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merge iid prediction fix #3

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merged 2 commits into from
Jun 24, 2024
Merged

merge iid prediction fix #3

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c78f11b
fix iid_effect predictions aknandi/disaggregation#90
simon-smart88 Jun 19, 2024
cd8556c
Merge branch 'timcdlucas:master' into terra
simon-smart88 Jun 24, 2024
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29 changes: 12 additions & 17 deletions R/predict.R
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Original file line number Diff line number Diff line change
Expand Up @@ -275,11 +275,7 @@ setup_objects <- function(model_output, newdata = NULL, predict_iid = FALSE) {
area_id =
factor(model_output$data$polygon_data$area_id))
}
shapefile_raster <- terra::rasterize(tmp_shp,
model_output$data$covariate_rasters,
field = 'area_id')
shapefile_ids <- terra::unique(shapefile_raster)
iid_objects <- list(shapefile_raster = shapefile_raster, shapefile_ids = shapefile_ids)
iid_objects <- list(shapefile = tmp_shp, template = model_output$data$covariate_rasters)
} else {
iid_objects <- NULL
}
Expand Down Expand Up @@ -320,31 +316,30 @@ predict_single_raster <- function(model_parameters, objects, link_function) {
}

if(!is.null(objects$iid_objects)) {
iid_ras <- objects$iid_objects$shapefile_raster

objects$iid_objects$shapefile$iid <- model_parameters$iideffect

iid_ras <- terra::rasterize(objects$iid_objects$shapefile, objects$iid_objects$template, field = 'iid')
iideffect_sd <- 1/sqrt(exp(model_parameters$iideffect_log_tau))
# todo
for(i in seq_along(model_parameters$iideffect)) {
targetvals <- terra::values(objects$iid_objects$shapefile_raster,
dataframe = FALSE, mat = FALSE)
whichvals <- which(targetvals == objects$iid_objects$shapefile_ids[1, i])
terra::values(iid_ras)[whichvals] <-
model_parameters$iideffect[i]
na_pixels <- which(is.na(terra::values(iid_ras, dataframe = FALSE, mat = FALSE)))

na_pixels <- which(is.na(terra::values(iid_ras, dataframe = FALSE, mat = FALSE)))
if (length(na_pixels) != 0){
na_iid_values <- stats::rnorm(length(na_pixels), 0, iideffect_sd)
terra::values(iid_ras)[na_pixels] <- na_iid_values
iid_ras[na_pixels] <- na_iid_values
}

if(terra::ext(iid_ras) != terra::ext(linear_pred)) {
# Extent of prediction space is different to the original model. Keep any overlapping iid values but predict to the new extent
raster_new_extent <- linear_pred
terra::values(raster_new_extent) <- NA
raster_new_extent[1:terra::ncell(raster_new_extent)] <- NA
#iid_ras <- terra::merge(iid_ras, raster_new_extent, ext = terra::ext(raster_new_extent))
# NOt sure why we no longer need the ext argument
# SS - added a crop which I think does the same thing
iid_ras <- terra::merge(iid_ras, raster_new_extent)
iid_ras <- terra::crop(iid_ras, raster_new_extent)
missing_pixels <- which(is.na(terra::values(iid_ras, dataframe = FALSE, mat = FALSE)))
missing_iid_values <- stats::rnorm(length(missing_pixels), 0, iideffect_sd)
terra::values(iid_ras)[missing_pixels] <- missing_iid_values
iid_ras[missing_pixels] <- missing_iid_values
}
linear_pred <- linear_pred + iid_ras
} else {
Expand Down
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