calculate incidence rate per 1000 person-years

opensafely · Apr 15, 2024 · fa263f4 · fa263f4
1 parent c92d63d
commit fa263f4
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Showing 13 changed files with 713 additions and 127 deletions.
diff --git a/.RData b/.RData
diff --git a/analysis/data_processing.R b/analysis/data_processing.R
diff --git a/analysis/dummydata/dummydata_adults.R b/analysis/dummydata/dummydata_adults.R
@@ -248,7 +248,9 @@ sim_list = lst(
 
   #date
   rsv_primary_day = bn_node(
-    ~ as.integer(runif(n = ..n, index_day, index_day + 365))
+    ~ ifelse(rsv_primary == TRUE, 
+             as.integer(runif(n = ..n, index_day, index_day + 365)), 
+             NA)
   ),
 
   #number of cases
@@ -263,7 +265,9 @@ sim_list = lst(
 
   #date
   rsv_secondary_day = bn_node(
-    ~ as.integer(runif(n = ..n, index_day, index_day + 365))
+    ~ ifelse(rsv_secondary == TRUE, 
+             as.integer(runif(n = ..n, index_day, index_day + 365)),
+             NA)
   ),
 
   #rsv secondary length of stay
@@ -283,7 +287,9 @@ sim_list = lst(
 
   #date
   flu_primary_day = bn_node(
-    ~ as.integer(runif(n = ..n, index_day, index_day + 365))
+    ~ ifelse(flu_primary == TRUE,
+             as.integer(runif(n = ..n, index_day, index_day + 365)),
+             NA)
   ),
 
   #number of cases
@@ -298,7 +304,9 @@ sim_list = lst(
 
   #date
   flu_secondary_day = bn_node(
-    ~ as.integer(runif(n = ..n, index_day, index_day + 365))
+    ~ ifelse(flu_secondary == TRUE,
+             as.integer(runif(n = ..n, index_day, index_day + 365)),
+             NA)
   ),
 
   #flu secondary length of stay
@@ -318,7 +326,9 @@ sim_list = lst(
 
   #date
   covid_primary_day = bn_node(
-    ~ as.integer(runif(n = ..n, index_day, index_day + 365))
+    ~ ifelse(covid_primary == TRUE,
+             as.integer(runif(n = ..n, index_day, index_day + 365)),
+             NA)
   ),
 
   #number of cases
@@ -333,7 +343,9 @@ sim_list = lst(
 
   #date
   covid_secondary_day = bn_node(
-    ~ as.integer(runif(n = ..n, index_day, index_day + 365))
+    ~ ifelse(covid_secondary == TRUE,
+             as.integer(runif(n = ..n, index_day, index_day + 365)),
+             NA)
   ),
 
   #covid secondary length of stay
@@ -353,7 +365,9 @@ sim_list = lst(
 
   #date
   overall_resp_primary_day = bn_node(
-    ~ as.integer(runif(n = ..n, index_day, index_day + 365))
+    ~ ifelse(overall_resp_primary == TRUE,
+             as.integer(runif(n = ..n, index_day, index_day + 365)),
+             NA)
   ),
 
   #number of cases
@@ -368,7 +382,9 @@ sim_list = lst(
 
   #date
   overall_resp_secondary_day = bn_node(
-    ~ as.integer(runif(n = ..n, index_day, index_day + 365))
+    ~ ifelse(overall_resp_secondary == TRUE,
+             as.integer(runif(n = ..n, index_day, index_day + 365)),
+             NA)
   ),
 
   #unspecified respiratory infection secondary length of stay
@@ -390,7 +406,9 @@ sim_list = lst(
 
   #date
   rsv_mortality_day = bn_node(
-    ~ as.integer(runif(n = ..n, index_day, index_day + 365)) 
+    ~ ifelse(rsv_mortality == TRUE,
+             as.integer(runif(n = ..n, index_day, index_day + 365)),
+             NA)
   ),
 
   #flu mortality
@@ -400,7 +418,9 @@ sim_list = lst(
 
   #date
   flu_mortality_day = bn_node(
-    ~ as.integer(runif(n = ..n, index_day, index_day + 365)) 
+    ~ ifelse(flu_mortality == TRUE,
+             as.integer(runif(n = ..n, index_day, index_day + 365)),
+             NA)
   ),
 
   #covid mortality
@@ -410,7 +430,9 @@ sim_list = lst(
 
   #date
   covid_mortality_day = bn_node(
-    ~ as.integer(runif(n = ..n, index_day, index_day + 365)) 
+    ~ ifelse(covid_mortality == TRUE,
+             as.integer(runif(n = ..n, index_day, index_day + 365)),
+             NA)
   ),
 
   #unspecified respiratory infection secondary care
@@ -420,7 +442,9 @@ sim_list = lst(
 
   #date
   overall_resp_mortality_day = bn_node(
-    ~ as.integer(runif(n = ..n, index_day, index_day + 365))
+    ~ ifelse(overall_resp_mortality == TRUE,
+             as.integer(runif(n = ..n, index_day, index_day + 365)),
+             NA)
   ),
 
   #all cause mortality
@@ -430,7 +454,9 @@ sim_list = lst(
 
   #date
   all_cause_mortality_day = bn_node(
-    ~ as.integer(runif(n = ..n, index_day, index_day + 365))
+    ~ ifelse(all_cause_mortality == TRUE,
+             as.integer(runif(n = ..n, index_day, index_day + 365)),
+             NA)
   ),
 
