inst/doc/vignette0.R

In msprog: Reproducible Assessment of Disability Course in Multiple Sclerosis

## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(
  collapse=TRUE,
  comment="#>"
)

## ----wrap-hook, include=FALSE-------------------------------------------------
library(knitr)
hook_output = knit_hooks$get("output")
knit_hooks$set(output = function(x, options) {
  # this hook is used only when the linewidth option is not NULL
  if (!is.null(n <- options$linewidth)) {
    x = xfun::split_lines(x) #substring(x, 4, nchar(x)))
    # any lines wider than n should be wrapped
    if (any(nchar(x) > n)) x = strwrap(x, width = n)
    x = paste0(paste(x, collapse = "\n#> "), "\n")
  }
  hook_output(x, options)
})

## -----------------------------------------------------------------------------
library(msprog)

## -----------------------------------------------------------------------------
head(toydata_visits)

## -----------------------------------------------------------------------------
head(toydata_relapses)

## -----------------------------------------------------------------------------
output_edss <- MSprog(data=toydata_visits, # data on visits
                 subj_col="id", value_col="EDSS", date_col="date", # specify column names
                 outcome="edss", # specify outcome type
                 relapse=toydata_relapses) # data on relapses

## -----------------------------------------------------------------------------
output_sdmt <- MSprog(data=toydata_visits, # data on visits
                 subj_col="id", value_col="SDMT", date_col="visit_day", # specify column names
                 outcome="sdmt", # specify outcome type
                 relapse=toydata_relapses, # data on relapses
                 date_format="day") # specify that dates are given as days

## ----indent="     "-----------------------------------------------------------
# print(output_edss$results, row.names=FALSE)
DT::datatable(output_edss$results, rownames=F,
              options = list(dom="t", scrollX=T, scrollY=F, paging = FALSE)
              )

## ----indent="     "-----------------------------------------------------------
# print(output_edss$event_count)
DT::datatable(output_edss$event_count,
              options = list(dom="t", scrollX=T, scrollY=F, paging = FALSE)
              )

## ----linewidth=90-------------------------------------------------------------
print(output_edss)

## -----------------------------------------------------------------------------
print(compute_delta(4, outcome="edss"))

## -----------------------------------------------------------------------------
print(compute_delta(10, outcome="t25fw"))

## -----------------------------------------------------------------------------
my_sdmt_delta <- function(x) {min(c(x/10, 3))}

## -----------------------------------------------------------------------------
print(my_sdmt_delta(50)) # my delta
print(compute_delta(50, outcome="sdmt")) # default delta

## ----eval=FALSE---------------------------------------------------------------
#  output <- MSprog(...
#                  outcome="sdmt", delta_fun=my_sdmt_delta,
#                   ...)

## -----------------------------------------------------------------------------
print(toydata_visits[toydata_visits$id==4, c("date", "EDSS")]) # EDSS visits

output <- MSprog(data=toydata_visits, 
                 subj_col="id", value_col="EDSS", date_col="date", outcome="edss", 
                 subjects=4,
                 relapse=toydata_relapses, 
                 event="multiple", baseline="fixed",  # <---
                 verbose=0)
# print(output$results, row.names=FALSE) # results
DT::datatable(output$results, rownames=F,
              options = list(dom="t", scrollX=T, scrollY=F, paging = FALSE)
              )

## -----------------------------------------------------------------------------
output <- MSprog(data=toydata_visits, 
                 subj_col="id", value_col="EDSS", date_col="date", outcome="edss", 
                 subjects=4,
                 relapse=toydata_relapses, 
                 event="multiple", baseline="roving",  # <---
                 verbose=0)
# print(output$results, row.names=FALSE) # results
DT::datatable(output$results, rownames=F,
              options = list(dom="t", scrollX=T, scrollY=F, paging = FALSE)
              )

## ----echo=FALSE, out.width="40%", fig.cap = "*Figure 2. Example of data with unscheduled visits.*"----
knitr::include_graphics("./unscheduled.png")

## ----eval=FALSE---------------------------------------------------------------
#  output <- MSprog(...
#                   validconf_col="scheduled",
#                   ...)

## ----eval=FALSE---------------------------------------------------------------
#  output <- MSprog(...
#                   relapse_indep=relapse_indep_from_bounds(p0, p1, e0, e1, c0, c1),
#                   ...)

## ----echo=FALSE, out.width="50%", fig.cap = "*Figure 1. Relapse-free intervals characterising PIRA, as defined by arguments `p0`, `p1`, `e0`, `e1`, `c0`, `c1`.*"----
knitr::include_graphics("./relapse_indep_def.png")

## -----------------------------------------------------------------------------
output <- MSprog(data=toydata_visits,
                 subj_col="id", value_col="EDSS", date_col="date", outcome="edss", 
                 event="multiple", RAW_PIRA=TRUE, baseline="roving", 
                 relapse=toydata_relapses) 

## -----------------------------------------------------------------------------
# print(output$event_count)
DT::datatable(output$event_count, 
              options = list(dom="t", scrollX=T, scrollY=F, paging = FALSE)
              )

## -----------------------------------------------------------------------------
# print(output$results, row.names=FALSE)
DT::datatable(output$results, rownames=F,
              options = list(dom="t", scrollX=T, scrollY=F, paging = FALSE)
              )

## -----------------------------------------------------------------------------
output <- MSprog(data=toydata_visits, 
                      subj_col="id", value_col="EDSS", date_col="date", 
                      outcome="edss", relapse=toydata_relapses, verbose=0,
                      include_dates=T, include_value=T, include_stable=F) # <---- !

# print(output$results, row.names=FALSE)
DT::datatable(output$results, rownames=F,
              options = list(dom="t", scrollX=T, scrollY=F, paging = FALSE)
              )

## -----------------------------------------------------------------------------
output <- MSprog(data=toydata_visits, 
                 subj_col="id", value_col="EDSS", date_col="date", outcome="edss",
                 event="multiple", baseline="roving", 
                 relapse=toydata_relapses, verbose=2)

## -----------------------------------------------------------------------------
# print(output$unconfirmed, row.names=FALSE)
DT::datatable(output$unconfirmed, rownames=F,
              options = list(dom="t", scrollX=T, scrollY=F, paging = FALSE)
              )

## -----------------------------------------------------------------------------
vm <- value_milestone(toydata_visits, milestone=6,
                 subj_col="id", value_col="EDSS", date_col="date",
                 outcome="edss", relapse=toydata_relapses,
                 verbose=0)

## -----------------------------------------------------------------------------
print(vm)