Package: HLMdiag 0.5.0

HLMdiag: Diagnostic Tools for Hierarchical (Multilevel) Linear Models

A suite of diagnostic tools for hierarchical (multilevel) linear models. The tools include not only leverage and traditional deletion diagnostics (Cook's distance, covratio, covtrace, and MDFFITS) but also convenience functions and graphics for residual analysis. Models can be fit using either lmer in the 'lme4' package or lme in the 'nlme' package.

Authors:Adam Loy [cre, aut], Jaylin Lowe [aut], Jack Moran [aut]

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HLMdiag.pdf |HLMdiag.html✨
HLMdiag/json (API)
NEWS

# Install 'HLMdiag' in R:

install.packages('HLMdiag', repos = c('https://aloy.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/aloy/hlmdiag/issues

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3

Datasets:

ahd - Methylprednisolone data
autism - Autism data
radon - Radon data
wages - Wages for male high school dropouts

On CRAN:

19 exports 16 stars 3.09 score 47 dependencies 7 dependents 4 mentions 161 scripts 1.1k downloads

Last updated 3 years agofrom:05b6aa27ce. Checks:OK: 1 NOTE: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 08 2024
R-4.5-win-x86_64	NOTE	Sep 08 2024
R-4.5-linux-x86_64	NOTE	Sep 08 2024
R-4.4-win-x86_64	NOTE	Sep 08 2024
R-4.4-mac-x86_64	NOTE	Sep 08 2024
R-4.4-mac-aarch64	NOTE	Sep 08 2024
R-4.3-win-x86_64	NOTE	Sep 08 2024
R-4.3-mac-x86_64	NOTE	Sep 08 2024
R-4.3-mac-aarch64	NOTE	Sep 08 2024

Exports:adjust_lmList case_delete compare_eb_ls covratio covtrace dotplot_diag extract_design hlm_augment hlm_influence hlm_resid leverage LSresids mdffits pull_resid resid_conditional resid_marginal rotate_ranef rvc varcomp.mer

Dependencies:cli colorspace cpp11 diagonals dplyr fansi farver generics ggplot2 ggrepel glue gtable hms isoband janitor labeling lattice lifecycle lubridate magrittr MASS Matrix mgcv munsell nlme pillar pkgconfig plyr purrr R6 RColorBrewer Rcpp RcppArmadillo reshape2 rlang scales snakecase stringi stringr tibble tidyr tidyselect timechange utf8 vctrs viridisLite withr

Influence Diagnostics

Jaylin Lowe, Jack Moran, Adam Loy

Rendered frominfluence_diagnostics.Rmdusingknitr::rmarkdown_notangleon Sep 08 2024.

Last update: 2021-05-01
Started: 2020-08-21

Residual Diagnostics

Jack Moran, Jaylin Lowe, Adam Loy

Rendered fromhlm_resid.Rmdusingknitr::rmarkdown_notangleon Sep 08 2024.

Last update: 2020-12-14
Started: 2020-08-21

Updated JSS code

Adam Loy

Rendered fromjss_update.Rmdusingknitr::rmarkdown_notangleon Sep 08 2024.

Last update: 2021-04-28
Started: 2020-12-03

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Fitting Common Models via 'lm'	adjust_lmList adjust_lmList,formula,data.frame-method adjust_lmList.formula
Methylprednisolone data	ahd
Autism data	autism
Case Deletion for 'mer'/'lmerMod' objects	case_delete case_delete.default case_delete.lme case_delete.lmerMod case_delete.mer
Visually comparing shrinkage and LS estimates	compare_eb_ls
Influence on precision of fixed effects in HLMs	covratio covratio.default covratio.lme covratio.lmerMod covratio.mer covtrace covtrace.default covtrace.lme covtrace.lmerMod covtrace.mer
Dot plots for influence diagnostics	dotplot_diag
Extracting covariance matrices from lme	extract_design
Calculating residuals and influence diagnostics for HLMs 'hlm_augment' is used to compute residuals, fitted values, and influence diagnostics for a hierarchical linear model. The residuals and fitted values are computed using Least Squares(LS) and Empirical Bayes (EB) methods. The influence diagnostics are computed through one step approximations.	hlm_augment hlm_augment.default hlm_augment.lmerMod
Calculating influence diagnostics for HLMs	hlm_influence hlm_influence.default hlm_influence.lme hlm_influence.lmerMod
Calculating residuals from HLMs	hlm_resid hlm_resid.default hlm_resid.lme hlm_resid.lmerMod
Diagnostic tools for hierarchical (multilevel) linear models	HLMdiag package-HLMdiag
Defunct functions in package HLMdiag	diagnostics ggplot_qqnorm group_qqnorm HLMdiag-defunct HLMresid HLMresid.default HLMresid.lmerMod HLMresid.mer
Deprecated functions in HLMdiag	HLMdiag-deprecated
Leverage for HLMs	leverage leverage.default leverage.lme leverage.lmerMod leverage.mer
Calculating least squares residuals	LSresids LSresids.default LSresids.lme LSresids.lmerMod LSresids.mer
Influence on fixed effects of HLMs	cooks.distance cooks.distance.lme cooks.distance.lmerMod cooks.distance.mer mdffits mdffits.default mdffits.lme mdffits.lmerMod mdffits.mer
Computationally Efficient HLM Residuals	pull_resid pull_resid.default pull_resid.lme pull_resid.lmerMod
Radon data	radon
Conditional residuals	resid_conditional resid_conditional.default resid_conditional.lme resid_conditional.lmerMod
Marginal residuals	resid_marginal resid_marginal.default resid_marginal.lme resid_marginal.lmerMod
Random effects residuals	resid_ranef
Calculate s-dimensional rotated random effects	rotate_ranef rotate_ranef.default rotate_ranef.lme rotate_ranef.lmerMod rotate_ranef.mer
Relative variance change for HLMs	rvc rvc.default rvc.lme rvc.lmerMod rvc.mer
Extracting variance components	varcomp.mer
Wages for male high school dropouts	wages