NEWS.md
In mcanouil/eggla: Early Growth Genetics Longitudinal Analysis

eggla 1.0.4

In README.Rmd,
docs: replace previous instructions with instructions using "lock" file for dependencies.
In vignettes/,
docs: remove outdated email address.

eggla 1.0.3

In R/*_aucs.R, R/*_slopes.R,
fix: sort rows by IDs (#127, thanks @DrGengWang).
fix: ensure denominator's length depends on the number of knots. (#127, thanks @DrGengWang)

In tests/testthat,
test: update snapshots

eggla 1.0.2

In R/*_aucs.R, R/*_slopes.R,
fix: use ID as character and use merge to combine data.frames/matrices.

In R, tests/testthat,
chore: replace 1: with seq_len and $ with [[.

In tests/testthat,
test: cleanup duplicated and outdated tests.
test: add snapshot tests.

eggla 1.0.1

In DESCRIPTION,
build: add growthcleanr GitHub repository as remote.

Full Changelog: https://github.com/mcanouil/eggla/compare/v1.0.0...v1.0.1

eggla 1.0.0

In inst/bin,
build: update PLINK2 to 5th of January 2024 version (Linux 64-bit build).
In .github,
build: upgrade BCFtools to 1.19.
build: upgrade R to 3.4.2.
In DESCRIPTION,
build: upgrade R packages to latest versions.

In inst/CITATION,
chore: convert CFF to bibentry.
In citation.cff,
chore: update citation file.
In R/gsp.R,
chore: add @export for S3 method.

Full Changelog: https://github.com/mcanouil/eggla/compare/v0.20.0...v1.0.0

eggla 0.20.0

In R, and vignettes/articles,
fix: add missing knot at 0.75 in linear splines model.

In .github,
chore: update infrastructure based on Devcontainer.

Full Changelog: https://github.com/mcanouil/eggla/compare/v0.19.6...v0.19.7

eggla 0.19.6

In R/run_eggla_gwas.R,
fix: GWAS results are now exported as a tab-delimited compressed file (i.e., txt.gz).

Full Changelog: https://github.com/mcanouil/eggla/compare/v0.19.5...v0.19.6

eggla 0.19.5

In R/egg_model.R,
fix: turns warnings into errors when fitting the model for the first time.

Full Changelog: https://github.com/mcanouil/eggla/compare/v0.19.4...v0.19.5

eggla 0.19.4

In R/on_attach.R, R/plot_aucs.R, R/plot_egg_aucs.R, R/predict_bmi.R, R/run_eggla_gwas.R, R/run_eggla_lmm.R,
fix: linters warnings.
In R/egg_model.R,
fix: in case or error, also increase the umber of EM iterations.

Full Changelog: https://github.com/mcanouil/eggla/compare/v0.19.3...v0.19.4

eggla 0.19.3

In R/run_eggla_gwas.R,
fix: update commands to get version.
fix: 'ax' replaced with 'omitted' in PLINK2 output.

Full Changelog: https://github.com/mcanouil/eggla/compare/v0.19.2...v0.19.3

eggla 0.19.2

In inst/bin,
build: update PLINK2 to 11th of April 2023 version (Linux 64-bit build).

In inst/CITATION,
chore: convert to bibentry.

Full Changelog: https://github.com/mcanouil/eggla/compare/v0.19.1...v0.19.2

eggla 0.19.1

In inst/CITATION, pkgdown/_pkgdown.yml, CITATION.cff, and DESCRIPTION,
chore: update domain

In R/eggla-packages.R,
docs: update domain.
In R/run_eggla_gwas.R,
docs: update missing argument.

Full Changelog: https://github.com/mcanouil/eggla/compare/v0.19.0...v0.19.1

eggla 0.19.0

In R/run_eggla_gwas.R,
fix: update path to files in example.
fix: check for samples in VCF files.
fix: leading zeros in IDs in dataset were removed.
fix: use PLINK2 to compute HWE P-value, N, alleles frequencies, and missing rate.
fix: use PLINK2 to compute MACH_R2 imputation score.
fix: use vep_file as the top level parameter instead of vep.
fix: remove --mach-r2-filter PLINK2 option.
In R/plot_aucs.R, R/plot_egg_aucs.R, and R/run_eggla_lmm.R,
fix: groupOnX argument of geom_quasirandom() is deprecated as of ggbeeswarm 0.7.1.
In R/plot_slopes.R and R/plot_egg_slopes.R,
fix: using size aesthetic for lines was deprecated.
In R/run_eggla_lmm(),
fix: bad copy/paste. (#100)
fix: wrong static title for residuals plot. (#102)
fix: update step parameter for adiposity peak/rebound prediction. (#98)
In R/compute_apar.R, R/compute_outliers.R, R/egg_correlations.R, R/egg_outliers.R, and R/predict_bmi.R,
fix: update step parameter for adiposity peak/rebound prediction. (#98)

chore: split .devcontainer settings into a separate repositories, i.e., .vscode and .devcontainer.

