Merge pull request #24 from UCD-SERG/scrub-vignette

add n, fixed antigen_isos bug
UCD-SERG · Nov 9, 2023 · b71947f · b71947f
2 parents 513c231 + 3313afd
commit b71947f
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diff --git a/R/est.incidence.by.R b/R/est.incidence.by.R
@@ -89,6 +89,7 @@ est.incidence.by <- function(
         fun = function(x)
           .optNll(
             dataList = x,
+            antigen_isos = antigen_isos,
             ...)
       )
     } |> system.time() -> time
@@ -122,6 +123,7 @@ est.incidence.by <- function(
       fits[[cur_stratum]] =
         .optNll(
           dataList = stratumDataList[[cur_stratum]],
+          antigen_isos = antigen_isos,
           verbose = verbose,
           ...)
 

diff --git a/R/get_strata.R b/R/get_strata.R
@@ -2,7 +2,8 @@ get_strata = function(data, strata_varnames)
 {
   to_return =
     data |>
-    distinct(across(any_of(strata_varnames))) |>
+    count(across(any_of(c(strata_varnames, "antigen_iso")))) |>
+    distinct(across(any_of(c(strata_varnames, "n")))) |>
     mutate(Stratum = paste("Stratum", row_number()))
 
 }