link_ae_inpatient breaks when using the record_id argument

[andreamazzella]

I tried using link_ae_inpatient to join some ecds data with sus data. I have an incident-specific patient identifier that I would like to keep in the linked dataset, so I used the record_id = argument.

hoslink <- link_ae_inpatient(
    ae = list(
        data = ecds,
        record_id = "patient_id",
        arrival_date = 'arrival_date',
        departure_date = 'departure_date',
        nhs_number = 'nhs_number',
        patient_dob = 'patient_birth_date',
        hospital_number = 'local_patient_identifier',
        org_code = 'organisation_code_of_provider'
    ),
    inp = list(
        data = sus,
        record_id = "patient_id",
        spell_start_date = 'spell_start_date',
        spell_id = 'mega_spell_id',
        nhs_number = 'nhs_number',
        patient_dob = 'birth_date',
        hospital_number = 'local_patient_identifier',
        org_code = 'organisation_code_code_of_provider'
    ),
    .forceCopy = FALSE
)

This results in the following error:

Error in data.table::fifelse(is.na(NULL), NULL, NULL) :
attempt to set an attribute on NULL

This seems to be because within the function code, line 474 (copied below) is expecting list ae to be 7-element long, but in this case we include also record_id, so it's an 8-element list.

ids <- as.vector(unlist(lapply(ae[c(4:length(ae))],`[[`,1)))

ids returns:

"departure_date" "nhs_number" "patient_birth_date" "local_patient_identifier" "organisation_code_of_provider"

So then in the for loop that follows (copied below), fifelse(is.na(departure_date.ae), ... doesn't find departure_date.ae and the function breaks.

  for(i in ids){
    link[,(i) := data.table::fifelse(is.na(v1),v2,v1),
         env = list(
           v1 = linknames[[i]][1],
           v2 = linknames[[i]][2]
         )
    ]
  }

I patched this in my code by changing line 474 to the following:

ids <- as.vector(unlist(lapply(ae[c(5:length(ae))],`[[`,1)))

But it would be good for this line of code to be robust enough to cover scenarios with and without record_id = argument in the link_ae_inpatient lists.