## ----echo=FALSE-----------------------------------------------------
options(prompt = "R> ",
        continue = "+  ",
        width = 70,
        useFancyQuotes = FALSE,
        digits = 3)
library("knitr")
opts_chunk$set(fig.path="fic-")

## ----message=FALSE--------------------------------------------------
library("fic")
wide.glm <- glm(low ~ lwtkg + age + smoke + ht + ui + smokeage + smokeui, 
                data = birthwt, family = binomial)

## -------------------------------------------------------------------
prob_logistic <- function(par, X)plogis(X %*% par)
vals.smoke <-    c(1, 58.24, 22.95, 1, 0, 0, 22.95, 0)
vals.nonsmoke <- c(1, 59.50, 23.43, 0, 0, 0, 0, 0)
X <- rbind("Smokers" = vals.smoke, "Non-smokers" = vals.nonsmoke)

## -------------------------------------------------------------------
prob_logistic(coef(wide.glm), X=X)

## -------------------------------------------------------------------
mod1.glm <- glm(low ~ lwtkg + age + smoke, data = birthwt, family = binomial)
mod2.glm <- glm(low ~ lwtkg + age + smoke + ht, data = birthwt,
                family = binomial)

## -------------------------------------------------------------------
inds <- rbind(mod1 = c(1,1,1,1,0,0,0,0),
              mod2 = c(1,1,1,1,1,0,0,0))
inds0 <- c(1,1,0,0,0,0,0,0)

## -------------------------------------------------------------------
fic1 <- fic(wide = wide.glm, inds = inds, inds0 = inds0,
            focus = prob_logistic, X=X)
fic1

## -------------------------------------------------------------------
combs <- all_inds(wide.glm, inds0)

## -------------------------------------------------------------------
combs <- subset(combs,
                !((smoke==0 & smokeage==1) |
                  (smoke==0 & smokeui==1) |
                  (age==0 & smokeage==1) |
                  (ui==0 & smokeui==1)))
ficres <- fic(wide = wide.glm, inds = combs, inds0 = inds0,
              focus = prob_logistic, X = X)

## ----birthwt,include=FALSE------------------------------------------
ggplot_fic(ficres)

## -------------------------------------------------------------------
summary(ficres)

## ----eval=FALSE-----------------------------------------------------
# fns <- list(coef = function(x)coef(x),
#             nobs = function(x)nobs(x),
#             vcov = function(x)vcov(x))
# fic1 <- fic(wide = wide.glm, inds = inds, inds0 = inds0,
#             focus = prob_logistic, fns = fns, X = X)

## -------------------------------------------------------------------
library("survival")
wide <- coxph(Surv(years, death==1) ~ sex + thick_centred + infilt + epith + 
                ulcer + depth + age, data = melanoma)

## -------------------------------------------------------------------
inds0 <- expand_inds(c(1,0,0,0,0,0,0), wide)
inds0

## ----eval=FALSE-----------------------------------------------------
# list(focus = fic:::cox_hr,
#      deriv = fic:::cox_hr_deriv,
#      dH = fic:::cox_hr_dH)
# list(focus = fic:::cox_cumhaz,
#      deriv = fic:::cox_cumhaz_deriv,
#      dH = fic:::cox_cumhaz_dH)
# list(focus = fic:::cox_survival,
#      deriv = fic:::cox_survival_deriv,
#      dH = fic:::cox_survival_dH)

## -------------------------------------------------------------------
combs <- all_inds(wide, inds0)

## -------------------------------------------------------------------
newdata <- with(melanoma,
                data.frame(sex = c("female","male"),
                           thick_centred = tapply(thick_centred, sex, mean),
                           infilt = 4, epith = 1, ulcer = 1, depth = 2,
                           age = tapply(age, sex, mean)))
X <- newdata_to_X(newdata, wide, intercept=FALSE)
ficall <- fic(wide, inds = combs, inds0 = inds0,
              focus = "survival", X = X, t = 5)

## ----melanoma,include=FALSE-----------------------------------------
ggplot_fic(ficall, ci = FALSE, xlim = c(0,1))

## -------------------------------------------------------------------
summary(ficall)

## ----echo=FALSE,eval=FALSE------------------------------------------
# par(mfrow = c(1,2))
# plot(ficall$FIC[ficall$vals=="female"], ficall$focus[ficall$vals=="female"],
#      xlim = c(0,30), ylim = c(0, 1),
#      ylab = "5yr survival estimates, women", xlab="FIC")
# plot(ficall$FIC[ficall$vals=="male"], ficall$focus[ficall$vals=="male"],
#      xlim = c(0,30), ylim = c(0.2, 0.9),
#      ylab = "5yr survival estimates, men", xlab = "FIC")