f78(["wahis_raster_template"]):::queued --> x27dbf0f2484063f3["wahis_outbreak_history"]:::queued
xe3c4533ec81ef618(["continent_polygon"]):::skipped --> xb49d77ffc5b097ae(["continent_bounding_box"]):::queued
x50d291d42ebde68c(["combined_anomalies_directory"]):::skipped --> x439c9f5bc1e96cd5(["combined_anomalies_AWS"]):::queued
xc61c34839fb8c873(["model_dates_selected"]):::queued --> x439c9f5bc1e96cd5(["combined_anomalies_AWS"]):::queued
xf9b79e824823a870["ndvi_anomalies"]:::queued --> x439c9f5bc1e96cd5(["combined_anomalies_AWS"]):::queued
x01b9e03cb52b7b05["weather_anomalies"]:::queued --> x439c9f5bc1e96cd5(["combined_anomalies_AWS"]):::queued
xf9b79e824823a870["ndvi_anomalies"]:::queued --> x144f59a0db036a4b(["ndvi_anomalies_AWS_upload"]):::queued
xe2329877730e44b5(["ndvi_anomalies_directory"]):::skipped --> x144f59a0db036a4b(["ndvi_anomalies_AWS_upload"]):::queued
x680f7450837c9229["forecasts_anomalies"]:::queued --> xcc18535b953bde28(["forecasts_anomalies_validate_AWS"]):::queued
x309ea01959a83a5a(["forecasts_validate_directory"]):::skipped --> xcc18535b953bde28(["forecasts_anomalies_validate_AWS"]):::queued
x021b0407fd88c849(["lead_intervals"]):::skipped --> xcc18535b953bde28(["forecasts_anomalies_validate_AWS"]):::queued
xc61c34839fb8c873(["model_dates_selected"]):::queued --> xcc18535b953bde28(["forecasts_anomalies_validate_AWS"]):::queued
x0548e231345702f7["nasa_weather_transformed"]:::queued --> xcc18535b953bde28(["forecasts_anomalies_validate_AWS"]):::queued
xbd6b5d8fe3154d5a["weather_historical_means"]:::queued --> xcc18535b953bde28(["forecasts_anomalies_validate_AWS"]):::queued
x27dbf0f2484063f3["wahis_outbreak_history"]:::queued --> x53890e32519c2cdc(["wahis_outbreak_history_AWS_upload"]):::queued
x338ce62055c4090f(["wahis_outbreak_history_animations_directory"]):::skipped --> x53890e32519c2cdc(["wahis_outbreak_history_AWS_upload"]):::queued
xba6244832b5285ba(["continent_raster_template"]):::queued --> x0548e231345702f7["nasa_weather_transformed"]:::queued
x84fbc80b775022e1(["nasa_weather_AWS"]):::queued --> x0548e231345702f7["nasa_weather_transformed"]:::queued
xc54ffbea58c4afd9(["nasa_weather_coordinates"]):::queued --> x0548e231345702f7["nasa_weather_transformed"]:::queued
x711dc87df29f0a9c(["nasa_weather_transformed_directory"]):::skipped --> x0548e231345702f7["nasa_weather_transformed"]:::queued
x0c2748f0f39a3907(["nasa_weather_years"]):::skipped --> x0548e231345702f7["nasa_weather_transformed"]:::queued
x3b5d33025a7856bb["ecmwf_forecasts_transformed"]:::queued --> xe017ffc3bafa162a(["ecmwf_forecasts_transformed_AWS_upload"]):::queued
x16ce463b7b647c1e(["ecmwf_forecasts_transformed_directory"]):::skipped --> xe017ffc3bafa162a(["ecmwf_forecasts_transformed_AWS_upload"]):::queued
x2b83f10567783884(["wahis_rvf_outbreaks_preprocessed"]):::queued --> x659aa62eded9787b(["wahis_outbreaks"]):::queued
xb49d77ffc5b097ae(["continent_bounding_box"]):::queued --> xa5bc51cd67d5e6c0(["modis_ndvi_task_id_continent"]):::queued
x3f3ba2f9e89a9591(["modis_ndvi_token"]):::completed --> xa5bc51cd67d5e6c0(["modis_ndvi_task_id_continent"]):::queued
x16e1cc582647deec["wahis_outbreak_history_animations"]:::queued --> x3a8830b5def8250b(["wahis_outbreak_history_animations_AWS_upload"]):::queued
x338ce62055c4090f(["wahis_outbreak_history_animations_directory"]):::skipped --> x3a8830b5def8250b(["wahis_outbreak_history_animations_AWS_upload"]):::queued
x5448b80c3909d641(["glw_directory"]):::skipped --> x01e625a4f1dd2c42(["glw_preprocessed_AWS_upload"]):::queued
x82990a83bfa4db45(["glw_preprocessed"]):::queued --> x01e625a4f1dd2c42(["glw_preprocessed_AWS_upload"]):::queued
