View source: R/create_sosvar.R
create_sosvar | R Documentation |
Calculates comorbidities and outcomes (including time to for the latter) from DIA, OP and ekod variables from National Patient Registry.
create_sosvar( type, name, sosdata, cohortdata, patid = lopnr, indexdate = indexdtm, add_unique, sosdate = sosdtm, censdate, allowedcenslimit = 0, noof = FALSE, comduration = FALSE, starttime = ifelse(type == "com", 0, 1), stoptime, diakod, opkod, ekod, diakodneg = FALSE, opkodneg = FALSE, ekodneg = FALSE, diavar = DIA_all, opvar = OP_all, evar = ekod_all, valsclass = "num", meta_reg = "NPR (in+out)", meta_pos, warnings = TRUE )
type |
Possible values are "out" and "com". Is the resulting variable an outcome (and time to is calculated) or comorbidity? |
name |
Name of resulting variable (prefix sos_out_ is added to outcome and sos_com_ to comorbidity). |
sosdata |
Data where DIA, OP, Ekod variables are found. |
cohortdata |
Data containing the cohort with at least columns patid and indexdate. |
patid |
Patient identifier. Default is lopnr. |
indexdate |
Index date for the patient (usually date of admission or discharge entered into SwedeHF). Default is indexdtm. |
add_unique |
If patid and indexdate are not unique in cohortdata, this identifies unique posts. |
sosdate |
Date of incident (comorbidity or outcome) in sosdata. Default is sosdtm. |
censdate |
Vector of dates. Only applicable for type = "out". Outcomes are allowed up until this day (usually date of death or end follow-up). |
allowedcenslimit |
Optional single value with allowed time unit between sosdate and censdate that still makes the sosdate be a valid event. Used for example when patients who are discharged day after death should still be counted as an event. Can cause unexpected results if the sos_data contains information > than last follow-up. |
noof |
Should comorbs/outcomes be number of or first? Default it first (FALSE). No time to is calculated for noof = TRUE and type = "out". |
comduration |
Should duration of the comorbidity be calculated (TRUE). Default is FALSE. |
starttime |
If type = "out" amount of time (in days) AFTER indexdate to start counting outcomes. If type = "com" amount of time (in days) PRIOR to indexdate. Indexdate = 0, all values prior to indexdate are negative. Default is 1 ("out") and 0 ("com"). |
stoptime |
If type = "out" amount of time (in days) AFTER indexdate to be counted. Note that censdate will be adjusted to stoptime. If type = "com" amount of time (in days) PRIOR to indexdate. Indexdate = 0, all values prior to indexdate are negative. Default is any time prior to starttime is considered a comorbidity and any time after starttime is considered an outcome. |
diakod |
String of icd codes as a regular expression defining the outcome/comorbidity. Should start with blank space " ". Also see diakodneg. |
opkod |
String of procedure codes as a regular expression defining the outcome/comorbidity. Should start with blank space " ". Also see opkodneg. |
ekod |
String of e codes as a regular expression defining the outcome/comorbidity. Should start with blank space " ". Also see ekodneg. |
diakodneg |
Should return non-matching codes in diakod? Default is FALSE. |
opkodneg |
Should return non-matching codes in opkod? Default is FALSE. |
ekodneg |
Should return non-matching codes in ekod? Default is FALSE. |
diavar |
Column where diakod is found. All codes should start with blank space " ". Default is DIA_all. |
opvar |
Column where opkod is found. All codes should start with blank space " ". Default is OP_all. |
evar |
Column where ekod is found. All codes should start with blank space " ". Default is ekod_all. |
valsclass |
optional argument specifying the class of the comorbidities/outcomes. Allowed values are "num" (numeric: 1, 0), "char" (character: "Yes", "No"), "fac" (factor: "Yes", "No"). Default is "num". |
meta_reg |
Optional argument specifying registries used. Printed in metadatatable. Default is "NPR (in+out)". |
meta_pos |
Optional argument specifying positions used to search for outcomes/comorbidities. Printed in metadatatable. |
warnings |
Should warnings be printed. Default is FALSE. |
dataset with column containing comorbidity/outcome. Also dataset metaout that writes directly to global enviroment with information on constructed variables.
prep_sosdata
create_deathvar
sos_data <- prep_sosdata(sos_data, evar = "ekod") rs_data <- create_sosvar( sosdata = sos_data, cohortdata = rs_data, patid = id, indexdate = indexdtm, sosdate = sosdtm, type = "com", name = "cv1y", diakod = " I", stoptime = -365.25, warnings = FALSE )
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