Merge pull request #65 from opensafely/update-long-covid-definition

Add code for therapeutics code graph

.devcontainer/Dockerfile

@@ -0,0 +1,31 @@
+FROM remlapmot/r-docker:2024-04-02-rstudio
+
+LABEL org.opencontainers.image.source https://github.com/opensafely/research-template
+
+# we are going to use an apt cache on the host, so disable the default debian
+# docker clean up that deletes that cache on every apt install
+RUN rm -f /etc/apt/apt.conf.d/docker-clean
+
+# Install python 3.10. This is the version used by the python-docker 
+# image, used for analyses using the OpenSAFELY pipeline.
+RUN --mount=type=cache,target=/var/cache/apt \
+    echo "deb http://ppa.launchpad.net/deadsnakes/ppa/ubuntu focal main" > /etc/apt/sources.list.d/deadsnakes-ppa.list &&\
+    /usr/lib/apt/apt-helper download-file 'https://keyserver.ubuntu.com/pks/lookup?op=get&search=0xf23c5a6cf475977595c89f51ba6932366a755776' /etc/apt/trusted.gpg.d/deadsnakes.asc &&\
+    apt update &&\
+    apt install -y curl python3.10 python3.10-distutils python3.10-venv &&\
+    # Pip for Python 3.10 isn't included in deadsnakes, so install separately
+    curl https://bootstrap.pypa.io/get-pip.py | python3.10 &&\
+    # Set default python, so that the Python virtualenv works as expected
+    rm /usr/bin/python3 && ln -s /usr/bin/python3.10 /usr/bin/python3
+
+# Copy the Python virtualenv from OpenSAFELY Python action image
+COPY --from=ghcr.io/opensafely-core/python:v2 /opt/venv /opt/venv
+
+# Create a local user and give it sudo (aka root) permissions
+RUN usermod -aG sudo rstudio
+RUN echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers
+
+# Required for installing opensafely cli
+ENV PATH="/home/rstudio/.local/bin:${PATH}"
+
+USER rstudio

.devcontainer/devcontainer.json

@@ -0,0 +1,43 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/python
+{
+    "name": "OpenSAFELY",
+    "image": "ghcr.io/opensafely/research-template:latest",
+    // Features to add to the dev container. More info: https://containers.dev/features.
+    "features": {
+        "ghcr.io/devcontainers/features/docker-in-docker:2": {
+            "moby": true,
+            "azureDnsAutoDetection": true,
+            "installDockerBuildx": true,
+            "version": "latest",
+            "dockerDashComposeVersion": "v2"
+        }
+    },
+    "postCreateCommand": "/bin/bash .devcontainer/postCreate.sh",
+    "postAttachCommand": {
+        "rstudio-start": "sudo rstudio-server start"
+    },
+    "forwardPorts": [
+        8787
+    ],
+    "portsAttributes": {
+        "8787": {
+            "label": "RStudio IDE"
+        }
+    },
+    // Configure tool-specific properties.
+    "customizations": {
+        "vscode": {
+            "extensions": [
+                "ms-python.python",
+                "ms-toolsai.jupyter",
+                "ms-toolsai.jupyter-renderers"
+            ]
+        }
+    },
+    // Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+    // "remoteUser": "root"
+    "remoteEnv": {
+        "MAX_WORKERS": "2"
+    }
+}

.devcontainer/postCreate.sh

@@ -0,0 +1,15 @@
+#!/bin/bash
+
+set -euo pipefail 
+
+pip3 install --user -r .devcontainer/requirements.in
+
+#set R working directory
+! grep -q `pwd` $R_HOME/etc/Rprofile.site && sudo tee -a $R_HOME/etc/Rprofile.site <<< "setwd(\"`pwd`\")"
+#set RStudio working directory
+! grep -q `pwd` ~/.config/rstudio/rstudio-prefs.json && cat ~/.config/rstudio/rstudio-prefs.json | jq ". + {\"initial_working_directory\":\"`pwd`\"}" >  ~/.config/rstudio/rstudio-prefs.json 
+
+#download and extract latest ehrql source
+wget https://github.com/opensafely-core/ehrql/archive/main.zip -P .devcontainer
+unzip -o .devcontainer/main.zip -d .devcontainer/
+rm .devcontainer/main.zip

