A mapping of diseases to their clinical features, represented as phecodes, is required for calculating phenotype risk scores.

## Usage

```
mapDiseaseToPhecode(
diseaseHpoMap = phers::diseaseHpoMap,
hpoPhecodeMap = phers::hpoPhecodeMap
)
```

## Arguments

- diseaseHpoMap
A data.table containing the mapping between diseases and HPO terms. Must have columns

`disease_id`

and`term_id`

. Default is the map included in this package.- hpoPhecodeMap
A data.table containing the mapping between HPO terms and phecodes. Must have columns

`term_id`

and`phecode`

. Default is the map included in this package.

## Examples

```
library('data.table')
library('survival')
# map ICD codes to phecodes
phecodeOccurrences = getPhecodeOccurrences(icdSample)
# calculate weights using the prevalence method
weightsPrev = getWeights(demoSample, phecodeOccurrences)
# calculate weights using the logistic method
weightsLogistic = getWeights(
demoSample, phecodeOccurrences, method = 'logistic', methodFormula = ~ sex)
# calculate weights using the loglinear method
phecodeOccurrences2 = phecodeOccurrences[, .(
num_occurrences = uniqueN(entry_date)), by = .(person_id, phecode)]
weightsLoglinear = getWeights(
demoSample, phecodeOccurrences2, method = 'loglinear', methodFormula = ~ sex)
# calculate weights using the cox method
phecodeOccurrences3 = phecodeOccurrences[, .(
first_occurrence_date = min(entry_date)) , by = .(person_id, phecode)]
phecodeOccurrences3 = merge(
phecodeOccurrences3, demoSample[, .(person_id, dob)], by = 'person_id')
phecodeOccurrences3[,
occurrence_age := as.numeric((first_occurrence_date - dob)/365.25)]
#> person_id phecode first_occurrence_date dob occurrence_age
#> 1: 1 365 2008-02-22 1999-09-03 8.472154
#> 2: 1 366 2006-02-15 1999-09-03 6.454358
#> 3: 1 735 2009-11-05 1999-09-03 10.175097
#> 4: 1 735.1 2009-11-05 1999-09-03 10.175097
#> 5: 2 442 2014-07-06 1995-09-26 18.777409
#> ---
#> 252: 49 474 2014-07-25 1999-10-21 14.759346
#> 253: 49 474.2 2014-07-25 1999-10-21 14.759346
#> 254: 49 496 2014-07-25 1999-10-21 14.759346
#> 255: 49 496.3 2014-07-25 1999-10-21 14.759346
#> 256: 49 963 2014-07-25 1999-10-21 14.759346
phecodeOccurrences3[, `:=`(first_occurrence_date = NULL, dob = NULL)]
#> person_id phecode occurrence_age
#> 1: 1 365 8.472154
#> 2: 1 366 6.454358
#> 3: 1 735 10.175097
#> 4: 1 735.1 10.175097
#> 5: 2 442 18.777409
#> ---
#> 252: 49 474 14.759346
#> 253: 49 474.2 14.759346
#> 254: 49 496 14.759346
#> 255: 49 496.3 14.759346
#> 256: 49 963 14.759346
demoSample3 = demoSample[, .(
person_id, sex,
first_age = as.numeric((first_visit_date - dob)/365.25),
last_age = as.numeric((last_visit_date - dob)/365.25))]
weightsCox = getWeights(
demoSample3, phecodeOccurrences3, method = 'cox', methodFormula = ~ sex)
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Ran out of iterations and did not converge
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Ran out of iterations and did not converge
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Ran out of iterations and did not converge
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
#> Warning: Loglik converged before variable 1 ; beta may be infinite.
```