## ----setup, include = FALSE---------------------------------------------------
evaluate_vignette <- requireNamespace("visreg", quietly = TRUE) & requireNamespace("splines", quietly = TRUE)
knitr::opts_chunk$set(
  collapse = TRUE, 
  eval = evaluate_vignette,
  results='hide',
  fig.show='all',
  comment = "#>"
)

## -----------------------------------------------------------------------------
library(casebase)
library(visreg)
library(splines)
library(ggplot2)
data("brcancer")
str(brcancer)

## ----results='show'-----------------------------------------------------------
mod_cb <- fitSmoothHazard(cens ~ ns(log(time), df = 3) + hormon,
                          data = brcancer,
                          time = "time")
summary(mod_cb)

## ----results='hide', fig.show='all'-------------------------------------------
plot(mod_cb,
     hazard.params = list(xvar = "time",
                          cond = list(hormon = 0),
                          alpha = 0.05)) +
  ggplot2::ggtitle("No Hormonal Therapy Hazard Function")

plot(mod_cb,
     hazard.params = list(xvar = "time",
                          cond = list(hormon = 1),
                          alpha = 0.05)) +
  ggplot2::ggtitle("Hormonal Therapy Hazard Function")

## -----------------------------------------------------------------------------
plot(mod_cb,
     hazard.params = list(xvar = "time",
                          by = "hormon",
                          alpha = 0.05)) +
  ggplot2::ylab("Hazard")

## -----------------------------------------------------------------------------
plot_results <- plot(mod_cb,
     hazard.params = list(xvar = "time",
                          by = "hormon",
                          alpha = 0.10,
                          plot = FALSE))

## ----results='show'-----------------------------------------------------------
head(plot_results$fit)

## -----------------------------------------------------------------------------
gg_object <- plot(mod_cb,
                  hazard.params = list(xvar = "time",
                                       by = "hormon",
                                       alpha = 0.20)) + # 80% CI
  ggplot2::ylab("Hazard")

## ----results='show'-----------------------------------------------------------
attr(gg_object,"class")

## -----------------------------------------------------------------------------
gg_object + 
  theme_minimal()+
  theme(legend.position = "bottom") + 
  labs(title = "Casebase") +
  scale_x_continuous(n.breaks = 10)

## ----results='show'-----------------------------------------------------------
mod_cb_tvc <- fitSmoothHazard(cens ~ hormon * ns(log(time), df = 3),
                              data = brcancer,
                              time = "time")
summary(mod_cb_tvc)

## -----------------------------------------------------------------------------
plot(mod_cb_tvc,
     hazard.params = list(xvar = "time",
                          by = "hormon",
                          alpha = 0.05)) +
  ggplot2::ylab("Hazard")

## ----results='show'-----------------------------------------------------------
mod_cb_tvc <- fitSmoothHazard(cens ~ estrec * ns(log(time), df = 3),
                              data = brcancer,
                              time = "time")
summary(mod_cb_tvc)

## -----------------------------------------------------------------------------
# computed at the 10th, 50th and 90th quantiles of estrec
plot(mod_cb_tvc,
     hazard.params = list(xvar = "time",
                          by = "estrec",
                          alpha = 1)) +
  ggplot2::ylab("Hazard")

## -----------------------------------------------------------------------------
# computed at quartiles of estrec
plot(mod_cb_tvc,
     hazard.params = list(xvar = c("time"),
                          by = "estrec",
                          alpha = 1,
                          breaks = 4)) +
  ggplot2::ylab("Hazard")

## -----------------------------------------------------------------------------
# computed where I want
plot(mod_cb_tvc,
     hazard.params = list(xvar = c("time"),
                          by = "estrec",
                          alpha = 1,
                          breaks = c(3,2200))) +
  ggplot2::ylab("Hazard")

## ----multiple-predictors, results='show'--------------------------------------
mod_cb_tvc <- fitSmoothHazard(cens ~ estrec * ns(log(time), df = 3) + 
                                horTh + 
                                age + 
                                menostat + 
                                tsize + 
                                tgrade + 
                                pnodes + 
                                progrec,
                              data = brcancer,
                              time = "time")
summary(mod_cb_tvc)

## ----many-predictors-plot, results='show', R.options=list(max.print=1)--------
plot(mod_cb_tvc,
     hazard.params = list(xvar = "time",
                          by = "estrec",
                          alpha = 1,
                          breaks = 2)) +
  ggplot2::ylab("Hazard")

## ----many-predictors-plot-2, results='show', R.options=list(max.print=1)------
plot(mod_cb_tvc,
     hazard.params = list(xvar = "time",
                          by = "estrec",
                          cond = list(tgrade = "III", age = 49),
                          alpha = 1,
                          breaks = 2)) +
  ggplot2::ylab("Hazard")

## ----eprchd, results='show'---------------------------------------------------
data("eprchd")
eprchd <- transform(eprchd, 
                    treatment = factor(treatment, levels = c("placebo","estPro")))
str(eprchd)

fit_mason <- fitSmoothHazard(status ~ treatment*time,
                             data = eprchd,
                             time = "time")
summary(fit_mason)

## ----plot-mason, results='show'-----------------------------------------------
newtime <- quantile(fit_mason[["originalData"]][[fit_mason[["timeVar"]]]], 
                    probs = seq(0.01, 0.99, 0.01))

# reference category
newdata <- data.frame(treatment = factor("placebo", 
                                         levels = c("placebo", "estPro")), 
                      time = newtime)
str(newdata)

plot(fit_mason, 
     type = "hr", 
     newdata = newdata,
     var = "treatment",
     increment = 1,
     xvar = "time",
     ci = T,
     rug = T)

## -----------------------------------------------------------------------------
plot(fit_mason, 
     type = "hr", 
     newdata = newdata,
     exposed = function(data) transform(data, treatment = "estPro"),
     xvar = "time",
     ci = T,
     rug = T)

## ----results='show'-----------------------------------------------------------
newdata <- data.frame(treatment = factor("estPro", 
                                         levels = c("placebo", "estPro")), 
                      time = newtime)
str(newdata)

levels(newdata$treatment)

## -----------------------------------------------------------------------------
plot(fit_mason, 
     type = "hr", 
     newdata = newdata,
     var = "treatment",
     increment = -1,
     xvar = "time",
     ci = TRUE,
     rug = TRUE)

## ----fig.show='none', results='show'------------------------------------------
result <- plot(fit_mason, 
               type = "hr", 
               newdata = newdata,
               var = "treatment",
               increment = -1,
               xvar = "time",
               ci = TRUE,
               rug = TRUE)
head(result)

## ----echo=FALSE, eval=TRUE----------------------------------------------------
print(sessionInfo(), locale = F)