traceplots_mplus: Extract and export Mplus trace and autocorrelation plots into...
In MaksimRudnev/LittleHelpers: Helpers for comparative studies

traceplots_mplus

R Documentation

Extract and export Mplus trace and autocorrelation plots into pdf

Description

The function exports all the available plots for each parameter and every chain. Therefore it can take a long time and the resulting pdf file can be large. Each page in pdf is for a specific parameter.

Usage

traceplots_mplus(
  x,
  is.file = F,
  pdffile = NULL,
  gg = T,
  param.id = NULL,
  raster = F,
  niter = NULL,
  chains = NULL,
  PSR = TRUE,
  PSR.version = "Rstan",
  ESS = T
)

Arguments

`x`	Either a model read by `readModels`, OR a gh5 file produced by Mplus (in Mplus it should be stated PLOTS: TYPE IS PLOT2;)
`is.file`	Logical, if x argument is file name. Default is FALSE, (i.e. it's an R object, a model read by `readModels`)
`pdffile`	File name of the pdf report to export all the plots. Defaults to an of x argument with a '.pdf' extension when is.file == TRUE, and extracts the original filename of the out file if x is a readModels object.
`gg`	Logical. Whether ggplot or base R graphics should be used. Default is ggplot which is slower but more flexible, e.g. with many chains.
`param.id`	Single interger or a vector. Single intterger shows 1:param.id parameters to plot, a vector shows parameters by their order id. If NULL (default), all the parameters are used.
`raster`	Logical. Currently not used. It was an option to convert vector plots to raster plots to save space and produce smaller pdfs. Currently not used.
`niter`	How many iterations should be shown on a traceplot. NULL (default) refers to all iterations. However, traceplots for long chains may result in highly overplotted graphics which are slow and take a lot of space on disk. A specified number will take a random sample of values from the iterations.
`PSR`	If PSR (R-hat) should be printed for each parameter. See `eachParamPSRMplus`.
`PSR.version`	Version of PSR; default is "Rstan" - the most up-to-date, provided by the Rstan::Rhat function (Vehtari et al., 2019). Other possible values: "Gelman" (Gelman et al. (2004)); or "Mplus" (Asparouhov and Muthen, 2010), and "Naive" which is a raw ratio of sum of a between- and within-chain variances to a within-chain variance.
`ESS`	Logical. If effective sample size should be printed on the plots. See `ess_bulk`

Examples


## Not run: 
m <- MplusAutomation::readModels("mybayes.out")
convergencePlotsMplus(m, niter = 5000, PSR.version = "Mplus")

# or directly from gh5 file:
convergencePlotsMplus("mybayes.gh5", param.id = 1, PSR.version = "Rstan", gg=F)

## End(Not run)

MaksimRudnev/LittleHelpers documentation built on Nov. 5, 2024, 10:16 p.m.