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## ----------------------------------------------------------------------------
## Author: Jason W. Morgan
## URL: http://leftcensored.skepsi.net
## Date: 2011.06.21
##
## Description: This file contains functions for extracting model summaries
## according to the requirements of mtable() and toLatex() available in the
## memisc packages.
##
## Note: This code is based heavily on the examples and functions provided by
## Martin Elff in his memisc package. If you find it useful, you should cite
## *his* work. You can find his website here: http://www.martin-elff.net
##
## Copyright 2011 Jason W. Morgan
##
## This program is free software: you can redistribute it and/or modify it
## under the terms of the GNU General Public License as published by the Free
## Software Foundation, either version 3 of the License, or (at your option)
## any later version.
##
## This program is distributed in the hope that it will be useful, but WITHOUT
## ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
## FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
## more details.
##
## You should have received a copy of the GNU General Public License along with
## this program. If not, see <http://www.gnu.org/licenses/>.
## ----------------------------------------------------------------------------
## ----------------------------------------------------------------------------
## Supported model types
## ----------------------------------------------------------------------------
##
## coxph, survreg - Cox proportional hazards models and parametric survival
## models from the survival library.
##
## aftreg, phreg, weibreg - parametric AFT, proportional hazards, and Weibull
## models available from the eha library.
##
## mer - multilevel mixed effects models as provided by the lme4 package. The
## model objects produced in the beta lme4a package are not supported.
##
## ----------------------------------------------------------------------------
## ----------------------------------------------------------------------------
## Summary functions for survival objects.
## ----------------------------------------------------------------------------
setSummaryTemplate(coxph = c("Log-likelihood" = "($logLik:f#)",
"AIC" = "($AIC:f#)",
"BIC" = "($BIC:f#)",
"N" = "($N:d)"))
setSummaryTemplate(survreg = c("Log-likelihood" = "($logLik:f#)",
"AIC" = "($AIC:f#)",
"BIC" = "($BIC:f#)",
"N" = "($N:d)"))
setSummaryTemplate(phreg = c("Log-likelihood" = "($logLik:f#)",
"AIC" = "($AIC:f#)",
"BIC" = "($BIC:f#)",
"N" = "($N:d)"))
getSummary.coxph <- function(obj, alpha = 0.05, ...) {
N <- obj$n
## Take the info right out of the object to guarantee that I get the right
## standard errors.
b <- coef(obj)
se <- sqrt(diag(vcov(obj)))
coef <- cbind(b, se, b / se, 1-pnorm(abs(b/se)))
lower <- qnorm(p = alpha/2, mean = coef[, 1], sd = coef[,2])
upper <- qnorm(p = 1 - alpha/2, mean = coef[, 1], sd = coef[,2])
coef <- cbind(coef, lower, upper)
# Patched by ME 2017-09-02
dn <- list(
rownames(coef),
c("est","se","stat","p","lwr","upr"),
rownames(attr(obj$terms,"factors"))[1]
)
dim(coef) <- c(dim(coef)[1],dim(coef)[2],1)
dimnames(coef) <- dn
ll <- obj$loglik[2]
K <- length(b)
AIC <- -2*ll + 2*K
BIC <- -2*ll + K*log(N)
sumstat <- c(logLik = ll, AIC = AIC, BIC = BIC, N = N)
list(coef = coef,
sumstat = sumstat,
contrasts = obj$contrasts,
xlevels = obj$xlevels,
call = obj$call)
}
getSummary.survreg <- function(obj, alpha = 0.05, ...) {
coef <- cbind(c(coef(obj), obj$scale), c(sqrt(diag(obj$var)),NA))
K <- length(coef) - 1
N <- obj$df.residual + K
stat <- coef[, 1] / coef[, 2]
pval <- 1-pnorm(abs(stat))
lower <- qnorm(p = alpha/2, mean = coef[, 1], sd = coef[,2])
upper <- qnorm(p = 1 - alpha/2, mean = coef[, 1], sd = coef[,2])
coef <- cbind(coef, stat, pval, lower, upper)
# Patched by ME 2017-09-02
dn <- list(
rownames(coef),
c("est","se","stat","p","lwr","upr"),
rownames(attr(obj$terms,"factors"))[1]
)
dim(coef) <- c(dim(coef)[1],dim(coef)[2],1)
dimnames(coef) <- dn
rownames(coef)[nrow(coef)] <- "scale"
pv <- c("(Intercept)",colnames(attr(obj$terms,"factors")))
pv <- match(pv,rownames(coef),nomatch=0)
distparms <- coef[-pv,,,drop=FALSE]
coef <- coef[pv,,,drop=FALSE]
ll <- obj$loglik[2]
AIC <- -2*ll + 2*K
BIC <- -2*ll + K*log(N)
sumstat <- c(logLik = ll, AIC = AIC, BIC = BIC, N = N)
list(coef = coef,
distparms = distparms,
sumstat = sumstat,
contrasts = obj$contrasts,
xlevels = obj$xlevels,
call = obj$call)
}
## aftreg(), phreg(), weibreg() are part of the eha package.
getSummary.aftreg <- function(obj, alpha = 0.05, ...) {
N <- obj$n
coef <- cbind(coef(obj), sqrt(diag(obj$var)))
stat <- coef[, 1] / coef[, 2]
pval <- 1-pnorm(abs(stat))
lower <- qnorm(p = alpha/2, mean = coef[, 1], sd = coef[, 2])
upper <- qnorm(p = 1 - alpha/2, mean = coef[, 1], sd = coef[, 2])
coef <- cbind(coef, stat, pval, lower, upper)
# Patched by ME 2017-09-02
dn <- list(
rownames(coef),
c("est","se","stat","p","lwr","upr"),
rownames(attr(obj$terms,"factors"))[1]
)
dim(coef) <- c(dim(coef)[1],dim(coef)[2],1)
dimnames(coef) <- dn
pv <- colnames(attr(obj$terms,"factors"))
pv <- match(pv,rownames(coef))
distparms <- coef[-pv,,,drop=FALSE]
coef <- coef[pv,,,drop=FALSE]
ll <- obj$loglik[2]
K <- length(coef[,1,])
AIC <- -2*ll + 2*K
BIC <- -2*ll + K*log(N)
sumstat <- c(logLik = ll, AIC = AIC, BIC = BIC, N = N)
list(coef = coef,
distparms = distparms,
sumstat = sumstat,
contrasts = obj$contrasts,
xlevels = obj$xlevels,
call = obj$call)
}
getSummary.phreg <- function(obj, alpha = 0.05, ...) {
getSummary.aftreg(obj, alpha = alpha, ...)
}
getSummary.weibreg <- function(obj, alpha = 0.05, ...) {
getSummary.aftreg(obj, alpha = alpha, ...)
}
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