John Lövrot lovrot

Installation on Mac OS X

brew install git
brew install git-flow

Biomarker: Predictive or Prognostic?
- Ballman KV (2015). J Clin Oncol 33(33):3968-71. PMID 26392104
Judging new markers by their ability to improve predictive accuracy
- Kattan MW (2003). J Natl Cancer Inst 95(9):634-5.

variableName	labelDescription	type	RClass	controlledTermsOrFormat	reference	comment
studyid	Study Identifier	Char	character		SDTM 2.2.4
siteid	Study Site Identifier	Char	character
usubjid	Unique Subject Identifier	Char	character		SDTM 2.2.4
subjid	Subject Identifier for the Study	Char	character
brthdtc	Date of Birth - Character	Char	character	ISO 8601	SDSIG 4.1.4.1
brthdtm	Date of Birth	Num	Date	R's Date class	SDSIG 4.1.4.3
age	Age at Reference Date	Num	integer		SDSIG 5.1.1
ageu	Age Units	Char	character	decades, years, months, days	SDSIG 5.1.1
agerfdt	Reference Date for Age	Char	character	ISO 8601, vaiable name, or free text (e.g. 'Diagnosis')		'rf' from CDISC naming fragments; 'dt' see SDSIG 4.1.4.2

KI Box uses the online file sharing and personal cloud content management service by Box.

	library(dplyr)
	library(tidyr)
	library(ggplot2)
	library(cgdsr)

	ggplot2::theme_set(theme_classic())

	conn <- CGDS("http://www.cbioportal.org/")

	test(conn)

	library(ggplot2)
	ggplot2::theme_set(theme_classic())

	## Create a dataframe with dummy data
	set.seed(123)
	n <- 20
	n_categories <- 5
	df <- data.frame(
	x = 1:n + rnorm(n),
	y = 1:n + rnorm(n),

	## A paraphrase of http://flowingdata.com/2014/12/01/pie-chart-pyramid/
	## See also https://github.com/lovrot/pie-chart-pyramid

	library(ggplot2)
	theme_set(theme_bw())

	palette_part <- c(
	"Sky"="deepskyblue3",
	"Sunny side of pyramid"="yellow1",
	"Shady side of pyramid"="yellow3")