compute.absolute.risk: Building and Applying an Absolute Risk Model
In iCARE: A Tool for Individualized Coherent Absolute Risk Estimation (iCARE)

Description Usage Arguments Details Value Examples

This function is used to build absolute risk models and apply them to estimate absolute risks.

computeAbsoluteRisk(model.formula = NULL, model.cov.info = NULL,
  model.snp.info = NULL, model.log.RR = NULL, model.ref.dataset = NULL,
  model.ref.dataset.weights = NULL, model.disease.incidence.rates,
  model.competing.incidence.rates = NULL, model.bin.fh.name = NA,
  n.imp = 5, apply.age.start, apply.age.interval.length,
  apply.cov.profile = NULL, apply.snp.profile = NULL, use.c.code = 1,
  return.lp = FALSE, return.refs.risk = FALSE)

`model.formula`	an object of class `formula`: a symbolic description of the model to be fitted, e.g. Y~Parity+FamilyHistory.
`model.cov.info`	contains information about the risk factors in the model ; a main list containing a list for each covariate, which must have the fields: `"name"` : a string with the covariate name, matching name in model.formula `"type"` : a string that is either "continuous" or "factor". If factor variable, then: `"levels"` : vector with strings of level names `"ref"` : optional field, string with name of referent level
`model.snp.info`	dataframe with three columns, named: [ "snp.name", "snp.odds.ratio", "snp.freq" ]
`model.log.RR`	vector with log odds ratios corresponding to the model params; no intercept; names must match design matrix arising from `model.formula` and `model.cov.info`; check names using function `check_design_matrix()`.
`model.ref.dataset`	dataframe of risk factors for a sample of subjects representative of underlying population, no missing values. Variables must be in same order with same names as in `model.formula`.
`model.ref.dataset.weights`	optional vector of sampling weights for `model.ref.dataset`.
`model.disease.incidence.rates`	two column matrix [ integer ages, incidence rates] or three column matrix [start age, end age, rate] with incidence rate of disease. Must fully cover age interval for estimation.
`model.competing.incidence.rates`	two column matrix [ integer ages, incidence rates] or three column matrix [start age, end age, rate] with incidence rate of competing events. Must fully cover age interval for estimation.
`model.bin.fh.name`	string name of family history variable, if in model. This must refer to a variable that only takes values 0,1, NA.
`n.imp`	integer value for number of imputations for handling missing SNPs.
`apply.age.start`	single integer or vector of integer ages for the start of the interval over which to compute absolute risk.
`apply.age.interval.length`	single integer or vector of integer years over which absolute risk should be computed.
`apply.cov.profile`	dataframe containing the covariate profiles for which absolute risk will be computed. Covariates must be in same order with same names as in `model.formula`.
`apply.snp.profile`	data frame with observed SNP data (coded 0,1, 2, or NA). May have missing values.
`use.c.code`	binary indicator of whether to run the c program for fast computation.
`return.lp`	binary indicator of whether to return the linear predictor for each subject in apply.cov.profile.
`return.refs.risk`	binary indicator of whether to return the absolute risk prediction for each subject in `model.ref.dataset`.

Individualized Coherent Absolute Risk Estimators (iCARE) is a tool that allows researchers to quickly build models for absolute risk and apply them to estimate individuals' risk based on a set of user defined input parameters. The software gives users the flexibility to change or update models rapidly based on new risk factors or tailor models to different populations based on the specification of simply three input arguments:

(1) a model for relative risk assumed to be externally derived
(2) an age-specific disease incidence rate and
(3) the distribution of risk factors for the population of interest.

The tool can handle missing information on risk factors for risk estimation using an approach where all estimates are derived from a single model through appropriate model averaging.

This function returns a list of results objects, including:

risk : absolute risk estimates over the specified interval for subjects given by apply.cov.profile
details: dataframe with the start of the interval, the end of the interval, the covariate profile, and the risk estimates for each individual
beta.used : the log odds ratios used in the model
lps : linear predictors for subjects in model.cov.profile, if requested by return.lp
refs.risk : absolute risk estimates for subjects in model.ref.dataset, if requested by return.refs.risk; computes for first age interval provided

data(bc_data, package="iCARE")
results = computeAbsoluteRisk(model.formula=bc_model_formula, 
                                 model.cov.info    = bc_model_cov_info,
                                 model.snp.info    = bc_72_snps,
                                 model.log.RR      = bc_model_log_or,
                                 model.ref.dataset = ref_cov_dat,
                                 model.disease.incidence.rates   = bc_inc,
                                 model.competing.incidence.rates = mort_inc, 
                                 model.bin.fh.name = "famhist",
                                 apply.age.start    = 50, 
                                 apply.age.interval.length = 30,
                                 apply.cov.profile  = new_cov_prof,
                                 apply.snp.profile  = new_snp_prof, 
                                 return.refs.risk   = TRUE)
summary(results)
plot(results, main="Risk")
boxplot(results$risk ~ new_cov_prof$famhist, na.rm=TRUE)