Augment data with information from a(n) rma objectSource:
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
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
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 at least all predictor
variable columns used to fit the model are present. If the original outcome
variable used to fit the model is not included in
newdata, then no
.resid column will be included in the output.
Augment will often behave differently depending on whether
newdata is given. 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
augment(fit) will return the augmented training data. In these
cases, augment tries to reconstruct the original data based on the model
object with 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. If a predictor enters the model as part
of a matrix of covariates, such as when the model formula uses
survival::Surv(), it is represented
as a matrix column.
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.
rma.mvmodels, should prediction intervals (
"prediction", default) or confidence intervals (
"confidence") intervals be returned? For
rma.unimodels, prediction intervals are always returned. For
rma.petomodels, confidence intervals are always returned.
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. Two exceptions here are:
tibble::tibble() with columns:
Fitted or predicted value.
Lower bound on interval for fitted values.
In meta-analysis, the moderators used to calculate the predicted values.
In meta-analysis, the level of the moderators used to calculate the predicted values.
The difference between observed and fitted values.
Standard errors of fitted values.
Upper bound on interval for fitted values.
The observed values for the individual studies
# load modeling library library(metafor) #> Loading required package: metadat #> Loading required package: numDeriv #> #> Loading the 'metafor' package (version 4.2-0). For an #> introduction to the package please type: help(metafor) #> #> Attaching package: ‘metafor’ #> The following object is masked from ‘package:car’: #> #> vif #> The following object is masked from ‘package:mclust’: #> #> hc # generate data and fit df <- escalc( measure = "RR", ai = tpos, bi = tneg, ci = cpos, di = cneg, data = dat.bcg ) meta_analysis <- rma(yi, vi, data = df, method = "EB") # summarize model fit with tidiers augment(meta_analysis) #> # A tibble: 13 × 6 #> .observed .fitted .se.fit .lower .upper .resid #> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> #> 1 -0.889 -0.801 0.411 -1.61 0.00524 -0.174 #> 2 -1.59 -1.26 0.354 -1.95 -0.561 -0.870 #> 3 -1.35 -0.990 0.437 -1.85 -0.134 -0.633 #> 4 -1.44 -1.40 0.138 -1.67 -1.13 -0.727 #> 5 -0.218 -0.287 0.212 -0.701 0.128 0.497 #> 6 -0.786 -0.785 0.0823 -0.946 -0.623 -0.0711 #> 7 -1.62 -1.25 0.370 -1.97 -0.523 -0.906 #> 8 0.0120 0.00301 0.0626 -0.120 0.126 0.727 #> 9 -0.469 -0.506 0.221 -0.939 -0.0740 0.246 #> 10 -1.37 -1.25 0.246 -1.73 -0.767 -0.656 #> 11 -0.339 -0.353 0.110 -0.568 -0.139 0.376 #> 12 0.446 -0.281 0.460 -1.18 0.621 1.16 #> 13 -0.0173 -0.145 0.244 -0.623 0.333 0.698