linERRscore: Compute the Firth-corrected score function

In sanderroberti/linearERRfit: Fit linear ERR models, including dose information to multiple locations

Description

Compute the Firth-corrected score for a matched case-control dataset

Usage

linERRscore(
  params,
  data,
  doses,
  set,
  status,
  loc,
  ccmethod,
  corrvars = NULL,
  repar = FALSE
)

Arguments

params	vector of parameters (β/ξ, α_2, ... , α_L, γ_1, ... , γ_p) for which to compute the modified score. Parameters α only need to be supplied when ccmethod="CL" or ccmethod="CCAL". Note that when repar=TRUE, ξ needs to be supplied
data	data frame containing matched case-control data, with a number of columns for doses to different locations, a column containing matched set numbers, a column containing the case's tumor location (value between 1 and the number of locations, with location x corresponding to the x-th column index in doses) and a column serving as a case-control indicator. Other covariates can also be included, in this case a parameter for each covariate column will be estimated. Hence factor variables need to be converted to dummy variables using model.matrix. If using ccmethod='meandose', a column for tumor location is still required but in this case the column can be a vector of ones.
doses	vector containing the indices of columns containing dose information.
set	column index containing matched set numbers.
status	column index containing case status.
loc	column index containing the location of the matched set's case's second tumor.
ccmethod	choice of method of analysis: one of meandose, CCML, CCAL or CL. Defaults to CCAL
corrvars	vector containing the indices of columns containing variables to be corrected for.
repar	reparametrize to β=exp(γ)? Note that this only affects the Firth modified score, not the original score. Defaults to FALSE.

Value

List object with components:

U	the original score
A	the modification to the score

The Firth corrected score is equal to U+A.

Examples

data(linearERRdata1)

# score in the truth
score1 <- linERRscore(params=c(.3,rep(-1.386294,4),log(2)),
data=linearERRdata1,set=1, doses=2:6, status=8, loc=7, corrvars=9,ccmethod="CCAL")

# score in the truth, reparametrized
score1_repar <- linERRscore(params=c(log(.3),rep(-1.386294,4),log(2)),
data=linearERRdata1,set=1, doses=2:6, status=8, loc=7, corrvars=9,ccmethod="CCAL", repar=TRUE)

score1$U # Original score
score1$U+score1$A # Firth score

score1_repar$U+score1_repar$A # Firth score under reparametrization

# score in 0
score2 <- linERRscore(params=c(0,rep(0,4),0),
data=linearERRdata1,set=1, doses=2:6, status=8, loc=7, corrvars=9, ccmethod="CCAL")

score2$U # Original score
score2$U+score2$A # Firth score

sanderroberti/linearERRfit documentation built on Nov. 8, 2021, 12:23 a.m.