Added all remaining with date of uk entry code

.github/workflows/test_runner.yaml

@@ -12,6 +12,6 @@ jobs:
     name: Test the project can run, using dummy data
     steps:
     - name: Checkout
-      uses: actions/checkout@v5
+      uses: actions/checkout@v6
     - name: Test that the project is runnable
       uses: opensafely-core/research-action@v2

analysis/dataset_definition_full_study_cohort.py

@@ -248,12 +248,27 @@
 
 dataset.date_of_first_migration_code = date_of_first_migration_code
 
+date_of_first_migration_code_withdoe = (
+    clinical_events.where((clinical_events.snomedct_code.is_in(codelists.all_migrant_codes)) | (clinical_events.snomedct_code.is_in(date_of_entry_code))) 
+    .where(clinical_events.date.is_on_or_between(patients.date_of_birth, study_end_date))
+    .where((clinical_events.date.is_on_or_before(patients.date_of_death)) | (patients.date_of_death.is_null()))
+    .sort_by(clinical_events.date)
+    .first_for_patient().date)
+
+dataset.date_of_first_migration_code_withdoe = date_of_first_migration_code_withdoe
+
 time_from_1st_pracreg_first_migration_code_days  = (date_of_first_migration_code - date_of_first_practice_registration).days
 time_from_1st_pracreg_first_migration_code_months  = (date_of_first_migration_code - date_of_first_practice_registration).months
 
 dataset.time_from_1st_pracreg_first_migration_code_days = time_from_1st_pracreg_first_migration_code_days
 dataset.time_from_1st_pracreg_first_migration_code_months  = time_from_1st_pracreg_first_migration_code_months 
 
+time_from_1st_pracreg_first_migration_code_days_withdoe  = (date_of_first_migration_code_withdoe - date_of_first_practice_registration).days
+time_from_1st_pracreg_first_migration_code_months_withdoe  = (date_of_first_migration_code_withdoe - date_of_first_practice_registration).months
+
+dataset.time_from_1st_pracreg_first_migration_code_days_withdoe = time_from_1st_pracreg_first_migration_code_days_withdoe
+dataset.time_from_1st_pracreg_first_migration_code_months_withdoe  = time_from_1st_pracreg_first_migration_code_months_withdoe 
+
 # time from birth to first migration code 
 
 time_from_birth_first_migration_code_days  = (date_of_first_migration_code - patients.date_of_birth).days
@@ -262,6 +277,12 @@
 dataset.time_from_birth_first_migration_code_days = time_from_birth_first_migration_code_days
 dataset.time_from_birth_first_migration_code_months  = time_from_birth_first_migration_code_months 
 
+time_from_birth_first_migration_code_days_withdoe  = (date_of_first_migration_code_withdoe - patients.date_of_birth).days
+time_from_birth_first_migration_code_months_withdoe  = (date_of_first_migration_code_withdoe - patients.date_of_birth).months
+
+dataset.time_from_birth_first_migration_code_days_withdoe = time_from_birth_first_migration_code_days_withdoe
+dataset.time_from_birth_first_migration_code_months_withdoe  = time_from_birth_first_migration_code_months_withdoe 
+
 dataset.configure_dummy_data(population_size=1000)
 show(dataset)
 

analysis/migration_coding.R

@@ -40,7 +40,10 @@ vars_to_summarise <- c(
 mig_vars <- c(
   "mig_status_2_cat",
   "mig_status_3_cat",
-  "mig_status_6_cat")
+  "mig_status_6_cat",
+  "mig_status_2_cat_withdoe",
+  "mig_status_3_cat_withdoe",
+  "mig_status_6_cat_withdoe")
 
