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cjabradshaw authored Nov 19, 2024
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Expand Up @@ -33,8 +33,8 @@ Fatima, SH, MA Judge, PN Le Souëf, CJA Bradshaw. Impact of climate change on di
- <code>DHSDiarrAnalysis.R</code>: R code to reproduce the resampled boosted regression tree analysis for determining the relationships between probability of diarrhoea, and socio-economic, maternal, child, climate data (full dataset).
- <code>DHSDiarrAnalysisIndaOnly.R</code>: R code to reproduce the resampled boosted regression tree analysis for determining the relationships between probability of diarrhoea, and socio-economic, maternal, child, climate data (India only).

## <a href="https://github.com/cjabradshaw/childDiarr/tree/main/data/brtdata">Data</a>
- <em>DHSclusterLevelDiarrData.csv.zst</em>: <a href="https://dhsprogram.com/data/">Demographic and Health Surveys</a> data summarised by cluster with central parameter (mean, proportion, etc.) and variance per cluster. Overlaid (cluster-level) climate data derived from <a href="https://www.worldclim.org/">WorldClim</a> <a href="https://www.worldclim.org/data/bioclim.html">bioclimatic variables</a> (mean annual temperature, temperature annual range, total annual precipitation, precipitation seasonality, and precipitation of the driest quarter). Unzip .csv data file prior to analysis. The file is a high-compression .zst of the .csv base file; use the following command in Terminal to decompress: <code>zstd -d 'DHSclusterLevelDiarrData.csv.zst'</code>
## Data
- <em>DHSclusterLevelDiarrData.csv.zst</em>: <a href="https://dhsprogram.com/data/">Demographic and Health Surveys</a> data summarised by cluster with central parameter (mean, proportion, etc.) and variance per cluster. Overlaid (cluster-level) climate data derived from <a href="https://www.worldclim.org/">WorldClim</a> <a href="https://www.worldclim.org/data/bioclim.html">bioclimatic variables</a> (mean annual temperature, temperature annual range, total annual precipitation, precipitation seasonality, and precipitation of the driest quarter). Unzip .csv data file prior to analysis. The file is a high-compression .zst of the .csv base file; use the following command in Terminal to decompress: <code>zstd -d 'DHSclusterLevelDiarrData.csv.zst'</code>. Due to licencing constraints, we are not permitted to post the summarised (cluster-level) data here.

## Required R libraries
- <code>cowplot</code>, <code>dismo</code>, <code>dplyr</code>, <code>foreign</code>, <code>gbm</code>, <code>GGally</code>, <code>ggplot2</code>, <code>ggpubr</code>, <code>gridExtra</code>, <code>haven</code>, <code>leaflet</code>, <code>mice</code>, <code>raster</code>, <code>reshape2</code>, <code>sf</code>, <code>sp</code>, <code>spatstat.random</code>, <code>tidyr</code>, <code>truncnorm</code>, <code>usdm</code>
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