This is the third step of codify() %>% classify() %>% index(). The function takes classified case data and calculates (weighted) index sums as specified by weights from a classcodes object.

index(classified, ...)

# S3 method for data.frame
index(classified, ...)

# S3 method for matrix
index(classified, index = NULL, cc = NULL, ...)

Arguments

classified

output from classify()

...

used internally

index

name of column with 'weights' from corresponding classcodes object. Can be NULL if the index is just a unweighted count of all identified groups.

cc

classcodes object. Can be NULL if a classcodes object is already available as an attribute of classified (which is often the case) and/or if index = NULL.

Value

Named numeric index vector with names corresponding to rownames(classified)

Details

Index weights for subordinate hierarchical classes (as identified by attr(cc, "hierarchy")) are excluded in presence of superior classes if index specified with argument index.

See also

Other verbs: categorize(), classify(), codify()

Examples

# Prepare some codified data with ICD-10 codes during 1 year (365 days) # before surgery x <- codify( ex_people, ex_icd10, id = "name", code = "icd10", date = "surgery", days = c(-365, 0), code_date = "admission" ) # Classify those patients by the Charlson comorbidity indices cl <- classify(x, "charlson")
#> Warning: 'classify()' does not preserve row order ('categorize()' does!)
#> Classification based on: icd10
# Calculate (weighted) index values head(index(cl)) # Un-weighted sum/no of conditions for each patient
#> index calculated as number of relevant categories
#> Connelly, Monta Garcia Hyett, Brenda Martinez Botello, Luz #> 0 0 0 #> Marton, Gabriella Mitchell, John Nelson, Cory #> 0 0 0
head(index(cl, "quan_original")) # Weighted index (Quan et al. 2005; see `?charlson`)
#> Connelly, Monta Garcia Hyett, Brenda Martinez Botello, Luz #> 0 0 0 #> Marton, Gabriella Mitchell, John Nelson, Cory #> 0 0 0
head(index(cl, "quan_updated")) # Weighted index (Quan et al. 2011; see `?charlson`)
#> Connelly, Monta Garcia Hyett, Brenda Martinez Botello, Luz #> 0 0 0 #> Marton, Gabriella Mitchell, John Nelson, Cory #> 0 0 0
# Tabulate index for all patients. # As expected, most patients are healthy and have index = 0/NA, # where NA indicates no recorded hospital visits # found in `ex_icd10` during codification. # In practice, those patients might be assumed to have 0 comorbidity as well. table(index(cl, "quan_original"), useNA = "always")
#> #> 0 1 2 3 6 <NA> #> 74 5 4 1 1 15
# If `cl` is a matrix without additional attributes (as imposed by `codify()`) # an explicit classcodes object must be specified by the `cc` argument cl2 <- as.matrix(cl) head(index(cl2, cc = "charlson"))
#> index calculated as number of relevant categories
#> Connelly, Monta Garcia Hyett, Brenda Martinez Botello, Luz #> 0 0 0 #> Marton, Gabriella Mitchell, John Nelson, Cory #> 0 0 0