Merge branch 'main' into reviewer-updates

.gitignore

@@ -10,3 +10,4 @@ analysis/.DS_Store
 .DS_Store
 !.gitkeep
 untitled folder/local run.do
+

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) University of Oxford
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

analysis/draw_rate_graphs.py

@@ -15,7 +15,7 @@
 
 df = pd.DataFrame()
 for f in groups:
-    df = df.append(pd.read_csv(f"released_output/rates_summary_{f}.csv"))
+    df = df.append(pd.read_csv(f"released_outputs/output/tabfig/rates_summary_{f}.csv"))
 df = df.replace(to_replace=dict(zip(old_names, new_names)))
 df = df.set_index(["group", "outcome", "time"])
 df = df.loc[df["variable"] == "Overall"]
@@ -27,7 +27,7 @@ def plot_rates(outcome_group, rows):
     for i, ax in enumerate(axes.flat):
         df_to_plot = df.loc[df.index.isin(rows, level=1)]
         df_to_plot = df_to_plot.loc[groups[i]]
-        df_to_plot = df_to_plot * 100
+        df_to_plot = df_to_plot * 120
         df_to_plot = df_to_plot.unstack(level=-1)
         errlo = df_to_plot["rate_ppm"] - df_to_plot["lc_ppm"]
         errhi = df_to_plot["uc_ppm"] - df_to_plot["rate_ppm"]
@@ -40,7 +40,7 @@ def plot_rates(outcome_group, rows):
         ax.set_title(titles[i], loc="left")
         ax.legend(loc=2).set_title("Time since hospital discharge")
         ax.set_xticklabels(labels)
-        ax.set_ylabel("Rate of each outcome (per 10,000 person months)")
+        ax.set_ylabel("Rate of each outcome (per 1,000 person years)")
         ax.grid(b=True, axis="y", color="#666666", linestyle="-", alpha=0.1)
         plt.tight_layout()
     plt.savefig(f"output/rate_graphs{outcome_group}.svg")

released_outputs/.gitignore

@@ -0,0 +1,2 @@
+metadata/*
+output/measure*

released_outputs/README.md

@@ -0,0 +1,36 @@
+# Table of contents
+
+* [.gitignore](.gitignore)
+* output
+  * [output/append_cohorts.txt](output/append_cohorts.txt)
+  * [output/competing_events.txt](output/competing_events.txt)
+  * [output/cox_models.txt](output/cox_models.txt)
+  * [output/matching_report_general_population.txt](output/matching_report_general_population.txt)
+  * output/tabfig
+    * [output/tabfig/an_descriptiveTable_covid.txt](output/tabfig/an_descriptiveTable_covid.txt)
+    * [output/tabfig/an_descriptiveTable_covid_community.txt](output/tabfig/an_descriptiveTable_covid_community.txt)
+    * [output/tabfig/an_descriptiveTable_gen_population.txt](output/tabfig/an_descriptiveTable_gen_population.txt)
+    * [output/tabfig/an_descriptiveTable_pneumonia.txt](output/tabfig/an_descriptiveTable_pneumonia.txt)
+    * [output/tabfig/an_descriptiveTable_pre_covid_discharged.txt](output/tabfig/an_descriptiveTable_pre_covid_discharged.txt)
+    * [output/tabfig/an_descriptiveTable_pre_pneum_discharged.txt](output/tabfig/an_descriptiveTable_pre_pneum_discharged.txt)
+    * [output/tabfig/cox_model_summary.csv](output/tabfig/cox_model_summary.csv)
+    * [output/tabfig/cox_model_summary_time_strat.csv](output/tabfig/cox_model_summary_time_strat.csv)
+    * [output/tabfig/cumInc_aki_cens_gp.svg](output/tabfig/cumInc_aki_cens_gp.svg)
+    * [output/tabfig/cumInc_dvt_cens_gp.svg](output/tabfig/cumInc_dvt_cens_gp.svg)
+    * [output/tabfig/cumInc_heart_failure_cens_gp.svg](output/tabfig/cumInc_heart_failure_cens_gp.svg)
+    * [output/tabfig/cumInc_mi_cens_gp.svg](output/tabfig/cumInc_mi_cens_gp.svg)
+    * [output/tabfig/cumInc_pe_cens_gp.svg](output/tabfig/cumInc_pe_cens_gp.svg)
+    * [output/tabfig/cumInc_stroke_cens_gp.svg](output/tabfig/cumInc_stroke_cens_gp.svg)
+    * [output/tabfig/fine_gray_summary.csv](output/tabfig/fine_gray_summary.csv)
+    * [output/tabfig/fine_gray_summary_time_strat.csv](output/tabfig/fine_gray_summary_time_strat.csv)
+    * [output/tabfig/fine_gray_summary_time_strat_age_sex.csv](output/tabfig/fine_gray_summary_time_strat_age_sex.csv)
+    * [output/tabfig/follow_up_summary.csv](output/tabfig/follow_up_summary.csv)
+    * [output/tabfig/outcomes_in_hosp_covid.csv](output/tabfig/outcomes_in_hosp_covid.csv)
+    * [output/tabfig/outcomes_in_hosp_pneumonia.csv](output/tabfig/outcomes_in_hosp_pneumonia.csv)
+    * [output/tabfig/rate_graphs_all.svg](output/tabfig/rate_graphs_all.svg)
+    * [output/tabfig/rate_graphs_cens_gp.svg](output/tabfig/rate_graphs_cens_gp.svg)
+    * [output/tabfig/rate_graphs_no_gp.svg](output/tabfig/rate_graphs_no_gp.svg)
+    * [output/tabfig/rates_summary_covid.csv](output/tabfig/rates_summary_covid.csv)
+    * [output/tabfig/rates_summary_covid_community.csv](output/tabfig/rates_summary_covid_community.csv)
+    * [output/tabfig/rates_summary_gen_population.csv](output/tabfig/rates_summary_gen_population.csv)
+    * [output/tabfig/rates_summary_pneumonia.csv](output/tabfig/rates_summary_pneumonia.csv)