.devcontainer/requirements.in

@@ -0,0 +1 @@
+opensafely

.gitignore

@@ -9,10 +9,12 @@ venv/
 .DS_Store
 .Rproj.user
 .Rhistory
+.devcontainer/ehrql-main
 reports/variation/*
 reports/coverage/table_prop_eligible_clinc_demo.csv
 reports/coverage/mabs_and_antivirals_coverage_report.html
 reports/coverage/figures/*
 reports/coverage/tables/*
-released_outputs/reports_wip/coverage/*
-reports/coverage_wip/*
+released_outputs/*
+reports/coverage_wip/*
+analysis/descriptive/mabs-and-avs-by-stp.html

.vscode/settings.json

@@ -1,7 +1,7 @@
 {
-    "python.linting.pylintEnabled": false,
-    "python.linting.flake8Enabled": true,
-    "python.linting.enabled": true,
+    "python.analysis.extraPaths": [".devcontainer/ehrql-main/"],
+    "python.defaultInterpreterPath": "/opt/venv/bin/python3.10",
+    "python.terminal.activateEnvironment": true,
     "data.preview.create.json.schema": false,
     "files.associations": {
         "*.feather": "arrow",

analysis/descriptive/coverage_report_data.R

@@ -751,3 +751,44 @@ groups2 <- groups2 %>%
 
 write_csv(rbind(all, groups) %>% filter(!is.na(tb)), fs::path(output_dir, "table_time_to_treat_redacted.csv"))
 write_csv(groups2, fs::path(output_dir, "table_time_to_treat_groups_redacted.csv"))
+
+
+# Treatment recording over time
+plot_data_treatment_codes <- data_processed_clean %>%
+  filter(!is.na(last_treatment_date)) %>%
+  select(last_treatment_date, last_treatment_type)  %>%
+  rbind(data_processed_clean %>%
+          filter(!is.na(last_treatment_date)) %>%
+          select(last_treatment_date, last_treatment_type) %>%
+          mutate(last_treatment_type = "All")) %>%
+  group_by(last_treatment_date, last_treatment_type) %>%
+  tally() %>%
+  group_by(last_treatment_type) %>%
+  arrange(last_treatment_type, last_treatment_date) %>%
+  complete(last_treatment_date = seq.Date(min(last_treatment_date, na.rm = T), max(last_treatment_date, na.rm = T), by="day"))  %>%
+  mutate(count = ifelse(is.na(n), 0, n),
+         count_redacted = plyr::round_any(count, 10),
+         count_redacted = ifelse(count < threshold, NA, count_redacted)) %>%
+          # cum_count = cumsum(count),
+          # cum_count_redacted =  plyr::round_any(cum_count, 10),
+          # cum_count_redacted = ifelse(cum_count < threshold, NA, cum_count_redacted)
+  select(-n) %>%
+  arrange(last_treatment_type, last_treatment_date)
+
+plot_order <- plot_data_treatment_codes %>%
+  group_by(last_treatment_type) %>%
+  mutate(order = max(count_redacted, na.rm = T)) %>%
+  arrange(desc(order)) %>%
+  filter(count_redacted == order) %>%
+  select(last_treatment_type, order) %>%
+  distinct()
+
+treatment_codes_plot_data <- plot_data_treatment_codes %>%
+  mutate(last_treatment_type = factor(last_treatment_type, levels = plot_order$last_treatment_type))
+
+write_csv(treatment_codes_plot_data %>% 
+            select(last_treatment_date, count_redacted, last_treatment_type),
+          fs::path(output_dir, "table_last_treatment_codes_redacted.csv"))
+write_csv(treatment_plot_data, fs::path(output_dir2, "table_last_treatment_codes.csv"))
+
+print("treatment_codes_plot_data saved")

