Merge pull request #13 from IDEELResearch/feature/mock_stave_prevalence

added example data and script to produce stave object and save to file

analysis/make_example_stave_output.R

@@ -0,0 +1,38 @@
+# make_example_stave_output.R
+#
+# Author: Bob Verity
+# Date: 2024-09-24
+#
+# Inputs: analysis/data/mock_stave.xlsx
+#
+# Outputs: analysis/data_derived/mock_stave_prevalence.rds
+#
+# Purpose:
+# Creates example STAVE output. Reads in example data, converts to stave,
+# calculates prevalence and saves to file.
+#
+# ------------------------------------------------------------------
+
+# install STAVE
+#devtools::install_github("mrc-ide/STAVE")
+library(STAVE)
+
+# import mock data
+file_path <- "analysis/data/mock_stave.xlsx"
+input_studies <- readxl::read_excel(file_path, sheet = "studies")
+input_surveys <- readxl::read_excel(file_path, sheet = "surveys")
+input_counts <- readxl::read_excel(file_path, sheet = "counts")
+
+# load into STAVE
+s <- STAVE_object$new()
+s$append_data(studies_dataframe = input_studies,
+              surveys_dataframe = input_surveys,
+              counts_dataframe = input_counts)
+
+# get prevalence
+p <- s$get_prevalence("crt:72:C")
+
+# save to file
+if (FALSE) {
+  saveRDS(p, file = "analysis/data_derived/mock_stave_prevalence.rds")
+}