NEWS.md file to track changes to the
package.cooks.distance() and mdffits() with
include.attr = TRUE now returns a tibble with column names
for the fixed effects in agreement with the fixef() output.hlm_resid() output is now
.id to avoid conflicts with id columnsAdded separate functions to calculate residuals for LMEs.
resid_marginal() calculates (raw, studentized, Pearson,
or Cholesky) marginal residuals.resid_conditional calculates (raw, studentized,
Pearson, or Cholesky) conditional residuals (i.e., error terms).resid_ranef calculates raw and standardized predicted
random effects.The following functions are now defunct
HLMresiddiagnosticsgroup_qqnormggplot_qqnormcase_delete function and accompaning functions for
lme objects from the nlme package. These
diagnostics are also avaliable for three-level models.hlm_resid for lme model objects and
three-level models.group parameter for influence diagnostics has been
changed to level in order to match the residual functions.
level defaults to NULL, which will delete individual
observations iteratively as group = NULL did.cooks.distance and mdffits functions
now only return the values as a numeric vector, instead of also
returning the beta values as attributes. If these attributes are
desired, the user can now set include.attr = TRUE, and a
tibble will be returned instead with the influence diagnostics and the
beta attributes.dotplot_diag function has been updated to be more
efficient. Additionally, it no longer places labels on the y-axis and
only labels the top five observations in order to improve
visibility.LSresid now returns only the residual values, excluding
the model framesim argument for LSresid has been
removedhlm_influence function has been added. This
function returns influence diagnostics appended to the model frame.hlm_resid function has been added. This function
returns residual diagnostics appended to the model frame.hlm_augment function has been added, which combines
hlm_influence and hlm_resid to return
influence diagnostics and residuals appended to the model frame.pull_resid function has been added. This funciton
returns a vector of a specified type of residual prioritizing
computational efficiency.delete parameter in case_delete,
hlm_influence, and hlm_augment now also
accepts character vectors at the second or third level. Observations or
groups to be deleted can be specified by row indices in a numeric vector
(as previously), or as character vectors of group level names found in
model@flist (lmerMod models) or model$groups
(lme models).cooks.distance and mdffits functions were
fixed to solve an issue with the number of columns.case_delete so that it works with
three level models.hlm_resid, hlm_influence, and
hlm_augment properly respect na.action and
work with models fit in nlmeLSresids doesn’t break with three-level models, or with
models containing tranformed variables.extractV.lme (and thus .lme_matrices) was
fixed to work with more complex covariance structures fit via nlme.ggplot2lmer function in
lme4or thelmefunction innlme. I am still working to implement these methods for higher-level models usinglme`.rotate_ranef function has been added. This function
rotates the random effects in an effort to find the least confounded
residuals for distributional assessment.LSresids was fixed for an issue with the order of the
resulting data frame.case_delete was fixed so that numeric group labels work
properly, which fixes an issue with rvc.group_qqnorm, by using
ppoints rather than .SampleQuantiles.case_delete.lmerMod, to use the
getME() function to extract n.HLMresid to a more appropriate definition: e / var().group_qqnormcooks.distance,
mdffits, covratio, covtrace,
rvc, and leverage for objects of class
mer.case_delete function, with corresponding S3 methods for
objects of class case_delete.leverage function has been added.case_delete and other deletion functions now allow for
the user to manually specify a subset to delete.dotplot_diag to accomodate
a more general usage.diagnostics no longer requires a model
parameter to be specified.delete parameter has been added to
case_delete to allow for manual specification of a subset
that should be deleted.case_delete the
user should specify group = NULL rather than
group = FALSE.