Version 0.5.0 ============= NEW FEATURES * Added 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. USE-VISIBLE CHANGES The following functions are now defunct * `HLMresid` * `diagnostics` * `group_qqnorm` * `ggplot_qqnorm` Version 0.4.0 ============= DEVELOPMENT * Influence diagnostics are now avaliable through the `case_delete` function and accompaning functions for `lme` objects from the `nlme` package. These diagnostics are also avaliable for three-level models. * Residual diagnostics are also now available via `hlm_resid` for `lme` model objects and three-level models. USER-VISIBLE CHANGES * The `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. * The `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. * The `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 frame * The `sim` argument for `LSresid` has been removed NEW FEATURES * The `hlm_influence` function has been added. This function returns influence diagnostics appended to the model frame. * The `hlm_resid` function has been added. This function returns residual diagnostics appended to the model frame. * The `hlm_augment` function has been added, which combines `hlm_influence` and `hlm_resid` to return influence diagnostics and residuals appended to the model frame. * The `pull_resid` function has been added. This funciton returns a vector of a specified type of residual prioritizing computational efficiency. * The `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). BUG FIXES * `cooks.distance` and `mdffits` functions were fixed to solve an issue with the number of columns. * Fixed an issue with `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 `nlme` * `LSresids` doesn't break with three-level models, or with models containing tranformed variables Version 0.3.1 ============= BUG FIXES * `.extractV.lme` (and thus `.lme_matrices`) was fixed to work with more complex covariance structures fit via nlme. * Updated package to work with the most recent version of `ggplot2` Version 0.3.0 ============= DEVELOPMENT * Influence diagnostics in HLMdiag 0.3.0 are available for two-level models fit using the `lmer` function in lme4` or the `lme` function in `nlme`. I am still working to implement these methods for higher-level models using `lme`. * HLMdiag no longer loads lme4 automatically (see above for the reason). NEW FEATURES * The `rotate_ranef` function has been added. This function rotates the random effects in an effort to find the least confounded residuals for distributional assessment. BUG FIXES * `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`. * Fixed an issue with `group_qqnorm`, by using `ppoints` rather than `.SampleQuantiles`. * Fixed an issue with `case_delete.lmerMod`, to use the `getME()` function to extract `n`. * A bug in the calculation of the Cholesky residuals was fixed (thanks to Harry Hiemstra for reporting the bug and the fix) Version 0.2.5 ============= * Fixed a compatibility issue with Rcpp Version 0.2.4 ============= * Added citation for the JSS paper * Fixed a bug with the calculation of Cook's distance Version 0.2.3 ============= * Added a function to calculate rotated random effects * Added new data sets * Maintenance for compatibility with lme4 1.0 and R 3.0.2 Version 0.2.2 ============= * Changed the standardization of the EB level-1 residuals in `HLMresid` to a more appropriate definition: e / var(\hat{e}). * Added functions to add compatibility with the development version of lme4. Version 0.2.1 ============= * Fixed a bug in `group_qqnorm` * Checked compatibility with R 2.15.3 Version 0.2.0 ============= DEVELOPMENT * Influence diagnostics in HLMdiag 0.2.0 are compatible with hierarchical (multilevel) linear models of any size and with models with crossed factors. * HLMdiag 0.2.0 offers significantly faster computation of the deletion diagnostics for fixed effects that are based on one-step approximations. * S3 methods have been created for `cooks.distance`, `mdffits`, `covratio`, `covtrace`, `rvc`, and `leverage` for objects of class `mer`. * Full deletions are still available using the `case_delete` function, with corresponding S3 methods for objects of class `case_delete`. NEW FEATURES * A `leverage` function has been added. * `case_delete` and other deletion functions now allow for the user to manually specify a subset to delete. OTHER USER-VISIBLE CHANGES * changes to the arguments of `dotplot_diag` to accomodate a more general usage. * `diagnostics` no longer requires a `model` parameter to be specified. * A `delete` parameter has been added to `case_delete` to allow for manual specification of a subset that should be deleted. * For observation-level deletion using `case_delete` the user should specify `group = NULL` rather than `group = FALSE`. Version 0.1.6 ============= * Updates for compatibility with ggplot2 >= 0.9.2 * Updates to NAMESPACE Version 0.1.5 ============= * Updates to NAMESPACE to fix compatibility issues Version 0.1.4 ============= * Updates for compatibility with ggplot2 0.9.0 Version 0.1.3 ============= * Added "marginal" residuals to the type argument for HLMresid. Version 0.1.2 ============= USER-VISIBLE CHANGES: * Removed the formula argument from LSresids. The formula is now obtained automatically from the mer object. Note: we are still working on automatic recognition of math operators such as log(), but anything in I() is recognized. * Added the function HLMresid, a wrapper that will extract both the LS and EB residuals given an mer object. * Added a level argument to LSresids, so the function can extract LS residuals from either level of the model. BUG FIXES: * Fixed the ordering of output from 'LSresids' to match the mode frame obtained from the mer object. Version 0.1.1 ============= * Created 'adjust_lmList' class to handle fitting separate linear models when a factor is constant across the group. * 'random_ls_coef' was removed and replaced by the 'coef' method for 'adjust_lmList' objects. * Added 'rvc' diagnostic. * Extended 'case_delete' from only handling deletion for fixed effects to also handling deletion for variance components. * Improved 'dotplot_diag' to handle modified dotplots.