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Code associated with Wood et al. 2019. "Precision mapping of snail habitat provides a powerful indicator of human schistosomiasis transmission." Proceedings of the National Academy of Sciences of the USA.
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README.md

Wood et al. 2019 PNAS

Code associated with Wood et al. 2019. "Precision mapping of snail habitat provides a powerful indicator of human schistosomiasis transmission." Proceedings of the National Academy of Sciences of the USA. https://doi.org/10.1073/pnas.1903698116. https://www.pnas.org/content/early/2019/10/22/1903698116.

This code refers to three datasets: one on the abundance and distribution of snails, which is available in its complete form (snail_data.csv), another on snail clusters as detected by SatScan software (cluster_data.csv), and another on the distribution of infection in people and the village-level habitat factors that predict those infections (summary_human_and_habitat_data.csv). Human data have been anonymized to protect patient privacy. In order to de-identify data, we present summary statistics for human infection at the level of village-year-class-sex. Anonymized data at the individual level may be released on a case-by-case basis. To discuss the possibility of obtaining anonymized data at the individual level, please contact the corresponding author, Chelsea Wood, at chelwood@uw.edu.

Because we can provide only de-identified (i.e., summarized) human infection data, some of the code herein refers to an individual-level dataset that is not provided. We hope that this code allows interested readers to understand each step of our analysis, even though they will not be able to re-create the analyses of human infection without the original dataset.

Data are available in this repository, and are also permanently archived in Dryad:

Wood, Chelsea et al. (2019), Precision mapping of snail habitat provides a powerful indicator of human schistosomiasis transmission, Dryad, Dataset, https://doi.org/10.5061/dryad.djh9w0vvt

Note that metadata files are provided for all of the data files (snail_data_metadata.csv, cluster_data_metadata.csv, and summary_human_and_habitat_data_metadata.csv).

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