remove missing population data

epiforecasts · Sep 11, 2024 · 3400e32 · 3400e32
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diff --git a/NEWS.md b/NEWS.md
@@ -1,6 +1,7 @@
 # socialmixr (development version)
 
 * The speed of loading surveys has been increased.
+* An error has been fixed causing NA contact matrices if any 5-year age band in the population data was missing.
 
 # socialmixr 0.3.2
 

diff --git a/R/contact_matrix.r b/R/contact_matrix.r
@@ -430,6 +430,8 @@ contact_matrix <- function(survey, countries = NULL, survey.pop, age.limits, fil
 
     # add upper.age.limit after sorting the survey.pop ages (and add maximum age > given ages)
     survey.pop <- survey.pop[order(lower.age.limit), ]
+    # if any lower age limits are missing remove them
+    survey.pop <- survey.pop[!is.na(population)]
     survey.pop$upper.age.limit <- unlist(c(
       survey.pop[-1, "lower.age.limit"],
       1 + max(