Merge pull request #35 from opensafely/add-16-17s

Add 16-17s and update report
opensafely · Sep 7, 2021 · 6fef31e · 6fef31e
2 parents ddc4edd + c63b522
commit 6fef31e
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Showing 67 changed files with 40,991 additions and 37,623 deletions.
diff --git a/analysis/study_definition_delivery_common.py b/analysis/study_definition_delivery_common.py
@@ -25,12 +25,6 @@
         age <= 120
         AND 
         age>=16
-        AND
-        (age >=18  
-        OR
-        shielded
-        OR
-        LD)
         """,
         registered=patients.registered_as_of(
             index_date, 
@@ -73,7 +67,7 @@
             "50-59": """ age >= 50 AND age < 60""",
             "60-69": """ age >= 60 AND age < 70""",
             "70-79": """ age >= 70 AND age < 80""",
-            "80+": """ age >=  80 AND age < 120""",  # age eligibility currently set at 80
+            "80+": """ age >=  80 AND age < 120""",  
         },
         return_expectations={
             "rate": "universal",
@@ -96,7 +90,8 @@
         {
             "0" : "DEFAULT",
             "0-15": """ age >= 0 AND age < 16 """,
-            "16-29": """ age >= 16 AND age < 30 """,
+            "16-17": """ age >= 16 AND age < 18 """,
+            "18-29": """ age >= 18 AND age < 30 """,
             "30-34": """ age >= 30 AND age < 35 """,
             "35-39": """ age >= 35 AND age < 40 """,
             "40-44": """ age >= 40 AND age < 45 """,
@@ -115,22 +110,23 @@
             "rate": "universal",
             "category": {
                 "ratios": {
-                    "0":0.0625,
-                    "0-15": 0.0625,
-                    "16-29": 0.0625,
-                    "30-34": 0.0625,
-                    "35-39": 0.0625,
-                    "40-44": 0.0625,
-                    "45-49": 0.0625,
-                    "50-54": 0.0625,
-                    "55-59": 0.0625,
-                    "60-64": 0.0625,
-                    "65-69": 0.0625,
-                    "70-74": 0.0625,
-                    "75-79": 0.0625,
-                    "80-84": 0.0625,
-                    "85-89": 0.0625,
-                    "90+": 0.0625
+                    "0":0.0125,
+                    "0-15": 0.065,
+                    "16-17": 0.065,
+                    "18-29": 0.065,
+                    "30-34": 0.065,
+                    "35-39": 0.065,
+                    "40-44": 0.065,
+                    "45-49": 0.065,
+                    "50-54": 0.065,
+                    "55-59": 0.065,
+                    "60-64": 0.065,
+                    "65-69": 0.065,
+                    "70-74": 0.065,
+                    "75-79": 0.065,
+                    "80-84": 0.065,
+                    "85-89": 0.065,
+                    "90+": 0.0125
                 }
             },
         },

diff --git a/lib/data_processing.py b/lib/data_processing.py
@@ -151,8 +151,9 @@ def load_data(input_file='input_delivery.csv.gz', input_path="output"):
         (df["age"]>=55),
         (df["age"]>=50),
         (df["age"]>=40),
-        (df["age"]>=30)]
-    choices = [3,1,2,4,5,6,7,8,9,10,11]
+        (df["age"]>=30),
+        (df["age"]>=18)]
+    choices = [3,1,2,4,5,6,7,8,9,10,11,12]
     # note the numbers here denote the desired sort order in which we want to look at these groups, not the priority order
 
     # create field "priority_group" which uses the appropriate value from `choices` according to the `conditions` met by each line of data. If none are met, assigns 0.

diff --git a/notebooks/diffable_python/opensafely_vaccine_report_overall.py b/notebooks/diffable_python/opensafely_vaccine_report_overall.py
@@ -61,7 +61,7 @@
 # <br>
 # - **<a href=#tables>Current vaccination coverage of each eligible population group, according to demographic/clinical features</a>**
 #   - Includes each of the groups above, plus <a href=#Cumulative-vaccination-figures-among-care-home-population>care home (65+)</a> and <a href=#Cumulative-vaccination-figures-among-Learning-Disabilities-(aged-16-64)-population>LD (aged 16-64)</a> populations.
-#   - **NEW** - tables now include <a href=#Cumulative-vaccination-figures-among-30-39-population>30-39</a> and <a href=#Cumulative-vaccination-figures-among-18-29-population>18-29</a> populations
+#   - **NEW** - tables now include <a href=#Cumulative-vaccination-figures-among-16-17-population>16-17</a>  population
 # <br>
 # <br>
 # - Appendix: <a href=#ethnicity>Proportion of each population group for whom ethnicity is known</a>

diff --git a/notebooks/diffable_python/population_characteristics.py b/notebooks/diffable_python/population_characteristics.py
@@ -82,7 +82,8 @@
         "50-54": 9,
         "40-49": 10,
         "30-39": 11,
-        "18-29": 0 
+        "18-29": 12,                
+        "16-17": 0 
         # NB if the population denominator is not included for the final group (0), the key must contain phrase "not in other eligible groups" so that data is presented appropriately
         }
 
@@ -115,6 +116,7 @@
                  "40-49":    u50,
                  "30-39":    u50,
                  "18-29":    u50,
+                 "16-17":    ["sex", "ethnicity_6_groups", "imd_categories"],
                  "LD (aged 16-64)":  ["sex", "ageband_5yr", "ethnicity_6_groups"],
                  "DEFAULT":   DEFAULT # other age groups
                 }
@@ -240,9 +242,11 @@
 
 second_dose_summarised_data_dict = summarise_data_by_group(df_dict_cum_second_dose, latest_date=latest_date, groups=groups)
 
+# + collapsed=true jupyter={"outputs_hidden": true}
 create_detailed_summary_uptake(second_dose_summarised_data_dict, formatted_latest_date, 
                                groups=groups,
                                savepath=savepath, vaccine_type="second_dose")
+# -
 
 # ## For comparison look at first doses UP TO 14 WEEKS AGO
 #

diff --git a/notebooks/diffable_python/second_doses.py b/notebooks/diffable_python/second_doses.py
@@ -84,14 +84,14 @@
 tablelist = find_and_sort_filenames("tables", by_demographics_or_population="population", 
                                     pre_string="among ", tail_string=" population.csv",
                                     population_subset="Cumulative first dose 14w ago",
-                                    files_to_exclude=["Cumulative first dose 14w ago vaccination figures among 16-64, not in other eligible groups shown population.csv"],
+                                    files_to_exclude=["Cumulative first dose 14w ago vaccination figures among 16-17 population.csv"],
                                     )
 
 # get 2nd dose figures for each group
 tablelist_2nd = find_and_sort_filenames("tables", by_demographics_or_population="population", 
                                         pre_string="among ", tail_string=" population.csv",
                                         population_subset="Cumulative second dose vaccination",
-                                        files_to_exclude=["Cumulative second dose vaccination figures among 16-64, not in other eligible groups shown population.cscv"],
+                                        files_to_exclude=["Cumulative second dose vaccination figures among 16-17 population.csv"],
                                         )
 
 

diff --git a/notebooks/opensafely_vaccine_report_overall.ipynb b/notebooks/opensafely_vaccine_report_overall.ipynb
diff --git a/notebooks/population_characteristics.ipynb b/notebooks/population_characteristics.ipynb