xc61c34839fb8c873(["model_dates_selected"]):::queued --> xcfd8f1e8f3ea9117["aggregated_data_rsa"]:::queued
x97fc33c6215703a3(["rsa_polygon"]):::skipped --> xcfd8f1e8f3ea9117["aggregated_data_rsa"]:::queued
x1f222a4448edddc4(["days_of_year"]):::skipped --> x42d785b9e0106385(["ndvi_historical_means_AWS"]):::queued
xb06c08f4a8f21445(["lag_intervals"]):::skipped --> x42d785b9e0106385(["ndvi_historical_means_AWS"]):::queued
x92b237aaa434cba4(["ndvi_date_lookup"]):::queued --> x42d785b9e0106385(["ndvi_historical_means_AWS"]):::queued
x7fef416d6ce259f3(["ndvi_historical_means_directory"]):::skipped --> x42d785b9e0106385(["ndvi_historical_means_AWS"]):::queued
x5130788afbe32544["modis_ndvi_transformed"]:::queued --> x92b237aaa434cba4(["ndvi_date_lookup"]):::queued
xa4eb23442420052a["sentinel_ndvi_transformed"]:::queued --> x92b237aaa434cba4(["ndvi_date_lookup"]):::queued
x659aa62eded9787b(["wahis_outbreaks"]):::queued --> xa33032ce29b67c7f(["wahis_distance_matrix"]):::queued
x39ef63e4c3553f78(["wahis_raster_template"]):::queued --> xa33032ce29b67c7f(["wahis_distance_matrix"]):::queued
x27dbf0f2484063f3["wahis_outbreak_history"]:::queued --> x16e1cc582647deec["wahis_outbreak_history_animations"]:::queued
x338ce62055c4090f(["wahis_outbreak_history_animations_directory"]):::skipped --> x16e1cc582647deec["wahis_outbreak_history_animations"]:::queued
x27dbf0f2484063f3["wahis_outbreak_history"]:::queued --> x2b50e7687b4412ab(["wahis_outbreak_history_animations_AWS"]):::queued
x338ce62055c4090f(["wahis_outbreak_history_animations_directory"]):::skipped --> x2b50e7687b4412ab(["wahis_outbreak_history_animations_AWS"]):::queued
x8894af119fe2eaa1(["landcover_directory"]):::skipped --> xbc982b2f29054bd9(["landcover_preprocessed_AWS_upload"]):::queued
xdecc37cc7e708cec(["landcover_preprocessed"]):::queued --> xbc982b2f29054bd9(["landcover_preprocessed_AWS_upload"]):::queued
x42a5375a64b48216(["aspect_directory"]):::skipped --> xfe5a910dc093a019(["aspect_preprocessed_AWS_upload"]):::queued
x155e2f0b29a20e05(["aspect_preprocessed"]):::queued --> xfe5a910dc093a019(["aspect_preprocessed_AWS_upload"]):::queued
x439c9f5bc1e96cd5(["combined_anomalies_AWS"]):::queued --> xfde5ff2681c50d89(["combined_anomalies"]):::queued
x50d291d42ebde68c(["combined_anomalies_directory"]):::skipped --> xfde5ff2681c50d89(["combined_anomalies"]):::queued
x680f7450837c9229["forecasts_anomalies"]:::queued --> xfde5ff2681c50d89(["combined_anomalies"]):::queued
xf9b79e824823a870["ndvi_anomalies"]:::queued --> xfde5ff2681c50d89(["combined_anomalies"]):::queued
x01b9e03cb52b7b05["weather_anomalies"]:::queued --> xfde5ff2681c50d89(["combined_anomalies"]):::queued
x42a5375a64b48216(["aspect_directory"]):::skipped --> x049b29595ee19108(["aspect_AWS"]):::queued
xba6244832b5285ba(["continent_raster_template"]):::queued --> x049b29595ee19108(["aspect_AWS"]):::queued
x9c9060069417a49a(["wahis_rvf_outbreaks_raw"]):::skipped --> x2b83f10567783884(["wahis_rvf_outbreaks_preprocessed"]):::queued
xfde5ff2681c50d89(["combined_anomalies"]):::queued --> xba5d6169ff0233fa(["combined_anomalies_AWS_upload"]):::queued
x50d291d42ebde68c(["combined_anomalies_directory"]):::skipped --> xba5d6169ff0233fa(["combined_anomalies_AWS_upload"]):::queued
xba6244832b5285ba(["continent_raster_template"]):::queued --> x82990a83bfa4db45(["glw_preprocessed"]):::queued
x71c93c84792ad529(["glw_AWS"]):::queued --> x82990a83bfa4db45(["glw_preprocessed"]):::queued
x5448b80c3909d641(["glw_directory"]):::skipped --> x82990a83bfa4db45(["glw_preprocessed"]):::queued
x4d4a15b2f0f1851f(["glw_urls"]):::skipped --> x82990a83bfa4db45(["glw_preprocessed"]):::queued
xba6244832b5285ba(["continent_raster_template"]):::queued --> x98b1351d966647f6(["elevation_AWS"]):::queued
