cch_tidiers {broom} | R Documentation |
Tidiers for case-cohort analyses: summarize each estimated coefficient, or test the overall model.
## S3 method for class 'cch' tidy(x, conf.level = 0.95, ...) ## S3 method for class 'cch' glance(x, ...)
x |
a "cch" object |
conf.level |
confidence level for CI |
... |
extra arguments (not used) |
It is not clear what an augment
method would look like,
so none is provided. Nor is there currently any way to extract the
covariance or the residuals.
All tidying methods return a data.frame without rownames, whose structure depends on the method chosen.
tidy
returns a data.frame with one row for each term
term |
name of term |
estimate |
estimate of coefficient |
stderror |
standard error |
statistic |
Z statistic |
p.value |
p-value |
conf.low |
low end of confidence interval |
conf.high |
high end of confidence interval |
glance
returns a one-row data.frame with the following
columns:
score |
score |
rscore |
rscore |
p.value |
p-value from Wald test |
iter |
number of iterations |
n |
number of predictions |
nevent |
number of events |
cch
if (require("survival", quietly = TRUE)) { # examples come from cch documentation subcoh <- nwtco$in.subcohort selccoh <- with(nwtco, rel==1|subcoh==1) ccoh.data <- nwtco[selccoh,] ccoh.data$subcohort <- subcoh[selccoh] ## central-lab histology ccoh.data$histol <- factor(ccoh.data$histol,labels=c("FH","UH")) ## tumour stage ccoh.data$stage <- factor(ccoh.data$stage,labels=c("I","II","III" ,"IV")) ccoh.data$age <- ccoh.data$age/12 # Age in years fit.ccP <- cch(Surv(edrel, rel) ~ stage + histol + age, data = ccoh.data, subcoh = ~subcohort, id= ~seqno, cohort.size = 4028) tidy(fit.ccP) # coefficient plot library(ggplot2) ggplot(tidy(fit.ccP), aes(x = estimate, y = term)) + geom_point() + geom_errorbarh(aes(xmin = conf.low, xmax = conf.high), height = 0) + geom_vline(xintercept = 0) # compare between methods library(dplyr) fits <- data_frame(method = c("Prentice", "SelfPrentice", "LinYing")) %>% group_by(method) %>% do(tidy(cch(Surv(edrel, rel) ~ stage + histol + age, data = ccoh.data, subcoh = ~subcohort, id= ~seqno, cohort.size = 4028, method = .$method))) # coefficient plots comparing methods ggplot(fits, aes(x = estimate, y = term, color = method)) + geom_point() + geom_errorbarh(aes(xmin = conf.low, xmax = conf.high)) + geom_vline(xintercept = 0) }