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LMMstar

Function for handling repeated measurements in R

https://github.com/bozenne/lmmstar

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    4 of 7 committers (57.1%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (17.7%) to scientific vocabulary

Keywords from Contributors

generalized-pairwise-comparisons non-parametric
Last synced: 10 months ago · JSON representation

Repository

Function for handling repeated measurements in R

Basic Info
Statistics
  • Stars: 4
  • Watchers: 4
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created almost 6 years ago · Last pushed 12 months ago
Metadata Files
Readme Changelog License

README.org 

#+BEGIN_HTML
CRAN version
Download count
Build status
Build status
License
#+END_HTML

#+BEGIN_SRC R :exports none :results output :session *R* :cache no
options(width = 100)
#+END_SRC

#+RESULTS:

* LMMstar: Repeated Measurement Models for Discrete Times

*LMMstar* stands for Linear Mixed Models - statistical analysis in
R. It is companion R package for the course "Statistical analysis of
correlated and repeated measurements for health science researchers"
taught by the section of Biostatistics of the University of
Copenhagen. It provides functions for computing summary statistics and
obtaining graphical displays of longitudinal data, as well as for
statistical modeling and statistical inference using mixed models. In
particular, it implements linear mixed models where the model for the
variance-covariance of the residuals is specified via patterns
(compound symmetry, toeplitz, unstructured, ...), possibly stratified
on a categorical variable. Statistical uncertainty for mean, variance,
and correlation parameters is performed based on the observed
information. Statistical testing can be performed for arbitrary linear
or non-linear combination(s) of model coefficients. For linear
combinations, a Satterthwaite approximation of the degrees of freedom
is available.  Normalized residuals are provided to assess model
misspecification. Predictions can be computed conditional to
covariates only or also to outcome values.

This package builds on existing software:
- =lava= for simulating data
- =multcomp= for adjusting for multiple comparisons
- =ggplot2= for graphical displays

** Installation

You can download the latest stable version on =CRAN= using:
#+BEGIN_SRC R :exports both :eval never
install.packages("LMMstar")
#+END_SRC

or download the development version from =GitHub=:
#+BEGIN_SRC R :exports both :eval never
library(remotes)
install_github("bozenne/LMMstar")
#+END_SRC

For the later you will need a fairly recent R version (>=4.0.0) and,
for windows users, [[https://cran.r-project.org/bin/windows/Rtools/][Rtools]]. You can check both using:
#+BEGIN_SRC R :exports both :results output :session *R* :cache no
paste0(R.Version()[c("major","minor")], collapse = ".")
pkgbuild::find_rtools()
#+END_SRC

#+RESULTS:
: [1] "4.1.1"
: [1] TRUE

** Export citation

#+BEGIN_SRC R :exports both :results output :session *R* :cache no
citation("LMMstar")
#+END_SRC

#+RESULTS:
#+begin_example

To cite the 'LMMstar' package in publications use the following text:

  Ozenne B, Forman J (2024). _LMMstar: Repeated measurement models for
  discrete times_. R package version 1.1.0.

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {LMMstar: Repeated measurement models for discrete times},
    author = {Brice Ozenne and Julie Forman},
    year = {2024},
    note = {R package version 1.1.0},
  }
#+end_example

** Functionalities
For an overview of the package see the following vignette [[./vignettes/overview.pdf]].

For an introduction to partial residual see this other vignette [[./vignettes/partial-residuals.pdf]]

Owner

  • Name: Ozenne
  • Login: bozenne
  • Kind: user
  • Location: Copenhagen

I'm a bio-statistician; you will find on my Github R packages implementing statistical developments, code related to articles, and setting for emacs.

GitHub Events

Total
  • Push event: 3
Last Year
  • Push event: 3

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 311
  • Total Committers: 7
  • Avg Commits per committer: 44.429
  • Development Distribution Score (DDS): 0.418
Past Year
  • Commits: 64
  • Committers: 2
  • Avg Commits per committer: 32.0
  • Development Distribution Score (DDS): 0.219
Top Committers
Name Email Commits
Brice Maxime Hugues Ozenne h****2@k****k 181
Brice Ozenne b****e@b****e 56
Brice Maxime Hugues Ozenne h****2@s****k 42
bozenne b****e@g****m 24
Brice Ozenne b****e@o****r 4
Julie Lyng Forman n****2@s****k 2
Karl Bang Christensen K****H@s****k 2
Committer Domains (Top 20 + Academic)
sund.root.ku.dk: 2 sund.ku.dk: 1 orange.fr: 1 briceozenne-pc76.home: 1 ku.dk: 1

Issues and Pull Requests

Last synced: over 1 year ago

All Time
  • Total issues: 3
  • Total pull requests: 0
  • Average time to close issues: 1 day
  • Average time to close pull requests: N/A
  • Total issue authors: 3
  • Total pull request authors: 0
  • Average comments per issue: 1.33
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • rvlenth (1)
  • manishasena (1)
  • bozenne (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 528 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 14
  • Total maintainers: 1
cran.r-project.org: LMMstar

Repeated Measurement Models for Discrete Times

  • Versions: 14
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 528 Last month
Rankings
Downloads: 18.4%
Stargazers count: 24.2%
Average: 27.3%
Forks count: 28.8%
Dependent packages count: 29.8%
Dependent repos count: 35.5%
Maintainers (1)
brice.mh.ozenne@gmail.com
Last synced: 10 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.5.0 depends
  • nlme * depends
  • Matrix * imports
  • copula * imports
  • emmeans * imports
  • ggplot2 * imports
  • lava * imports
  • multcomp * imports
  • numDeriv * imports
  • sandwich * imports
  • AICcmodavg * suggests
  • Publish * suggests
  • R.rsp * suggests
  • asht * suggests
  • data.table * suggests
  • ggpubr * suggests
  • lattice * suggests
  • lme4 * suggests
  • lmerTest * suggests
  • mice * suggests
  • mvtnorm * suggests
  • nlmeU * suggests
  • optimx * suggests
  • psych * suggests
  • qqtest * suggests
  • reshape2 * suggests
  • testthat * suggests
.github/workflows/r.yml actions
  • actions/checkout v3 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-tinytex v2 composite