Merge pull request #549 from HopkinsIDD/dev_undo_set_precision

remove set precision
HopkinsIDD · Oct 2, 2023 · 2e538f9 · 2e538f9
2 parents 8e822e7 + 642d407
commit 2e538f9
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Showing 2 changed files with 3 additions and 5 deletions.
diff --git a/packages/taxdat/R/shapefile_utils.R b/packages/taxdat/R/shapefile_utils.R
@@ -15,14 +15,12 @@ clip_shapefiles_to_adm0 <- function(iso_code,
     iso_code = iso_code,
     admin_levels = c(0),
     lps = shapefiles
-  ) %>% 
-    sf::st_set_precision(1e8)
+  ) 
 
   sf::st_crs(adm0_geom) <- sf::st_crs(shapefiles) ## same crs needed for st_intersection
 
   # Drop data with no intersections
   shapefiles <- shapefiles %>% 
-    sf::st_set_precision(1e8) %>% 
     dplyr::mutate(adm0_intersect = sf::st_intersects(shapefiles$geom, adm0_geom$geom, sparse = FALSE) %>% 
                     as.vector())
 

diff --git a/packages/taxdat/R/stan_input_helpers.R b/packages/taxdat/R/stan_input_helpers.R
@@ -995,7 +995,7 @@ get_censoring_inds <- function(ind_mapping_resized,
       # Get all tfracs for the given observation
       tfracs <- ind_mapping_resized$tfrac[ind_mapping_resized$map_obs_loctime_obs == x]
       # Define right-censored if any tfrac is smaller than 95% of the time slice
-      ifelse(any(tfracs <= censoring_thresh), "right-censored", "full")
+      ifelse(any(tfracs < censoring_thresh), "right-censored", "full")
     })
 }
 
@@ -2059,7 +2059,7 @@ update_stan_data_indexing <- function(stan_data,
   stan_data$M <- length(unique(ind_mapping_resized$map_obs_loctime_obs))
 
   # Define censored observations
-  stan_data$censored  <- as.array(ind_mapping_resized$tfrac <= config$censoring_thresh)
+  stan_data$censored  <- as.array(ind_mapping_resized$tfrac < config$censoring_thresh)
 
   for (var in names(ind_mapping_resized)) {
     if (var == "map_obs_loctime_obs") {