released_outputs/output/append_cohorts.txt

@@ -0,0 +1,109 @@
+-------------------------------------------------------------------------------
+      name:  <unnamed>
+       log:  /workspace/output/append_cohorts.txt
+  log type:  text
+ opened on:  13 Jun 2021, 10:04:50
+
+. 
+. * Gen flag for covid patients  (case = 1)
+. use $outdir/cohort_rates_covid, replace
+
+. gen case = 1 
+
+. append using $outdir/cohort_rates_pneumonia, force
+(label diabcat already defined)
+(label reduced_kidney_function_cat2lab already defined)
+(label cancer already defined)
+(label bpcat already defined)
+(label asthmacat already defined)
+(label obese4cat already defined)
+(label bmicat already defined)
+(label agegroup already defined)
+(label region_7 already defined)
+(label region_9 already defined)
+(label ethnicity_lab already defined)
+(label smoke already defined)
+(label imd already defined)
+(label sexLab already defined)
+
+. replace case = 0 if case ==.
+(127,715 real changes made)
+
+. 
+. * count patients from pneumonia group who are among Covid group
+. bysort patient_id: gen flag = _n
+
+. safecount if flag == 2
+  3,535
+
+. 
+. noi di "number of patients in both cohorts is `r(N)'"
+number of patients in both cohorts is 3535
+
+. 
+. drop flag 
+
+. save $outdir/combined_covid_pneumonia.dta, replace
+(note: file /workspace/output/combined_covid_pneumonia.dta not found)
+file /workspace/output/combined_covid_pneumonia.dta saved
+
+. 
+. 
+. 
+. *****************************************************************************
+> ***
+. * Append covid/gen pop. cohorts 
+. 
+. * Gen flag for covid patients  (case = 1)
+. use $outdir/cohort_rates_covid, replace
+
+. gen case = 1 
+
+. append using $outdir/cohort_rates_gen_population, force
+(label diabcat already defined)
+(label reduced_kidney_function_cat2lab already defined)
+(label cancer already defined)
+(label bpcat already defined)
+(label asthmacat already defined)
+(label obese4cat already defined)
+(label bmicat already defined)
+(label agegroup already defined)
+(label region_7 already defined)
+(label region_9 already defined)
+(label ethnicity_lab already defined)
+(label smoke already defined)
+(label imd already defined)
+(label sexLab already defined)
+
+. replace case = 0 if case ==.
+(0 real changes made)
+
+. 
+. 
+. * count patients from pneumonia group who are among Covid group
+. bysort patient_id: gen flag = _n
+
+. safecount if flag == 2
+  1,404
+
+. 
+. noi di "number of patients in both cohorts is `r(N)'"
+number of patients in both cohorts is 1404
+
+. 
+. drop flag 
+
+. save $outdir/combined_covid_gen_population.dta, replace
+(note: file /workspace/output/combined_covid_gen_population.dta not found)
+file /workspace/output/combined_covid_gen_population.dta saved
+
+. 
+. 
+. 
+. 
+. log close
+      name:  <unnamed>
+       log:  /workspace/output/append_cohorts.txt
+  log type:  text
+ closed on:  13 Jun 2021, 10:04:54
+-------------------------------------------------------------------------------