Package: eggla 1.0.1

eggla: Early Growth Genetics Longitudinal Analysis

Tools for longitudinal analysis within the EGG (Early Growth Genetics) Consortium (<http://egg-consortium.org/>).

Authors:Mickaël Canouil [aut, cre], Nicole Warrington [aut], Kimberley Burrows [aut], Anni Heiskala [aut]

eggla_1.0.1.tar.gz
eggla_1.0.1.zip(r-4.5)eggla_1.0.1.zip(r-4.4)eggla_1.0.1.zip(r-4.3)
eggla_1.0.1.tgz(r-4.4-any)eggla_1.0.1.tgz(r-4.3-any)
eggla_1.0.1.tar.gz(r-4.5-noble)eggla_1.0.1.tar.gz(r-4.4-noble)
eggla_1.0.1.tgz(r-4.4-emscripten)eggla_1.0.1.tgz(r-4.3-emscripten)
eggla.pdf |eggla.html✨
eggla/json (API)
NEWS

# Install 'eggla' in R:
install.packages('eggla', repos = c('https://mcanouil.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/mcanouil/eggla/issues

Datasets:
  • bmigrowth - BMI Measurements For 100 Individuals From 0 To 17 Years.

On CRAN:

geneticsgrowth-curvesinfancylongitudinal-analysismixed-effects-modelsspline-regression

20 exports 2 stars 1.00 score 92 dependencies 19 scripts

Last updated 7 months agofrom:eceaaa8752. Checks:OK: 4 ERROR: 1 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 23 2024
R-4.5-winOKAug 23 2024
R-4.5-linuxERRORAug 24 2024
R-4.4-winOKAug 23 2024
R-4.4-macNOTEJul 24 2024
R-4.3-winOKAug 23 2024
R-4.3-macNOTEJul 24 2024

Exports:compute_aparcompute_aucscompute_correlationscompute_outlierscompute_slopesegg_aucsegg_correlationsegg_modelegg_outliersegg_slopesgspplot_aucsplot_egg_aucsplot_egg_slopesplot_residualsplot_slopespredict_bmirun_eggla_gwasrun_eggla_lmmtime_model

Dependencies:backportsbayestestRbeeswarmbitbit64broombroom.mixedclicliprcodacodetoolscolorspacecommonmarkcpp11crayoncurldata.tabledatawizarddigestdistributionaldoParalleldplyrfansifarverforcatsforeachfurrrfuturefuture.applygenericsggbeeswarmggdistggplot2ggtextglobalsgluegridtextgrowthcleanrgtablehavenhmsinsightisobanditeratorsjpeglabelinglabelledlatticelifecyclelistenvmagrittrmarkdownMASSMatrixmgcvmunsellnlmenumDerivparallellypatchworkperformancepillarpkgconfigplyrpngprettyunitsprogresspurrrquadprogR.methodsS3R.ooR.utilsR6RColorBrewerRcppreadrrlangscalesstringistringrtibbletidyrtidyselecttzdbutf8vctrsviporviridisLitevroomwithrxfunxml2

Get Started with 'eggla'

Mickaël Canouil, Ph.D. ([email protected])

Rendered fromeggla.Rmdusingknitr::rmarkdownon Aug 23 2024.

Last update: 2024-01-30
Started: 2022-05-03

Readme and manuals

Help Manual

Help pageTopics
BMI Measurements For 100 Individuals From 0 To 17 Years.bmigrowth
Compute adiposity peak (AP) and adiposity rebound (AR).compute_apar
Compute area under the curves for several intervals using a model fitted by 'time_model()'.compute_aucs
Compute the derived parameters correlations from a cubic splines mixed-effects model by 'time_model()'.compute_correlations
Compute outliers detection in derived parameters from a cubic splines mixed-effects model by 'time_model()'.compute_outliers
Predict average slopes for several intervals using a model fitted by 'time_model()'.compute_slopes
Derived areas under the curve from a cubic splines mixed-effects model by 'egg_model()'.egg_aucs
Compute the derived parameters correlations from a cubic splines mixed-effects model by 'egg_model()'.egg_correlations
Fit a cubic splines mixed model.egg_model
Compute outliers detection in AUCs/Slopes derived parameters from a cubic splines mixed-effects model by 'egg_model()'.egg_outliers
Derived slopes from a cubic splines mixed-effects model by 'egg_model()'.egg_slopes
General regression splines with variable degrees and ness, smoothing splines.gsp
Plot derived area under the curves from a model fitted by 'time_model()'.plot_aucs
Plot derived area under the curves from a model fitted by 'egg_model()'.plot_egg_aucs
Plot derived slopes from a model fitted by 'egg_model()'.plot_egg_slopes
Plot several residuals plots for diagnostics.plot_residuals
Plot derived slopes from a model fitted by 'time_model()'.plot_slopes
Predict BMI for a range of ages from a model fit.predict_bmi
Perform GWAS using PLINK2 (and BCFtools)run_eggla_gwas
Perform EGG longitudinal analysis and derived areas under the curves and slopes.run_eggla_lmm
Fit one of three mixed model.time_model