Nothing
## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----eval=FALSE---------------------------------------------------------------
# install.packages("finalfit")
## -----------------------------------------------------------------------------
library(finalfit)
explanatory = c("age.factor", "extent.factor", "perfor.factor")
dependent = 'mort_5yr'
colon_s %>%
finalfit_newdata(explanatory = explanatory, newdata = list(
c("<40 years", "Submucosa", "No"),
c("<40 years", "Submucosa", "Yes"),
c("<40 years", "Adjacent structures", "No"),
c("<40 years", "Adjacent structures", "Yes") )) -> newdata
newdata
## -----------------------------------------------------------------------------
colon_s %>%
glmmulti(dependent, explanatory) %>%
boot_predict(newdata,
estimate_name = "Predicted probability of death",
R=100, boot_compare = FALSE,
digits = c(2,3))
## ----eval=FALSE---------------------------------------------------------------
# knitr::kable(table, row.names = FALSE, align = c("l", "l", "l", "r"))
## -----------------------------------------------------------------------------
colon_s %>%
glmmulti(dependent, explanatory) %>%
boot_predict(newdata,
estimate_name = "Predicted probability of death",
#compare_name = "Absolute risk difference",
R=100, digits = c(2,3))
## ----eval=FALSE---------------------------------------------------------------
# library(finalfit)
# library(ggplot2)
# theme_set(theme_bw())
#
# explanatory = c("nodes", "extent.factor", "perfor.factor")
# dependent = 'mort_5yr'
#
# colon_s %>%
# finalfit_newdata(explanatory = explanatory, rowwise = FALSE,
# newdata = list(
# rep(seq(0, 30), 4),
# c(rep("Muscle", 62), rep("Adjacent structures", 62)),
# c(rep("No", 31), rep("Yes", 31), rep("No", 31), rep("Yes", 31))
# )
# ) -> newdata
#
# colon_s %>%
# glmmulti(dependent, explanatory) %>%
# boot_predict(newdata, boot_compare = FALSE,
# R=100, condense=FALSE) %>%
# ggplot(aes(x = nodes, y = estimate, ymin = estimate_conf.low,
# ymax = estimate_conf.high, fill=extent.factor))+
# geom_line(aes(colour = extent.factor))+
# geom_ribbon(alpha=0.1)+
# facet_grid(.~perfor.factor)+
# xlab("Number of postive lymph nodes")+
# ylab("Probability of death")+
# labs(fill = "Extent of tumour", colour = "Extent of tumour")+
# ggtitle("Probability of death by lymph node count")
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