build: upgrade PLINK2 and BCFtools to latest versions.
build: update R packages to latest versions.

Full Changelog: https://github.com/mcanouil/eggla/compare/v0.18.5...v0.19.0

eggla 0.18.5

In R/egg_correlations.R,
docs: fix wrong return value in documentation.

Full Changelog: https://github.com/mcanouil/eggla/compare/v0.18.4...v0.18.5

eggla 0.18.4

In DESCRIPTION,
chore: update email address.

Full Changelog: https://github.com/mcanouil/eggla/compare/v0.18.3...v0.18.4

eggla 0.18.3

In R/run_eggla_gwas.R,
fix: HWE_P should be NA for imputed variants.

Full Changelog: https://github.com/mcanouil/eggla/compare/v0.18.2...v0.18.3

eggla 0.18.2

In R/egg_correlations.R and R/run_eggla_lmm.R,
fix: parameters table not properly filtered and omitting missing values.

Full Changelog: https://github.com/mcanouil/eggla/compare/v0.18.1...v0.18.2

eggla 0.18.1

In R/run_eggla_gwas.R,
fix: info_type description given to genotyped variants.

Full Changelog: https://github.com/mcanouil/eggla/compare/v0.18.0...v0.18.1

eggla 0.18.0

In R/run_eggla_lmm.R and R/egg_correlations.R,
feat: perform correlations between all parameters.

Full Changelog: https://github.com/mcanouil/eggla/compare/v0.17.5...v0.18.0

eggla 0.17.5

In vignettes/articles/adiposity-peak-rebound.Rmd,
style: remove top ticks for AP/AR.

Full Changelog: https://github.com/mcanouil/eggla/compare/v0.17.4...v0.17.5

eggla 0.17.4

In R/run_eggla_gwas.R,
fix: rename R2 to INFO if exists.
In vignettes/articles/models-diagnostics.Rmd,
revert: set back knots to original values for diagnostics.
fix: hardcode performance metrics to avoid changes due to performance updates.
fix: eval to FALSE to set w/o AR1.

In vignettes/articles/models-diagnostics.Rmd,
docs: new section to update and tidy perf data.

In vignettes/articles/adiposity-peak-rebound.Rmd, vignettes/articles/run-cubic-splines.Rmd, and vignettes/articles/models-diagnostics.Rmd,
style: homogenise all figures with the new theme.

Full Changelog: https://github.com/mcanouil/eggla/compare/v0.17.3...v0.17.4

eggla 0.17.3

In R/run_eggla_lmm.R,
fix: order derived parameter for outlier figure.

Full Changelog: https://github.com/mcanouil/eggla/compare/v0.17.2...v0.17.3

eggla 0.17.2

In R/compute_apar.R,
fix: update filter that removed all AR estimates and add a control for AR > AP.
In vignettes/articles/adiposity-peak-rebound.Rmd,
fix: missplaced parenthesis.

Full Changelog: https://github.com/mcanouil/eggla/compare/v0.17.1...v0.17.2

eggla 0.17.1

In R/compute_outliers.R, R/egg_outliers.R, and R/run_eggla_lmm.R,
fix: only allow one value for outlier_method.
In R/plot_egg_slopes.R and R/plot_slopes.R,
fix: uses GAM with cubic splines every time.

style: set default ggplot2 theme to a modified version of theme_minimal() and colour/fill scales to "viridis".
style: use Okabe Ito colour palette.

Full Changelog: https://github.com/mcanouil/eggla/compare/v0.17.0...v0.17.1

eggla 0.17.0

In R/run_eggla_lmm.R, R/compute_outliers.R, and R/egg_outliers.R,
feat: new arg to pass on the outlier method.
feat: new arg to pass on the outlier method threshold.
feat: now exclude flagged outliers by setting their values to NA.