analysis/descriptive/crude_outcomes.Rmd

@@ -685,7 +685,7 @@ sgtf_outcomes <- data_processed_clean %>%
     # Redact values < threshold
     count = ifelse(count < threshold, NA, as.numeric(count)),
     covid_positive_test = ifelse(covid_positive_test < threshold, NA, covid_positive_test),
-    covid_hospital_admission = ifelse(covid_hospital_admission < threshold, NA, as.numeric(covid_hospital_admission)),
+    covid_hospital_admission = ifelse(covid_hospital_admission < threshold, NA_integer_, as.numeric(covid_hospital_admission)),
     covid_hospitalisation_critical_care = ifelse(covid_hospitalisation_critical_care < threshold, NA, as.numeric(covid_hospitalisation_critical_care)),
     covid_death = ifelse(covid_death < threshold, NA, as.numeric(covid_death)),
     any_death = ifelse(any_death < threshold, NA, as.numeric(any_death)),

analysis/descriptive/mabs-and-avs-by-stp.Rmd

@@ -498,8 +498,8 @@ table_elig_treat_redacted <- table_elig_treat %>%
     Paxlovid = plyr::round_any(as.numeric(Paxlovid), 10),
     Sotrovimab = plyr::round_any(as.numeric(Sotrovimab), 10),
     Remdesivir = plyr::round_any(as.numeric(Remdesivir), 10),
-    Molnupiravir = plyr::round_any(Molnupiravir, 10),
-    Casirivimab = plyr::round_any(Casirivimab, 10)) %>%
+    Molnupiravir = plyr::round_any(as.numeric(Molnupiravir), 10),
+    Casirivimab = plyr::round_any(as.numeric(Casirivimab), 10)) %>%
   arrange(desc(decile)) %>%
   mutate(Paxlovid_perc = paste(round(Paxlovid/Treated*100, digits = 0), " (",
                                round((Paxlovid/Treated - 1.96*sqrt((Paxlovid/Treated)*(1-Paxlovid/Treated)/Treated))*100, digits = 0),

analysis/process/process_data.R

@@ -59,6 +59,12 @@ data_extract0 <- read_csv(
     remdesivir_covid_therapeutics = col_date(format = "%Y-%m-%d"),
     molnupiravir_covid_therapeutics = col_date(format = "%Y-%m-%d"),
     casirivimab_covid_therapeutics = col_date(format = "%Y-%m-%d"),
+
+    paxlovid_covid_therapeutics_last = col_date(format = "%Y-%m-%d"),
+    sotrovimab_covid_therapeutics_last = col_date(format = "%Y-%m-%d"),
+    remdesivir_covid_therapeutics_last = col_date(format = "%Y-%m-%d"),
+    molnupiravir_covid_therapeutics_last = col_date(format = "%Y-%m-%d"),
+    casirivimab_covid_therapeutics_last = col_date(format = "%Y-%m-%d"),
 
     # ELIGIBILITY CRITERIA VARIABLES ----
     covid_test_positive = col_logical(),
@@ -120,7 +126,7 @@ data_extract0 <- read_csv(
     serious_mental_illness_nhsd = col_logical(),
     sickle_cell_disease_nhsd = col_date(format = "%Y-%m-%d"),
     vaccination_status = col_character(),
-    first_lc_code_date = col_date(format = "%Y-%m-%d"),
+    first_long_covid = col_date(format = "%Y-%m-%d"),
 