   ##exclusion criteria

diff --git a/analysis/dummydata/dummydata_children_and_adolescents.R b/analysis/dummydata/dummydata_children_and_adolescents.R
@@ -157,7 +157,9 @@ sim_list = lst(
 
   #date
   rsv_primary_day = bn_node(
-    ~ as.integer(runif(n = ..n, index_day, index_day + 365))
+    ~ ifelse(rsv_primary == TRUE, 
+             as.integer(runif(n = ..n, index_day, index_day + 365)), 
+             NA)
   ),
 
   #number of cases
@@ -172,7 +174,9 @@ sim_list = lst(
 
   #date
   rsv_secondary_day = bn_node(
-    ~ as.integer(runif(n = ..n, index_day, index_day + 365))
+    ~ ifelse(rsv_secondary == TRUE, 
+             as.integer(runif(n = ..n, index_day, index_day + 365)),
+             NA)
   ),
 
   #rsv secondary length of stay
@@ -192,7 +196,9 @@ sim_list = lst(
 
   #date
   flu_primary_day = bn_node(
-    ~ as.integer(runif(n = ..n, index_day, index_day + 365))
+    ~ ifelse(flu_primary == TRUE,
+             as.integer(runif(n = ..n, index_day, index_day + 365)),
+             NA)
   ),
 
   #number of cases
@@ -207,7 +213,9 @@ sim_list = lst(
 
   #date
   flu_secondary_day = bn_node(
-    ~ as.integer(runif(n = ..n, index_day, index_day + 365))
+    ~ ifelse(flu_secondary == TRUE,
+             as.integer(runif(n = ..n, index_day, index_day + 365)),
+             NA)
   ),
 
   #flu secondary length of stay
@@ -227,7 +235,9 @@ sim_list = lst(
 
   #date
   covid_primary_day = bn_node(
-    ~ as.integer(runif(n = ..n, index_day, index_day + 365))
+    ~ ifelse(covid_primary == TRUE,
+             as.integer(runif(n = ..n, index_day, index_day + 365)),
+             NA)
   ),
 
   #number of cases
@@ -242,7 +252,9 @@ sim_list = lst(
 
   #date
   covid_secondary_day = bn_node(
-    ~ as.integer(runif(n = ..n, index_day, index_day + 365))
+    ~ ifelse(covid_secondary == TRUE,
+             as.integer(runif(n = ..n, index_day, index_day + 365)),
+             NA)
   ),
 
   #covid secondary length of stay
@@ -262,7 +274,9 @@ sim_list = lst(
 
   #date
   overall_resp_primary_day = bn_node(
-    ~ as.integer(runif(n = ..n, index_day, index_day + 365))
+    ~ ifelse(overall_resp_primary == TRUE,
+             as.integer(runif(n = ..n, index_day, index_day + 365)),
+             NA)
   ),
 
   #number of cases
@@ -277,7 +291,9 @@ sim_list = lst(
 
   #date
   overall_resp_secondary_day = bn_node(
-    ~ as.integer(runif(n = ..n, index_day, index_day + 365))
+    ~ ifelse(overall_resp_secondary == TRUE,
+             as.integer(runif(n = ..n, index_day, index_day + 365)),
+             NA)
   ),
 
   #unspecified respiratory infection secondary length of stay
@@ -299,7 +315,9 @@ sim_list = lst(
 
   #date
   rsv_mortality_day = bn_node(
-    ~ as.integer(runif(n = ..n, index_day, index_day + 365)) 
+    ~ ifelse(rsv_mortality == TRUE,
+             as.integer(runif(n = ..n, index_day, index_day + 365)),
+             NA)
   ),
 
   #flu mortality
@@ -309,7 +327,9 @@ sim_list = lst(
 
   #date
   flu_mortality_day = bn_node(
-    ~ as.integer(runif(n = ..n, index_day, index_day + 365)) 
+    ~ ifelse(flu_mortality == TRUE,
+             as.integer(runif(n = ..n, index_day, index_day + 365)),
+             NA)
   ),
 
   #covid mortality
@@ -319,7 +339,9 @@ sim_list = lst(
 
   #date
   covid_mortality_day = bn_node(
-    ~ as.integer(runif(n = ..n, index_day, index_day + 365)) 
+    ~ ifelse(covid_mortality == TRUE,
+             as.integer(runif(n = ..n, index_day, index_day + 365)),
+             NA)
   ),
 
   #unspecified respiratory infection secondary care
@@ -329,7 +351,9 @@ sim_list = lst(
 
   #date
   overall_resp_mortality_day = bn_node(
-    ~ as.integer(runif(n = ..n, index_day, index_day + 365))
+    ~ ifelse(overall_resp_mortality == TRUE,
+             as.integer(runif(n = ..n, index_day, index_day + 365)),
+             NA)
   ),
 
   #all cause mortality
@@ -339,7 +363,9 @@ sim_list = lst(
 
   #date
   all_cause_mortality_day = bn_node(
-    ~ as.integer(runif(n = ..n, index_day, index_day + 365))
+    ~ ifelse(all_cause_mortality == TRUE,
+             as.integer(runif(n = ..n, index_day, index_day + 365)),
+             NA)
   ),
 
   #care home resident