broom: tidy.mjoint – R documentation

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tidy.mjoint

Tidy a(n) mjoint object

Description

Tidy summarizes information about the components of a model. A model component might be a single term in a regression, a single hypothesis, a cluster, or a class. Exactly what tidy considers to be a model component varies across models but is usually self-evident. If a model has several distinct types of components, you will need to specify which components to return.

Usage

## S3 method for class 'mjoint'
tidy(
  x,
  component = "survival",
  conf.int = FALSE,
  conf.level = 0.95,
  boot_se = NULL,
  ...
)

Arguments

`x`	An `mjoint` object returned from `joineRML::mjoint()`.
`component`	Character specifying whether to tidy the survival or the longitudinal component of the model. Must be either `"survival"` or `"longitudinal"`. Defaults to `"survival"`.
`conf.int`	Logical indicating whether or not to include a confidence interval in the tidied output. Defaults to `FALSE`.
`conf.level`	The confidence level to use for the confidence interval if `conf.int = TRUE`. Must be strictly greater than 0 and less than 1. Defaults to 0.95, which corresponds to a 95 percent confidence interval.
`boot_se`	Optionally a `bootSE` object from `joineRML::bootSE()`. If specified, calculates confidence intervals via the bootstrap. Defaults to `NULL`, in which case standard errors are calculated from the empirical information matrix.
`...`	Additional arguments. Not used. Needed to match generic signature only. Cautionary note: Misspelled arguments will be absorbed in `...`, where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass `conf.lvel = 0.9`, all computation will proceed using `conf.level = 0.95`. Additionally, if you pass `newdata = my_tibble` to an `augment()` method that does not accept a `newdata` argument, it will use the default value for the `data` argument.

Value

A tibble::tibble() with columns:

`conf.high`	Upper bound on the confidence interval for the estimate.
`conf.low`	Lower bound on the confidence interval for the estimate.
`estimate`	The estimated value of the regression term.
`p.value`	The two-sided p-value associated with the observed statistic.
`statistic`	The value of a T-statistic to use in a hypothesis that the regression term is non-zero.
`std.error`	The standard error of the regression term.
`term`	The name of the regression term.

Examples

if (requireNamespace("joineRML", quietly = TRUE)) {

## Not run: 
# Fit a joint model with bivariate longitudinal outcomes
library(joineRML)
data(heart.valve)
hvd <- heart.valve[!is.na(heart.valve$log.grad) &
  !is.na(heart.valve$log.lvmi) &
  heart.valve$num <= 50, ]
fit <- mjoint(
  formLongFixed = list(
    "grad" = log.grad ~ time + sex + hs,
    "lvmi" = log.lvmi ~ time + sex
  ),
  formLongRandom = list(
    "grad" = ~ 1 | num,
    "lvmi" = ~ time | num
  ),
  formSurv = Surv(fuyrs, status) ~ age,
  data = hvd,
  inits = list("gamma" = c(0.11, 1.51, 0.80)),
  timeVar = "time"
)

# Extract the survival fixed effects
tidy(fit)

# Extract the longitudinal fixed effects
tidy(fit, component = "longitudinal")

# Extract the survival fixed effects with confidence intervals
tidy(fit, ci = TRUE)

# Extract the survival fixed effects with confidence intervals based
# on bootstrapped standard errors
bSE <- bootSE(fit, nboot = 5, safe.boot = TRUE)
tidy(fit, boot_se = bSE, ci = TRUE)

