In raredd/trainr: Analysis project and presentation.

library('knitr')

## package options
opts_knit$set(eval.after = 'fig.cap', progress = TRUE,  width = 80, 
              verbose = TRUE, par = TRUE)

## global chunk options:
opts_chunk$set(cache = FALSE, tidy = FALSE, echo = FALSE,
               dev.args = list(antialias = 'none', bg = 'transparent'),
               dev = 'CairoPNG', dpi = 150, fig.align = 'center',
               warning = FALSE, message = FALSE)


knit_hooks$set(par = function(before, options, envir) {
                 if (before && options$fig.show != 'none') 
                   par(mar = c(4,4,.1,.1), cex.lab = .95, cex.axis = .9, 
                       mgp = c(2,.7,0), tcl = -.3)
                 },
               plot = function(x, options) {
                 fig_fn = paste0(opts_knit$get('base.url'),
                                 paste(x, collapse = '.'))
                 fig.cap <- knitr:::.img.cap(options)
                 style = c('display:block',
                           sprintf('margin: %s;',
                                   switch(options$fig.align,
                                          left = 'auto auto auto 0',
                                          center = 'auto',
                                          right = 'auto 0 auto auto')))
                 addon_args <- ''
                 fig_number_txt <- ''
                 cntr <- getOption('figure_counter', FALSE)
                 if (cntr != FALSE) {
                   if (is.logical(cntr))
                     cntr <- 1
                   ## figure_counter_str allows for custom figure text, 
                   ## eg, <b> Figure %s:</b>
                   ## the %s allows for setting the counter manually to 1a, 1b, 
                   ## etc if needed
                   fig_number_txt <- 
                     sprintf(getOption('figure_counter_str', 'Figure %s: '),
                             ifelse(getOption('figure_counter_roman', FALSE),
                                    as.character(as.roman(cntr)), 
                                    as.character(cntr)))
                   if (is.numeric(cntr))
                     options(figure_counter = cntr + 1)
                   }
                 paste0("<figure><img src='", fig_fn, "'"," ", addon_args,
                        paste0(" style='", paste(style, collapse = '; '), 
                               "'"),'>',
                        '<figcaption>', fig_number_txt, fig.cap, 
                        '</figcaption></figure>')
                 })

## fonts for images
library('Cairo')
CairoFonts(regular = 'Arial:style=Regular',
           bold = 'Arial:style=Bold',
           italic = 'Arial:style=Italic',
           bolditalic = 'Arial:style=Bold Italic,BoldItalic',
           symbol = 'Symbol')

GCB vs non-GCB in DLBCL (15-000)

A comparison of clinical outcomes by genetic subtype in patients with newly diagnosed DLBCL

Most recent compile: r as.character(format(Sys.Date(), format = '%d %B %Y'))

Department of Biostatistics and Computational Biology
Dana Farber Cancer Institute

Statisticians:
Robert Redd, email

All analyses were performed using r R.Version()$version.string and packages survival vr packageVersion('survival') for time-to-event analyses; and knitr vr packageVersion('knitr') for reproducible research.

Summary

The primary outcome was - overall response rate (ORR)

The secondary outcomes were: - rate of PR, CR or better
- progression-free survival
- overall survival

Some patients responsed and there were some toxicities. This summary should be written better.

Statistical considerations

Responses to study treatment were reported as proportions with 95% exact binomial confidence intervals. Time-to-event endpoints were summarized using the Kaplan-Meier method with variance estimated using the log-log transformation.

raredd/trainr documentation built on May 27, 2019, 2:03 a.m.