In R/compute_outliers.R,
fix: replace AP greater than 2 by NA.

In tests,
test: no longer uses snapshots.

In pkgdown/_pkgdown.yml,
style: separate the run_eggl_*() functions from the rest.

Full Changelog: https://github.com/mcanouil/eggla/compare/v0.16.0...v0.17.0

eggla 0.16.0

In R/run_eggla_lmm.R,
feat: draw outlier figure for all derived parameters.

In R/compute_outliers.R and R/egg_outliers.R,
fix: id column matching across parameters now properly works.
In R/run_eggla_gwas.R,
fix: CRAN checks notes.
In R/compute_apar.R, R/plot_aucs.R, R/plot_egg_aucs.R, R/plot_egg_slopes.R, R/plot_residuals.R, R/plot_slopes.R, vignettes/articles/adiposity-peak-rebound.Rmd, vignettes/articles/model-selection.Rmd, vignettes/articles/models-diagnostics.Rmd, and vignettes/articles/run-cubic-splines.Rmd,
fix: standardise ggplot default theme and fix gt tables.

Full Changelog: https://github.com/mcanouil/eggla/compare/v0.15.0...v0.16.0

eggla 0.15.0

In R/compute_outliers.R and R/egg_outliers.R,
feat: now detects outliers for all slopes together, all AUCs together and for individual slopes, AUCs, AP (BMI and age), and AR (BMI and age).

Full Changelog: https://github.com/mcanouil/eggla/compare/v0.14.0...v0.15.0

eggla 0.14.0

refactor!: no longer rely on renv.

In R/run_eggla_lmm.R,
feat: add diagnostics output to a "to-send" folder to avoid mistakenly send individual-level data.
In R/run_eggla_gwas.R,
fix: now uses the filled INFO field of VCF and compute required columns for meta-analysis.

Full Changelog: https://github.com/mcanouil/eggla/compare/v0.13.1...v0.14.0

eggla 0.13.1

In pkgdown/_pkgdown.yml,
chore: update template to "minty".

Full Changelog: https://github.com/mcanouil/eggla/compare/v0.13.0...v0.13.1

eggla 0.13.0

In R/*.R,
fix: knots default value is now c(1, 8, 12).
In R/run_eggla_gwas.R,
refactor: path argument has been renamed working_directory for consistency with run_eggla_lmm().

In R/compute_apar.R and R/predict_bmi.R,
feat: filter argument filter predicted values table in case of multiple measurements.
In R/run_eggla_lmm.R,
feat: filter_apar argument to be passed to compute_apar() and predict_bmi().
In R/run_eggla_gwas.R,
feat: now performs GWAS of BMI and age at adiposity peak and rebound in addition to slopes and AUCs.
feat: now has a clean argument which clean intermediary files stored in working_directory.
feat: new use_info argument to indicate if INFO field should be extracted (default is FALSE).

In R/run_eggla_lmm.R,
fix: now checks if IDs are unique.
fix: properly export BMI and age at adiposity peak and rebound.
fix: PLINK2 and BCFTools binary path checks.
In R/run_eggla_gwas.R,
fix: now check for individuals in common between phenotypes and genotypes before processing the VCF files.
In DESCRIPTION,
fix: move some packages from suggests to imports (e.g., ggtext, ggdist, etc.)
fix: now uses growthcleaner from CRAN.

In .devcontainer and inst/setup,
refactor: improve Docker build process and add devcontainer ability.
In pkgdown/_pkgdown.yml,
refactor: reorder sections to focus on the main functions first.

Full Changelog: <https://github.com/mcanouil/eggla/compare/v0.12.3...v0.13.0>

eggla 0.12.3

In DESCRIPTION,
fix: depends on R >= 4.2.0.

In R/run_eggla_gwas.R,
fix: BCFtools filters as parameter with non by default.
fix: ensure 'id_column' is of type character.

In insta/vcf and data-raw/bmigrowth.R,
chore: add VCF files to test run_eggla_gwas().

In inst/setup/eggla-example.R,
test: add run_eggla_gwas in docker build test example.
In tests/testthat/test-run_eggla.R,
test: new tests for run_eggla functions.

Full Changelog: <https://github.com/mcanouil/eggla/compare/v0.12.2...v0.12.3>

eggla 0.12.2

In R/run_eggla_gwas.R,
fix: the condition has length > 1.

