diff --git a/vignettes/forestly.Rmd b/vignettes/forestly.Rmd index 8172b0c..85d9382 100644 --- a/vignettes/forestly.Rmd +++ b/vignettes/forestly.Rmd @@ -94,12 +94,20 @@ We then define the related population (`population = "apat"`) and observation (` ```{r} meta <- meta |> define_population( - name = "apat", group = "TRTA", id = "USUBJID", - subset = SAFFL == "Y", label = "All Patient as Treated" + name = "apat", + group = "TRTA", + id = "USUBJID", + subset = SAFFL == "Y", + label = "All Patient as Treated", + var = c("USUBJID", "SAFFL", "TRTA", "SITEID", "SEX", "RACE", "AGE") ) |> define_observation( - name = "apat", group = "TRTA", - subset = SAFFL == "Y", label = "All Patient as Treated" + name = "apat", + group = "TRTA", + subset = SAFFL == "Y", + label = "All Patient as Treated", + var = c("USUBJID", "SAFFL", "TRTA", "AEDECOD", "AEBODSYS", + "AEREL", "AESER", "AEOUT", "AEACN", "AESDTH", "ASTDT", "AENDT") ) ``` @@ -110,7 +118,8 @@ meta <- meta |> name = "any", subset = NULL, label = "Any AEs", - var = "AEDECOD", soc = "AEBODSYS" + var = "AEDECOD", + soc = "AEBODSYS" ) ``` For drug related AEs (`"drug-related"`), its filter is `AEREL %in% c("PROBABLE", "POSSIBLE")`. @@ -118,9 +127,10 @@ For drug related AEs (`"drug-related"`), its filter is `AEREL %in% c("PROBABLE", meta <- meta |> define_parameter( name = "drug-related", - subset = toupper(AREL) == "RELATED", + subset = toupper(AEREL) %in% c("PROBABLE", "POSSIBLE"), label = "Drug-related AEs", - var = "AEDECOD", soc = "AEBODSYS" + var = "AEDECOD", + soc = "AEBODSYS" ) ``` Similarly, we define serious AE and drug related serious AEs. @@ -130,13 +140,15 @@ meta <- meta |> name = "serious", subset = AESER == "Y", label = "Serious AEs", - var = "AEDECOD", soc = "AEBODSYS" + var = "AEDECOD", + soc = "AEBODSYS" ) |> define_parameter( name = "drug-related-serious", - subset = AESER == "Y" & AEREL %in% c("PROBABLE", "POSSIBLE"), + subset = AESER == "Y" & toupper(AEREL) %in% c("PROBABLE", "POSSIBLE"), label = "Drug-related serious AEs", - var = "AEDECOD", soc = "AEBODSYS" + var = "AEDECOD", + soc = "AEBODSYS" ) ```