update to est_mobility output, init vignettes

.Rbuildignore

@@ -6,3 +6,4 @@ model/
 src/
 docs/
 pkgdown/
+^vignettes/articles$

DESCRIPTION

@@ -58,3 +58,4 @@ Depends:
   grDevices,
   utils,
   methods
+Config/Needs/website: rmarkdown

R/est_WASH_coverage.R

@@ -297,25 +297,28 @@ est_WASH_coverage <- function(PATHS) {
      print(weights_table)
 
 
-     path1 <- file.path(PATHS$MODEL_INPUT, "WASH_data_weights.csv")
-     path2 <- file.path(PATHS$DOCS_TABLES, "WASH_data_weights.csv")
-
-     write.csv(weights_table, file=path1, row.names = FALSE)
-     write.csv(weights_table, file=path2, row.names = FALSE)
-
+     path <- file.path(PATHS$DOCS_TABLES, "WASH_data_weights.csv")
+     write.csv(weights_table, file=path, row.names = FALSE)
      message("WASH weights table saved here:")
-     message(path1)
-     message(path2)
+     message(path)
+
 
 
+     param_df <- make_param_df(variable_name = 'theta',
+                               variable_description = 'WASH coverage',
+                               parameter_distribution = 'point',
+                               j = wash_data$iso_code,
+                               parameter_name = 'mean',
+                               parameter_value = wash_data$Weighted_Mean_WASH)
 
-     wash_weight_mean <- wash_data[,c("Country", "iso_code", "Weighted_Mean_WASH")]
 
-     path1 <- file.path(PATHS$MODEL_INPUT, "WASH_weighted_mean_theta.csv")
+     path1 <- file.path(PATHS$MODEL_INPUT, "param_theta_WASH.csv")
      path2 <- file.path(PATHS$DOCS_TABLES, "WASH_weighted_mean_theta.csv")
 
-     write.csv(wash_weight_mean, file=path1, row.names = FALSE)
-     write.csv(wash_weight_mean, file=path2, row.names = FALSE)
+     write.csv(param_df, file=path1, row.names = FALSE)
+
+     write.csv(wash_data[,c("Country", "iso_code", "Weighted_Mean_WASH")],
+               file=path2, row.names = FALSE)
 
      message("WASH weighted mean (tau) saved here:")
      message(path1)

R/est_mobility.R

@@ -167,21 +167,17 @@ est_mobility <- function(PATHS) {
      param_df_point <- make_param_df(
           variable_name = "tau",  # Assuming 'tau' represents travel probabilities
           variable_description = "Country-level travel probabilities",
-          parameter_distribution = "beta",
-          i = df_travel_prob$iso_code,  # i is set to the iso_code
-          j = NA,             # j is not applicable in this case
-          t = NA,             # t is not applicable in this case
-          parameter_name = "point",
+          parameter_distribution = "point",
+          i = df_travel_prob$iso_code,
+          parameter_name = "mean",
           parameter_value = df_travel_prob$mean
      )
 
      param_df_stoch <- make_param_df(
           variable_name = "tau",  # Assuming 'tau' represents travel probabilities
           variable_description = "Country-level travel probabilities",
           parameter_distribution = "beta",
-          i = df_travel_prob$iso_code,  # i is set to the iso_code
-          j = NA,             # j is not applicable in this case
-          t = NA,             # t is not applicable in this case
+          i = df_travel_prob$iso_code,
           parameter_name = c(rep("shape1", nrow(df_travel_prob)), rep("shape2", nrow(df_travel_prob))),
           parameter_value = c(df_travel_prob$shape1, df_travel_prob$shape2)
      )
@@ -190,12 +186,26 @@ est_mobility <- function(PATHS) {
      param_df <- param_df[order(param_df$i),]
 
      utils::write.csv(param_df, file.path(PATHS$MODEL_INPUT, "param_tau_departure.csv"), row.names = FALSE)
-     utils::write.csv(mod_mobility_summary, file.path(PATHS$MODEL_INPUT, "param_diffusion_model.csv"), row.names = TRUE)
 
+     tmp <- melt(pi)
+
+     param_df <- make_param_df(
+          variable_name = "pi",  # Assuming 'tau' represents travel probabilities
+          variable_description = "Probability of travel from i to j",
+          parameter_distribution = "point",
+          i = tmp$origin,
+          j = tmp$destination,
+          parameter_name = 'mean',
+          parameter_value = tmp$value
+     )
+
+     utils::write.csv(param_df, file.path(PATHS$MODEL_INPUT, "param_pi_diffusion.csv"), row.names = FALSE)
+
+
+     #utils::write.csv(mod_mobility_summary, file.path(PATHS$MODEL_INPUT, "param_diffusion_model.csv"), row.names = TRUE)
 
-     utils::write.csv(df_travel_prob[,c("country", "iso_code", "mean", "sd", "ci_lo", "ci_hi")],
-                      file.path(PATHS$MODEL_INPUT, "pred_tau_departure.csv"), row.names = FALSE)
-     utils::write.csv(melt(pi), file.path(PATHS$MODEL_INPUT, "pred_pi_diffusion.csv"), row.names = FALSE)
+     #utils::write.csv(df_travel_prob[,c("country", "iso_code", "mean", "sd", "ci_lo", "ci_hi")],
+     #                 file.path(PATHS$MODEL_INPUT, "pred_tau_departure.csv"), row.names = FALSE)
 
 
      message("Mobility model fitting complete.")

docs/_pkgdown.yml

@@ -27,8 +27,10 @@ navbar:
   - text: Vignettes
     href: articles/index.html
     menu:
+      - text: Project setup
+        href: articles/Project-setup.html
       - text: Running MOSAIC
-        href: articles/LAUNCH.html
+        href: articles/Running-MOSAIC.html
   right:
   - icon: fa-github
     href: https://github.com/InstituteforDiseaseModeling/MOSAIC-pkg