Full Changelog: <https://github.com/mcanouil/eggla/compare/v0.12.1...v0.12.2>

eggla 0.12.1

In R/run_eggla_gwas.R,
fix: wrong variable in "results" input check condition.

Full Changelog: <https://github.com/mcanouil/eggla/compare/v0.12.0...v0.12.1>

eggla 0.12.0

In R/run_eggla_lmm.R,
fix: improve data transformation/cleaning (#38).
fix: allow to output directories path and no zip archives when zip is not available (#41).
fix: remove dates from model object filename.
In R/run_eggla_gwas.R,
fix: allow to use directories path or zip archives as results (#41).
fix: rename results_zip argument to results.

In R/run_eggla_lmm.R,
feat: add knots and period parameters (#37).
feat: add clean parameter to clean directories when archives are successfully created (#41).

chore: remove version from CFF file.

style: remove break line in badges section.

Full Changelog: <https://github.com/mcanouil/eggla/compare/v0.11.2...v0.12.0>

eggla 0.11.2

fix: uses general Zenodo DOI.

Full Changelog: <https://github.com/mcanouil/eggla/compare/v0.11.1...v0.11.2>

eggla 0.11.1

chore: add DOI and citation files.

In vinettes/eggla.Rmd,
fix: uses latest moving tag.

Full Changelog: <https://github.com/mcanouil/eggla/compare/v0.11.0...v0.11.1>

eggla 0.11.0

run_eggla() has been renamed to run_eggla_lmm().
do_eggla_gwas() has been renamed to run_eggla_gwas().

In R/run_eggla_lmm.R,
fix: exclude rds from being included in archive.
In R/run_eggla_gwas.R,
fix: improve and add messages.
fix: ensure "data" is a data.frame or a path read in a data.frame.
fix: allows binary path to be an actual binary path.
fix: now returns results files path, input parameters zip file, and text file with software versions.
fix: collapse vector of covariates into an atomic string to be added in the results files.

In inst/bin,
feat: add PLINK2 binary internally.
In R/run_eggla_lmm.R,
feat: eggla model call is now written in a file.
In R/egg_correlations() and R/compute_correlations(),
feat: add correlation figure/table. (#22)
In R/egg_outliers() and R/compute_outliers(),
feat: add function to check. (#22)

In tests/testhat:
test: add tests for plot functions.
test: add more tests for time_model() and egg_model().
test: add tests for *_correlations() and *_outliers() functions.

Full Changelog: <https://github.com/mcanouil/eggla/compare/v0.10.4...v0.11.0>

eggla 0.10.4

In R/do_eggla_gwas.R,
Fix: plink2 binary path modified outside download if statement.
Fix: merge not cartesian by keeping only first measures of each individuals (#20).
In inst/setup/Dockerfile, inst/setup/pkg.lock, inst/setup/renv.lock, anddata-raw/lock.R,
Fix: add all data.table dependencies.
In R/, tests/, and vignettes/,
fix: documentation consistency with code, i.e., replaced "AR1" with "CAR1" (#21).

Full Changelog: <https://github.com/mcanouil/eggla/compare/v0.10.3...v0.10.4>

eggla 0.10.3

In inst/Dockerfile,
Build: add PLINK2 and install all eggla's dependencies, including suggests.
In R/do_eggla_gwas.R,
Fix: no longer relies on URL for PLINK2 since only alpha dynamic URL remains.
In vignettes/eggla.Rmd:
Chore: remove unused eval = FALSE chunk option.
Fix: remove renv code in the Docker section.
Fix: set properly the working directory.

Full Changelog: <https://github.com/mcanouil/eggla/compare/v0.10.2...v0.10.3>

eggla 0.10.2

In R/egg_model.R,
Fix: try without CAR1 before reducing random effect. (#18)

Full Changelog: <https://github.com/mcanouil/eggla/compare/v0.10.1...v0.10.2>

eggla 0.10.1

In R/egg_slopes.R, R/plot_egg_slopes.R, R/egg_aucs.R, and R/plot_egg_aucs.R,
Fix: hardcoded knots, now as an argument. (#16, #17)

Full Changelog: <https://github.com/mcanouil/eggla/compare/v0.10.0...v0.10.1>

eggla 0.10.0

In R/predict_bmi.R (#14),
Feat: new function to predict BMI from a lme model object, from egg_model() or time_model().