     # COVID VARIENT
     sgtf = col_character(),
@@ -151,7 +157,13 @@ if(Sys.getenv("OPENSAFELY_BACKEND") %in% c("", "expectations")){
            remdesivir_covid_therapeutics = as.Date(ifelse(!is.na(remdesivir_covid_therapeutics), date, NA), origin = "1970-01-01"),
            molnupiravir_covid_therapeutics = as.Date(ifelse(!is.na(molnupiravir_covid_therapeutics), date, NA),  origin = "1970-01-01"),
            casirivimab_covid_therapeutics = as.Date(ifelse(!is.na(casirivimab_covid_therapeutics), date, NA),  origin = "1970-01-01"),
-
+
+          paxlovid_covid_therapeutics_last = as.Date(ifelse(!is.na(paxlovid_covid_therapeutics_last), date, NA),  origin = "1970-01-01"),
+           sotrovimab_covid_therapeutics_last = as.Date(ifelse(!is.na(sotrovimab_covid_therapeutics_last), date, NA),  origin = "1970-01-01"),
+           remdesivir_covid_therapeutics_last = as.Date(ifelse(!is.na(remdesivir_covid_therapeutics_last), date, NA), origin = "1970-01-01"),
+           molnupiravir_covid_therapeutics_last = as.Date(ifelse(!is.na(molnupiravir_covid_therapeutics_last), date, NA),  origin = "1970-01-01"),
+           casirivimab_covid_therapeutics_last = as.Date(ifelse(!is.na(casirivimab_covid_therapeutics_last), date, NA),  origin = "1970-01-01"),
+
            covid_positive_test_30_days_post_elig_or_treat = as.Date(ifelse(covid_positive_test_30_days_post_elig_or_treat > covid_test_positive_date + 30,
                                                                    covid_positive_test_30_days_post_elig_or_treat, NA),  origin = "1970-01-01"))
 
@@ -192,6 +204,19 @@ data_processed <- data_extract %>%
       treatment_date == casirivimab_covid_therapeutics ~ "Casirivimab", 
       TRUE ~ NA_character_),
 
+    # last MAB or Antiviral recorded
+    last_treatment_date = as.Date(pmin(paxlovid_covid_therapeutics_last, sotrovimab_covid_therapeutics_last, 
+                                  remdesivir_covid_therapeutics_last, molnupiravir_covid_therapeutics_last, 
+                                  casirivimab_covid_therapeutics_last, na.rm = TRUE), origin = "1970-01-01"),
+    last_treatment_type = case_when(
+      last_treatment_date == paxlovid_covid_therapeutics_last ~ "Paxlovid", 
+      last_treatment_date == sotrovimab_covid_therapeutics_last ~ "Sotrovimab", 
+      last_treatment_date == remdesivir_covid_therapeutics_last ~ "Remdesivir", 
+      last_treatment_date == molnupiravir_covid_therapeutics_last ~ "Molnupiravir", 
+      last_treatment_date == casirivimab_covid_therapeutics_last ~ "Casirivimab", 
+      TRUE ~ NA_character_),
+
+
 
     # ELIGIBILITY VARIABLES ----
 
@@ -212,7 +237,7 @@ data_processed <- data_extract %>%
     sickle_cell_disease_nhsd = ifelse(!is.na(sickle_cell_disease_nhsd), 1, 0),
 
     ## Long COVID
-    long_covid = ifelse(!is.na(first_lc_code_date), 1, 0),
+    long_covid = ifelse(!is.na(first_long_covid), 1, 0),
 
     # Combine subgoups of rare neurological conditions cohort
     rare_neurological_conditions_nhsd =  pmin(multiple_sclerosis_nhsd, motor_neurone_disease_nhsd, myasthenia_gravis_nhsd,
@@ -561,6 +586,9 @@ data_processed_clean <- data_processed_combined %>%
     # Treatment
     paxlovid_covid_therapeutics, sotrovimab_covid_therapeutics, remdesivir_covid_therapeutics, molnupiravir_covid_therapeutics, 
     casirivimab_covid_therapeutics, treatment_date, treatment_type,
+
+    # Last treatment code recorded 
+    last_treatment_date, last_treatment_type,
 
     # High risk cohort
     downs_syndrome, solid_cancer, haematological_disease, renal_disease, liver_disease, imid, immunosupression,