# Augment original data with fitted longitudinal values and residuals
hvd2 <- augment(fit)

# Extract model statistics
glance(fit)

## End(Not run)
}

broom

Convert Statistical Objects into Tidy Tibbles

v0.7.10

MIT + file LICENSE

Authors

David Robinson [aut], Alex Hayes [aut] (<https://orcid.org/0000-0002-4985-5160>), Simon Couch [aut, cre] (<https://orcid.org/0000-0001-5676-5107>), Indrajeet Patil [ctb] (<https://orcid.org/0000-0003-1995-6531>), Derek Chiu [ctb], Matthieu Gomez [ctb], Boris Demeshev [ctb], Dieter Menne [ctb], Benjamin Nutter [ctb], Luke Johnston [ctb], Ben Bolker [ctb], Francois Briatte [ctb], Jeffrey Arnold [ctb], Jonah Gabry [ctb], Luciano Selzer [ctb], Gavin Simpson [ctb], Jens Preussner [ctb], Jay Hesselberth [ctb], Hadley Wickham [ctb], Matthew Lincoln [ctb], Alessandro Gasparini [ctb], Lukasz Komsta [ctb], Frederick Novometsky [ctb], Wilson Freitas [ctb], Michelle Evans [ctb], Jason Cory Brunson [ctb], Simon Jackson [ctb], Ben Whalley [ctb], Karissa Whiting [ctb], Yves Rosseel [ctb], Michael Kuehn [ctb], Jorge Cimentada [ctb], Erle Holgersen [ctb], Karl Dunkle Werner [ctb] (<https://orcid.org/0000-0003-0523-7309>), Ethan Christensen [ctb], Steven Pav [ctb], Paul PJ [ctb], Ben Schneider [ctb], Patrick Kennedy [ctb], Lily Medina [ctb], Brian Fannin [ctb], Jason Muhlenkamp [ctb], Matt Lehman [ctb], Bill Denney [ctb] (<https://orcid.org/0000-0002-5759-428X>), Nic Crane [ctb], Andrew Bates [ctb], Vincent Arel-Bundock [ctb] (<https://orcid.org/0000-0003-2042-7063>), Hideaki Hayashi [ctb], Luis Tobalina [ctb], Annie Wang [ctb], Wei Yang Tham [ctb], Clara Wang [ctb], Abby Smith [ctb] (<https://orcid.org/0000-0002-3207-0375>), Jasper Cooper [ctb] (<https://orcid.org/0000-0002-8639-3188>), E Auden Krauska [ctb] (<https://orcid.org/0000-0002-1466-5850>), Alex Wang [ctb], Malcolm Barrett [ctb] (<https://orcid.org/0000-0003-0299-5825>), Charles Gray [ctb] (<https://orcid.org/0000-0002-9978-011X>), Jared Wilber [ctb], Vilmantas Gegzna [ctb] (<https://orcid.org/0000-0002-9500-5167>), Eduard Szoecs [ctb], Frederik Aust [ctb] (<https://orcid.org/0000-0003-4900-788X>), Angus Moore [ctb], Nick Williams [ctb], Marius Barth [ctb] (<https://orcid.org/0000-0002-3421-6665>), Bruna Wundervald [ctb] (<https://orcid.org/0000-0001-8163-220X>), Joyce Cahoon [ctb] (<https://orcid.org/0000-0001-7217-4702>), Grant McDermott [ctb] (<https://orcid.org/0000-0001-7883-8573>), Kevin Zarca [ctb], Shiro Kuriwaki [ctb] (<https://orcid.org/0000-0002-5687-2647>), Lukas Wallrich [ctb] (<https://orcid.org/0000-0003-2121-5177>), James Martherus [ctb] (<https://orcid.org/0000-0002-8285-3300>), Chuliang Xiao [ctb] (<https://orcid.org/0000-0002-8466-9398>), Joseph Larmarange [ctb], Max Kuhn [ctb], Michal Bojanowski [ctb], Hakon Malmedal [ctb], Clara Wang [ctb], Sergio Oller [ctb], Luke Sonnet [ctb], Jim Hester [ctb], Cory Brunson [ctb], Ben Schneider [ctb], Bernie Gray [ctb] (<https://orcid.org/0000-0001-9190-6032>), Mara Averick [ctb], Aaron Jacobs [ctb], Andreas Bender [ctb], Sven Templer [ctb], Paul-Christian Buerkner [ctb], Matthew Kay [ctb], Erwan Le Pennec [ctb], Johan Junkka [ctb], Hao Zhu [ctb], Benjamin Soltoff [ctb], Zoe Wilkinson Saldana [ctb], Tyler Littlefield [ctb], Charles T. Gray [ctb], Shabbh E. Banks [ctb], Serina Robinson [ctb], Roger Bivand [ctb], Riinu Ots [ctb], Nicholas Williams [ctb], Nina Jakobsen [ctb], Michael Weylandt [ctb], Lisa Lendway [ctb], Karl Hailperin [ctb], Josue Rodriguez [ctb], Jenny Bryan [ctb], Chris Jarvis [ctb], Greg Macfarlane [ctb], Brian Mannakee [ctb], Drew Tyre [ctb], Shreyas Singh [ctb], Laurens Geffert [ctb], Hong Ooi [ctb], Henrik Bengtsson [ctb], Eduard Szocs [ctb], David Hugh-Jones [ctb], Matthieu Stigler [ctb], Hugo Tavares [ctb] (<https://orcid.org/0000-0001-9373-2726>), R. Willem Vervoort [ctb], Brenton M. Wiernik [ctb], Josh Yamamoto [ctb], Jasme Lee [ctb], Taren Sanders [ctb] (<https://orcid.org/0000-0002-4504-6008>)

Initial release