 rounding <- function(vars) {
   case_when(vars == 0 ~ 0,
@@ -56,10 +59,17 @@ migration_coding_summary <- cohort %>%
   group_by(migration_scheme, migration_status) %>%
   summarise(
     n = rounding(n()),
+    # excluding date of uk entry code
     total_migration_codes = rounding(sum(number_of_migration_codes)),
     median_migration_codes = median(number_of_migration_codes, na.rm = TRUE),
     q25_migration_codes = quantile(number_of_migration_codes, 0.25, na.rm = TRUE),
     q75_migration_codes = quantile(number_of_migration_codes, 0.75, na.rm = TRUE),
+    # including date of uk entry code
+    total_migration_codes_withdoe = rounding(sum(number_of_migration_codes_withdoe)),
+    median_migration_codes_withdoe = median(number_of_migration_codes_withdoe, na.rm = TRUE),
+    q25_migration_codes_withdoe = quantile(number_of_migration_codes_withdoe, 0.25, na.rm = TRUE),
+    q75_migration_codes_withdoe = quantile(number_of_migration_codes_withdoe, 0.75, na.rm = TRUE),
+    # excluding date of uk entry code
     median_time_from_1st_pracreg_first_migration_code_days = median(time_from_1st_pracreg_first_migration_code_days, na.rm = TRUE),
     q25_time_from_1st_pracreg_first_migration_code_days = quantile(time_from_1st_pracreg_first_migration_code_days, 0.25, na.rm = TRUE),
     q75_time_from_1st_pracreg_first_migration_code_days = quantile(time_from_1st_pracreg_first_migration_code_days, 0.75, na.rm = TRUE),
@@ -72,6 +82,19 @@ migration_coding_summary <- cohort %>%
     median_time_from_birth_first_migration_code_months = median(time_from_birth_first_migration_code_months, na.rm = TRUE),
     q25_time_from_birth_first_migration_code_months = quantile(time_from_birth_first_migration_code_months, 0.25, na.rm = TRUE),
     q75_time_from_birth_first_migration_code_months = quantile(time_from_birth_first_migration_code_months, 0.75, na.rm = TRUE),
+    # including date of uk entry code
+    median_time_from_1st_pracreg_first_migration_code_days_withdoe = median(time_from_1st_pracreg_first_migration_code_days, na.rm = TRUE),
+    q25_time_from_1st_pracreg_first_migration_code_days_withdoe = quantile(time_from_1st_pracreg_first_migration_code_days, 0.25, na.rm = TRUE),
+    q75_time_from_1st_pracreg_first_migration_code_days_withdoe = quantile(time_from_1st_pracreg_first_migration_code_days, 0.75, na.rm = TRUE),
+    median_time_from_1st_pracreg_first_migration_code_months_withdoe = median(time_from_1st_pracreg_first_migration_code_months , na.rm = TRUE),
+    q25_time_from_1st_pracreg_first_migration_code_months_withdoe = quantile(time_from_1st_pracreg_first_migration_code_months , 0.25, na.rm = TRUE),
+    q75_time_from_1st_pracreg_first_migration_code_months_withdoe = quantile(time_from_1st_pracreg_first_migration_code_months , 0.75, na.rm = TRUE),
+    median_time_from_birth_first_migration_code_days_withdoe = median(time_from_birth_first_migration_code_days, na.rm = TRUE),
+    q25_time_from_birth_first_migration_code_days_withdoe = quantile(time_from_birth_first_migration_code_days, 0.25, na.rm = TRUE),
+    q75_time_from_birth_first_migration_code_days_withdoe = quantile(time_from_birth_first_migration_code_days, 0.75, na.rm = TRUE),
+    median_time_from_birth_first_migration_code_months_withdoe = median(time_from_birth_first_migration_code_months, na.rm = TRUE),
+    q25_time_from_birth_first_migration_code_months_withdoe = quantile(time_from_birth_first_migration_code_months, 0.25, na.rm = TRUE),
+    q75_time_from_birth_first_migration_code_months_withdoe = quantile(time_from_birth_first_migration_code_months, 0.75, na.rm = TRUE),
     .groups = "drop"
   ) 
 

analysis/migration_coding_combinations.R

@@ -44,7 +44,9 @@ migration_code_combinations_summary <- cohort %>%
         if (immig_status_excl_refugee_asylum) "immig_status_excl_refugee_asylum",
         if (refugee_asylum_status) "refugee_asylum_status",
         if (english_not_main_language) "english_not_main_language",
-        if (interpreter_required) "interpreter_required"
+        if (interpreter_required) "interpreter_required",
+        if (trafficking) "trafficking",
+        if (date_of_uk_entry) "date_of_uk_entry"
       ),
       collapse = "; "
     ),

analysis/process_full_cohort_data_migration_types.R

@@ -32,6 +32,7 @@ cohort <- read_feather(cohort_file) %>%
 
 migration_type_vars <- c("any_migrant", 
                          "not_born_in_uk", 
+                         "date_of_uk_entry",
                          "immig_status_excl_refugee_asylum", 
                          "refugee_asylum_status",
                          "english_not_main_language",

project.yaml

@@ -55,6 +55,30 @@ actions:
       moderately_sensitive:
         csv: output/tables/demographics_full_study_cohort_6cat.csv
 
+  generate_demographics_full_study_table_2cat_withdoe:
+    run: r:latest analysis/process_full_cohort_data.R output/tables/demographics_full_study_cohort_2cat_withdoe.csv mig_status_2_cat_withdoe
+    needs:
+    - generate_full_study_cohort
+    outputs:
+      moderately_sensitive:
+        csv: output/tables/demographics_full_study_cohort_2cat_withdoe.csv
+
+  generate_demographics_full_study_table_3cat_withdoe:
+    run: r:latest analysis/process_full_cohort_data.R output/tables/demographics_full_study_cohort_3cat_withdoe.csv mig_status_3_cat_withdoe
+    needs:
+    - generate_full_study_cohort
+    outputs:
+      moderately_sensitive:
+        csv: output/tables/demographics_full_study_cohort_3cat_withdoe.csv
+
+  generate_demographics_full_study_table_6cat_withdoe:
+    run: r:latest analysis/process_full_cohort_data.R output/tables/demographics_full_study_cohort_6cat_withdoe.csv mig_status_6_cat_withdoe
+    needs:
+    - generate_full_study_cohort
+    outputs:
+      moderately_sensitive:
+        csv: output/tables/demographics_full_study_cohort_6cat_withdoe.csv
+
   generate_demographics_full_study_table_migration_types:
     run: r:latest analysis/process_full_cohort_data_migration_types.R 
     needs:
@@ -143,7 +167,6 @@ actions:
       moderately_sensitive:
         csv: output/tables/demographics_census_2011_cohort_6cat_withdoe.csv
 
-
   generate_demographics_census_2021_study_table_2cat_withdoe:
     run: r:latest analysis/process_census_cohort_data.R output/cohorts/census_2021_study_cohort.arrow output/tables/demographics_census_2021_cohort_2cat_withdoe.csv mig_status_2_cat_withdoe
     needs: