When trying to replace values, “missing values are not allowed in subscripted assignments of data frames”

You can use ifelse, like so

pe94.person$foo <- ifelse(!is.na(pe94.person$H01) & pe94.person$H01 == 12, 0, pe94.person$H03)

check if foo meets your criteria and then go ahead and assign it to pe94.person$H03 directly. I find it safer to assign it a new variable and usually use that in subsequent analysis.

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