x0381132b9136146c(["elevation_directory"]):::skipped --> x98b1351d966647f6(["elevation_AWS"]):::queued
xb06c08f4a8f21445(["lag_intervals"]):::skipped --> xc61c34839fb8c873(["model_dates_selected"]):::queued
x01b9e03cb52b7b05["weather_anomalies"]:::queued --> xc567f473073bf453(["weather_anomalies_AWS_upload"]):::queued
xf94f7486eed9869c(["weather_anomalies_directory"]):::skipped --> xc567f473073bf453(["weather_anomalies_AWS_upload"]):::queued
xbd6b5d8fe3154d5a["weather_historical_means"]:::queued --> xf8b72b30842f6a3c(["weather_historical_means_AWS_upload"]):::queued
x4407a62768444c3e(["weather_historical_means_directory"]):::skipped --> xf8b72b30842f6a3c(["weather_historical_means_AWS_upload"]):::queued
xba6244832b5285ba(["continent_raster_template"]):::queued --> x84fbc80b775022e1(["nasa_weather_AWS"]):::queued
xc54ffbea58c4afd9(["nasa_weather_coordinates"]):::queued --> x84fbc80b775022e1(["nasa_weather_AWS"]):::queued
x711dc87df29f0a9c(["nasa_weather_transformed_directory"]):::skipped --> x84fbc80b775022e1(["nasa_weather_AWS"]):::queued
x0c2748f0f39a3907(["nasa_weather_years"]):::skipped --> x84fbc80b775022e1(["nasa_weather_AWS"]):::queued
xb06c08f4a8f21445(["lag_intervals"]):::skipped --> x0df1395319c2f010(["weather_anomalies_AWS"]):::queued
xc61c34839fb8c873(["model_dates_selected"]):::queued --> x0df1395319c2f010(["weather_anomalies_AWS"]):::queued
x0548e231345702f7["nasa_weather_transformed"]:::queued --> x0df1395319c2f010(["weather_anomalies_AWS"]):::queued
xf94f7486eed9869c(["weather_anomalies_directory"]):::skipped --> x0df1395319c2f010(["weather_anomalies_AWS"]):::queued
xbd6b5d8fe3154d5a["weather_historical_means"]:::queued --> x0df1395319c2f010(["weather_anomalies_AWS"]):::queued
x30a742f54b518a5f(["augmented_data_rsa_directory"]):::skipped --> x30a742f54b518a5f(["augmented_data_rsa_directory"]):::skipped
xdc94d22b863438a5(["nasa_weather_variables"]):::skipped --> xdc94d22b863438a5(["nasa_weather_variables"]):::skipped
end
linkStyle 0 stroke-width:0px;</code></pre>
<p>Many of the computational steps can be time consuming and either
depend on or produce large files. In order to speed up the pipeline,
intermediate files can be stored on the cloud for rapid retrieval and
portability between pipeline instances. We currently use an AWS <a href="https://aws.amazon.com/s3/">S3 bucket</a> for this purpose. The
pipeline will still run without access to cloud storage but the user can
benefit from adapt the <code>_targets.R</code> file to use their own
object storage repository. AWS access keys and bucket ID are stored in
the <code>.env</code> file.</p>
<p>For handling gridded binary weather data, this pipeline uses the <a href="https://confluence.ecmwf.int/display/ECC">ecCodes</a> package
which can be installed on OSX using <code>homebrew</code>:</p>
<pre><code>brew install eccodes</code></pre>
<p>and on Ubuntu using apt-get</p>
<pre><code>sudo apt update
sudo apt install eccodes</code></pre>
<p>EHA users: see the <code>stripts/</code> repository to be able to
directly download data from AWS outside of the targets workflow.</p>
<p>Follow the links for more information about:</p>
<ul>
<li><a href="https://ecohealthalliance.github.io/eha-ma-handbook/3-projects.html#targets"><code>targets</code></a></li>
<li><a href="https://ecohealthalliance.github.io/eha-ma-handbook/3-projects.html#package-management-with-renv"><code>renv</code></a></li>
<li><a href="https://ecohealthalliance.github.io/eha-ma-handbook/16-encryption.html">git-crypt</a></li>
<li><a href="https://github.com/ecohealthalliance/building-blocks-of-reproducibility">Reproducible
workflows</a></li>
</ul>
</body>
</html>