Merge pull request #38 from vimc/vimc-7312

Vimc 7312: update to recognise MenCWYX burden outcomes

Author: kgaythorpe

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: vimpact
 Title: Vaccine Impact Calculation
-Version: 0.1.2
+Version: 0.1.3
 Authors@R:
     c(person(given = "Rich",
              family = "FitzJohn",
@@ -34,6 +34,6 @@ Suggests:
     RSQLite,
     withr
 Remotes: reside-ic/fakerbase
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 VignetteBuilder: knitr
 Config/testthat/edition: 3

NEWS.md

@@ -1,3 +1,7 @@
+# vimpact 0.1.3
+
+* Recognise new burden outcomes.
+
 # vimpact 0.1.2
 
 * Add to readme installation instruction.

R/impact_central.R

@@ -1,7 +1,8 @@
 get_raw_impact_details <- function(con, meta1, burden_outcome, is_under5 = FALSE, countries_to_extract = NULL){
   #verify parameters
   stopifnot(nrow(meta1) == 2L)
-  stopifnot(burden_outcome %in% c("deaths", "cases", "dalys", "yll"))
+  stopifnot(burden_outcome %in% c("deaths", "cases", "dalys", "yll",
+                                  "deaths_cwyx", "cases_cwyx", "dalys_cwyx", "yll_cwyx")) # _cwyx outcomes are MenA specific.
   stopifnot(is_under5 %in% c(TRUE, FALSE))
 
   #preparation
@@ -12,10 +13,18 @@ get_raw_impact_details <- function(con, meta1, burden_outcome, is_under5 = FALSE
     k <- 2
   } else if(burden_outcome == "dalys"){
     k <- 3
-  }else if(burden_outcome == "yll"){
+  } else if(burden_outcome == "yll"){
     k <- 4
+  } else if(burden_outcome == "deaths_cwyx"){
+    k <- 5
+  } else if(burden_outcome == "cases_cwyx"){
+    k <- 6
+  } else if(burden_outcome == "dalys_cwyx"){
+    k <- 7
+  } else if(burden_outcome == "yll_cwyx"){
+    k <- 8
   } else {
-    stop("Can only take burden outcome as one of deaths, cases, dalys, yll")
+    stop("Can only take burden outcome as one of deaths, cases, dalys, yll, deaths_cwyx, cases_cwyx, dalys_cwyx, yll_cwyx")
   }
 
   # determine whether a recipe is for routine or campaign vaccine delivery

R/impact_meta.R

@@ -213,22 +213,22 @@ replace_burden_outcome <- function(burden_outcomes, a){
     }
     m2 <- m
     ii <- 1
-    k <- grepl("deaths", v)
+    k <- grepl("deaths", v) & !grepl("cwyx", v)
     if(any(k)){
       m2[ii] <- m[k]
       ii <- ii+1
     }
-    k <- grepl("cases", v)
+    k <- grepl("cases", v) & !grepl("cwyx", v)
     if(any(k)){
       m2[ii] <- m[k]
       ii <- ii+1
     }
-    k <- grepl("dalys", v)
+    k <- grepl("dalys", v) & !grepl("cwyx", v)
     if(any(k)){
       m2[ii] <- m[k]
       ii <- ii+1
     }
-    k <- grepl("yll", v)
+    k <- grepl("yll", v) & !grepl("cwyx", v)
     if(any(k)){
       m2[ii] <- m[k]
       ii <- ii+1