msboxes_R: msboxes_R

In nskourlis/MSMplus: Prepare MSMplus input files and locally deploys the MSMplus app

msboxes_R

Description

msboxes_R will create a json file containing parameters that will help MSMplus to automatically create the multi-state graph of each specific setting. However, the user has the option to design and create the multistate graph within the app as well.

Usage

msboxes_R(
  data,
  id,
  yb,
  xb,
  boxwidth = 0.1,
  boxheight = 0.1,
  tstop,
  vartime = 1,
  tmatrix,
  scale = 1,
  msm = FALSE,
  jsonpath = NULL,
  name = "msboxes_R.json"
)

Arguments

data	Provide a dataset that is properly formatted for a multi-state analysis (eg. after msprep())
id	Provide an indentity variable
yb	Provide a vector of values for the y coordinates of the state boxes of the multi-state graph you want to create
xb	Provide a vector of values for the x coordinates of the state boxes of the multi-state graph you want to create
boxwidth	Provide the width of the state boxes of the multi-state graph you want to create (default 0.1)
boxheight	Provide the height of the state boxes of the multi-state graph you want to create (default 0.1)
tstop	Provide the Tstop variable of your dataset
vartime	A vector of time points at which the user wants to count the number of people in each state and the number of people that have made each transition
tmatrix	The transition matrix (e.g transMat(x = list(c(2, 3),c(3), c() )) ).
scale	rescale time value
msm	In case the msm package is used, the function uses statetable.msm to calculate the frequencies.Default: FALSE
jsonpath	specify the path of the folder that the json file should be saved, Default: "" saves the json file to the current working directory
name	Specify the name of the output json file, Default: 'msboxes_R.json'

Details

DETAILS

Value

Nstates, Ntransitions, xvalues, yvalues,boxwidth, boxheight, statenames, transnames, the start and end coordinates of the arrows that connect the state boxes, tmat, number of people in each state and the number of people that have made each transition

Examples

## Not run: 

 #EXAMPLE
 
 library("mstate")
 library("dplyr")
 library("RJSONIO")
head(ebmt)

tmat <- transMat(x = list(c(2, 3),c(3), c() ), names = c("Transplant", "Platelet Recovery", "Relapse/Death" ) )

ebmt$age2=  recode(ebmt$age, ">40" =0, "20-40"=1,"<=20" =0 )
ebmt$age3=  recode(ebmt$age, ">40" =1, "20-40"=0,"<=20" =0 )

msebmt <- msprep(data = ebmt, trans = tmat, time = c(NA, "prtime", "rfstime"), status = c(NA, "prstat", "rfsstat"), keep=c("age2","age3"))


results=MSMplus::msboxes_R(data=msebmt,id= msebmt$id, yb=c(0.3,0.5,0.75),
                              xb=c(0.5,0.2,0.7),boxwidth=0.1,boxheight=0.1,
                              tmatrix= tmat, tstop=msebmt$Tstop,vartime=c(seq(0,10,by=1)),scale=365.25,
                              jsonpath="", name="msboxes_EBMT_R.json" ) 

results
 

## End(Not run)

nskourlis/MSMplus documentation built on Dec. 7, 2023, 4:53 a.m.