`R/survival-coxph-tidiers.R`

`augment.coxph.Rd`

Augment accepts a model object and a dataset and adds
information about each observation in the dataset. Most commonly, this
includes predicted values in the `.fitted`

column, residuals in the
`.resid`

column, and standard errors for the fitted values in a `.se.fit`

column. New columns always begin with a `.`

prefix to avoid overwriting
columns in the original dataset.

Users may pass data to augment via either the `data`

argument or the
`newdata`

argument. If the user passes data to the `data`

argument,
it **must** be exactly the data that was used to fit the model
object. Pass datasets to `newdata`

to augment data that was not used
during model fitting. This still requires that all columns used to fit
the model are present.

Augment will often behavior different depending on whether `data`

or
`newdata`

is specified. This is because there is often information
associated with training observations (such as influences or related)
measures that is not meaningfully defined for new observations.

For convenience, many augment methods provide default `data`

arguments,
so that `augment(fit)`

will return the augmented training data. In these
cases augment tries to reconstruct the original data based on the model
object, with some varying degrees of success.

The augmented dataset is always returned as a tibble::tibble with the
**same number of rows** as the passed dataset. This means that the
passed data must be coercible to a tibble. At this time, tibbles do not
support matrix-columns. This means you should not specify a matrix
of covariates in a model formula during the original model fitting
process, and that `splines::ns()`

, `stats::poly()`

and
`survival::Surv()`

objects are not supported in input data. If you
encounter errors, try explicitly passing a tibble, or fitting the original
model on data in a tibble.

We are in the process of defining behaviors for models fit with various na.action arguments, but make no guarantees about behavior when data is missing at this time.

# S3 method for coxph augment(x, data = NULL, newdata = NULL, type.predict = "lp", type.residuals = "martingale", ...)

x | A |
---|---|

data | A |

newdata | A |

type.predict | Character indicating type of prediction to use. Passed
to the |

type.residuals | Character indicating type of residuals to use. Passed
to the |

... | Additional arguments. Not used. Needed to match generic
signature only. |

When the modeling was performed with `na.action = "na.omit"`

(as is the typical default), rows with NA in the initial data are omitted
entirely from the augmented data frame. When the modeling was performed
with `na.action = "na.exclude"`

, one should provide the original data
as a second argument, at which point the augmented data will contain those
rows (typically with NAs in place of the new columns). If the original data
is not provided to `augment()`

and `na.action = "na.exclude"`

, a
warning is raised and the incomplete rows are dropped.

na.action

Other coxph tidiers: `glance.coxph`

,
`tidy.coxph`

Other survival tidiers: `augment.survreg`

,
`glance.aareg`

, `glance.cch`

,
`glance.coxph`

, `glance.pyears`

,
`glance.survdiff`

,
`glance.survexp`

,
`glance.survfit`

,
`glance.survreg`

, `tidy.aareg`

,
`tidy.cch`

, `tidy.coxph`

,
`tidy.pyears`

, `tidy.survdiff`

,
`tidy.survexp`

, `tidy.survfit`

,
`tidy.survreg`

A `tibble::tibble()`

with columns:

Fitted / predicted value.

Residuals of fitted values. TODO -- document when present. Residuals on which data set?

Standard errors of fitted values. TODO -- prediction or mean interval?

#> # A tibble: 2 x 5 #> term estimate std.error statistic p.value #> <chr> <dbl> <dbl> <dbl> <dbl> #> 1 age 0.0170 0.00922 1.85 0.0646 #> 2 sex -0.513 0.167 -3.06 0.00218#> # A tibble: 2 x 5 #> term estimate std.error statistic p.value #> <chr> <dbl> <dbl> <dbl> <dbl> #> 1 age 1.02 0.00922 1.85 0.0646 #> 2 sex 0.599 0.167 -3.06 0.00218lp <- augment(cfit, lung) risks <- augment(cfit, lung, type.predict = "risk") expected <- augment(cfit, lung, type.predict = "expected") glance(cfit)#> # A tibble: 1 x 15 #> n nevent statistic.log p.value.log statistic.sc p.value.sc statistic.wald #> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> #> 1 228 165 14.1 0.000857 13.7 0.00105 13.5 #> # ... with 8 more variables: p.value.wald <dbl>, r.squared <dbl>, #> # r.squared.max <dbl>, concordance <dbl>, std.error.concordance <dbl>, #> # logLik <dbl>, AIC <dbl>, BIC <dbl># also works on clogit models resp <- levels(logan$occupation) n <- nrow(logan) indx <- rep(1:n, length(resp)) logan2 <- data.frame( logan[indx,], id = indx, tocc = factor(rep(resp, each=n)) ) logan2$case <- (logan2$occupation == logan2$tocc) cl <- clogit(case ~ tocc + tocc:education + strata(id), logan2) tidy(cl)#> # A tibble: 9 x 5 #> term estimate std.error statistic p.value #> <chr> <dbl> <dbl> <dbl> <dbl> #> 1 toccfarm -1.90 1.38 -1.37 1.70e- 1 #> 2 toccoperatives 1.17 0.566 2.06 3.91e- 2 #> 3 toccprofessional -8.10 0.699 -11.6 4.45e-31 #> 4 toccsales -5.03 0.770 -6.53 6.54e-11 #> 5 tocccraftsmen:education -0.332 0.0569 -5.84 5.13e- 9 #> 6 toccfarm:education -0.370 0.116 -3.18 1.47e- 3 #> 7 toccoperatives:education -0.422 0.0584 -7.23 4.98e-13 #> 8 toccprofessional:education 0.278 0.0510 5.45 4.94e- 8 #> 9 toccsales:education NA 0 NA NAglance(cl)#> # A tibble: 1 x 13 #> n nevent statistic.log p.value.log statistic.sc p.value.sc statistic.wald #> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> #> 1 4190 838 666. 1.90e-138 682. 5.01e-142 414. #> # ... with 6 more variables: p.value.wald <dbl>, r.squared <dbl>, #> # r.squared.max <dbl>, logLik <dbl>, AIC <dbl>, BIC <dbl>