fixed bugs in the keep population flag. (#874)

- filter out where gender not 1 or 2
- deal with negative ages where dob is after mid point of year
- previously filtered cases where dod was before midpoint, but was also
accidentally removing cases with missing death dates! Now fixed.
- added filter for nsu only once calculations are done

R/add_keep_population_flag.R

@@ -24,6 +24,7 @@ add_keep_population_flag <- function(individual_file, year) {
     year_available <- pop_estimates %>%
       dplyr::pull(year) %>%
       unique()
+
     if (calendar_year %in% year_available) {
       pop_estimates <- pop_estimates %>%
         dplyr::filter(year == calendar_year)
@@ -70,17 +71,18 @@ add_keep_population_flag <- function(individual_file, year) {
     # If they don't have a locality, they're no good as we won't have an estimate to match them against.
     # Same for age and gender.
     nsu_keep_lookup <- individual_file %>%
+      dplyr::filter(gender == 1 | gender == 2) %>%
       dplyr::filter(!is.na(locality), !is.na(age)) %>%
       # Remove people who died before the mid-point of the calender year.
       # This will make our numbers line up better with the methodology used for the mid-year population estimates.
-      # anyone who died 5 years before the file shouldn't be in it anyway...
-      dplyr::filter(death_date > mid_year | nsu != 0) %>%
+      dplyr::filter(death_date > mid_year | is.na(death_date) | nsu != 0) %>%
       # Calculate the populations of the whole SLF and of the NSU.
       dplyr::group_by(locality, age_group, gender) %>%
       dplyr::mutate(
         nsu_population = sum(nsu),
         total_source_population = dplyr::n()
       ) %>%
+      dplyr::filter(nsu == 1) %>%
       dplyr::left_join(pop_estimates,
         by = c("locality", "age_group", "gender")
       ) %>%
@@ -137,7 +139,7 @@ add_age_group <- function(data, age_var_name) {
   data <- data %>%
     dplyr::mutate(
       age_group = dplyr::case_when(
-        {{ age_var_name }} >= 0 & {{ age_var_name }} <= 4 ~ "0-4",
+        {{ age_var_name }} >= -1 & {{ age_var_name }} <= 4 ~ "0-4",
         {{ age_var_name }} >= 5 & {{ age_var_name }} <= 14 ~ "5-14",
         {{ age_var_name }} >= 15 & {{ age_var_name }} <= 24 ~ "15-24",
         {{ age_var_name }} >= 25 & {{ age_var_name }} <= 34 ~ "25-34",