plotModelValidation: Model Validation Plot

In iCARE: A Tool for Individualized Coherent Absolute Risk Estimation (iCARE)

Description

This function is used to create plots for model calibration, model discrimination and incidence rates.

Usage

plotModelValidation(study.data, validation.results,
                    dataset = "Example Dataset",
                    model.name = "Example Model",
                    x.lim.absrisk = "",
                    y.lim.absrisk = "", 
                    x.lab.absrisk = "Expected Absolute Risk (%)", 
                    y.lab.absrisk = "Observed Absolute Risk (%)", 
                    x.lim.RR = "",
                    y.lim.RR = "", x.lab.RR = "Expected Relative Risk", 
                    y.lab.RR = "Observed Relative Risk",
                    risk.score.plot.kernel = "gaussian",
                    risk.score.plot.bandwidth = "nrd0",
                    risk.score.plot.percent.smooth = 50)

Arguments

study.data	See ModelValidation
validation.results	List returned from ModelValidation
dataset	Name and type of dataset to be displayed in the output, e.g., "PLCO Full Cohort" or "Full Cohort Simulation"
model.name	Name of the model to be displayed in output, e.g., "Synthetic Model" or "Simulation Setting"
x.lim.absrisk	Vector of length two specifying the x-axes limits in the absolute risk calibration plot. If not specified, then default limits will be computed.
y.lim.absrisk	Vector of length two specifying the y-axes limits in the absolute risk calibration plot. If not specified, then default limits will be computed.
x.lab.absrisk	String specifying the x-axes label in the absolute risk calibration plot. The default is "Expected Absolute Risk (%)".
y.lab.absrisk	String specifying the y-axes label in the absolute risk calibration plot. The default is "Observed Absolute Risk (%)."
x.lim.RR	Vector of length two specifying the x-axes limits in the relative risk calibration plot. If not specified, then default limits will be computed.
y.lim.RR	Vector of length two specifying the y-axes limits in the relative risk calibration plot. If not specified, then default limits will be computed.
x.lab.RR	String specifying the x-axes label in the relative risk calibration plot. The default is "Expected Relative Risk".
y.lab.RR	String specifying the y-axes label in the relative risk calibration plot. The default is "Observed Relative Risk".
risk.score.plot.kernel	Character string giving the smoothing kernel to be used by the density function used internally to plot the density of the risk scores. It should be one of "gaussian", "rectangular", "triangular", "epanechnikov", "biweight", "cosine" or "optcosine", with default "gaussian".
risk.score.plot.bandwidth	The options for bandwidth selection used by the density function internally to plot the density of the risk scores. The options are one of the following: "nrd0", "nrd", "ucv", "bcv", "SJ-ste", "SJ-dpi" with the default being "nrd0". More information on these different options is available in the help pages that can be accessed from R using the command ?bw.nrd.
risk.score.plot.percent.smooth	Percentage of the number of sample points used for determining the number of equally spaced points at which the density of the risk score is to be estimated. This number supplies the input parameter "n" to the density function used internally to plot the densities of the risk score. The default value is 50.

Value

This function returns NULL

See Also

ModelValidation

Examples

data(bc_data, package="iCARE")
validation.cohort.data$inclusion = 0
subjects_included = intersect(validation.cohort.data$id, 
                              validation.nested.case.control.data$id)
validation.cohort.data$inclusion[subjects_included] = 1

validation.cohort.data$observed.followup = validation.cohort.data$study.exit.age - 
  validation.cohort.data$study.entry.age

selection.model = glm(inclusion ~ observed.outcome 
                      * (study.entry.age + observed.followup), 
                      data = validation.cohort.data, 
                      family = binomial(link = "logit"))

validation.nested.case.control.data$sampling.weights =
  selection.model$fitted.values[validation.cohort.data$inclusion == 1]

set.seed(50)

data = validation.nested.case.control.data

snpDat     = bc_72_snps
form       = diagnosis ~ famhist + as.factor(parity)
info       = list(bc_model_cov_info[[1]], bc_model_cov_info[[3]])
vars       = all.vars(form)[-1]
risk.model = list(model.formula = form,
                  model.cov.info = info,
                  model.snp.info = snpDat,
                  model.log.RR = bc_model_log_or[c(1, 8:11)],
                  model.ref.dataset = ref_cov_dat[, vars],
                  model.ref.dataset.weights = NULL,
                  model.disease.incidence.rates = bc_inc,
                  model.competing.incidence.rates = mort_inc,
                  model.bin.fh.name = "famhist",
                  apply.cov.profile = data[,vars],
                  apply.snp.profile = data[,snpDat$snp.name],
                  n.imp = 5, use.c.code = 1, return.lp = TRUE,
                  return.refs.risk = TRUE)

# Not run since it can take a few minutes
#output = ModelValidation(study.data = data, total.followup.validation = TRUE,
#          predicted.risk.interval = NULL, iCARE.model.object = risk.model,
#          number.of.percentiles = 10)

plot(output)

iCARE documentation built on Nov. 8, 2020, 5:25 p.m.