Change default period to the following time windows for predicting 'linear' slopes from the model:
0-0.5 years (Infancy – same as previously).
1.5-3.5 years (Childhood – reduced the upper bound from 5 years).
6.5-10 years (Pre-pubertal – increased the lower bound from 6 years).
12-17 years (adolescence – same as previously).

In R/compute_apar.R (#14),
Fix: grep instead of any/grepl.
Refactor: inherits params from predict_bmi().
Fix: uses predict_bmi() internally.
In R/plot_slopes.R, and R/plot_egg_slopes.R,
Fix: grep instead of any/grepl.
Fix: uses GAM 'y ~ s(x, bs = "cr")'.
In vignettes/articles/adiposity-peak-rebound.Rmd; vignettes/articles/models-diagnostics.Rmd, and vignettes/articles/run-cubic-splines.Rmd (#14, #15),
Fix: uses GAM 'y ~ s(x, bs = "cr")' and predict_bmi().
In vignettes/eggla.Rmd,
Fix: "-it" instead of "--detach" for Docker command.

Full Changelog: <https://github.com/mcanouil/eggla/compare/v0.9.1...v0.10.0>

eggla 0.9.1

In R/egg_model.R, R/egg_model.R, R/run_eggla.R, and R/do_eggla_gwas,
Feat: add quiet to silent the messages.

Full Changelog: <https://github.com/mcanouil/eggla/compare/v0.9.0...v0.9.1>

eggla 0.9.0

In inst/setup/Dockerfile,
Feat: add script example (inst\setup\eggla-example.R) to run on dataset included in eggla.
In R/egg_model.R,
Feat: allow to specify the knots for the splines, i.e., no longer hardcoded.

In R/egg_model.R,
Fix: hardcoded "ID" for individual specification in random effect.
In R/time_model.R,
Fix: hardcoded "ID" for individual specification in random effect by adding id_var arg.
In vignettes/eggla.Rmd (renamed/moved from vignettes/articles/run-eggla.Rmd),
Fix: use Rscript instead of R --no-save --no-restore --quiet.

In vignettes/eggla.Rmd,
Docs: complete GWAS sections.
Docs: add Docker section.

Full Changelog: <https://github.com/mcanouil/eggla/compare/v0.8.1...v0.9.0>

eggla 0.8.1

In inst/setup/Dockerfile,
Feat: Docker image built automatically "devel" from "main" and "tag" from "releases".

Full Changelog: <https://github.com/mcanouil/eggla/compare/v0.8.0...v0.8.1>

eggla 0.8.0

In R/compute_apar.R,
Feat: allow to compute adiposity peak and adiposity rebound on raw data from a "lme" model object.
Refactor: rename arguments.
In tests, DESCRIPTION,
Feat: now uses the third edition of testthat.

In R/do_eggla_gwas.R,
Fix: no visible global function definition for 'patterns'.

In inst/setup,
build: update lock files from renv and pak based on local package.
In data-raw/lock.R,
build: update script to work on local version for both renv and pak.

Full Changelog: <https://github.com/mcanouil/eggla/compare/v0.7.0...v0.8.0>

eggla 0.7.0

In R/compute_apar.R,
Feat: Allows to define the range in which to compute adiposity peak and adiposity rebound.
In R/egg_model.R, R/time_model.R,
Feat: Allows to use (or not) AR(1) auto-correlation in the model, if TRUE (default: FALSE), the function will try without if all models fail.

In vignettes/articles/run-eggla.Rmd, vignettes/articles/models-diagnostics.Rmd,
Fix: Uses CAR1 by default in vignettes, only to speed-up computation.

Full Changelog: <https://github.com/mcanouil/eggla/compare/v0.6.1...v0.7.0>

eggla 0.6.1

In R/compute_apar.R,
Fix: returns only the first local maxima (adiposity peak) and minima (adiposity rebound).

Full Changelog: <https://github.com/mcanouil/eggla/compare/v0.6.0...v0.6.1>

eggla 0.6.0

In R/do_eggla_gwas.R:
Feat: Function to run GWAS on eggla results using PLINK2 (and BCFtools).
In vignettes/articles/run_eggla,
Feat: Add "GWAS" step.
Refactor: use "R EOF" syntax.

In R/run_eggla.R:
Fix: Rename (add "s") AUCs csv output file for consistency.
Docs: Add missing documentation for parameters.
In R/plot_slopes.R:
Fix: hardcoded "age" variable.
Fix: ignore case in variable search.
In R/plot_egg_slopes.R:
Fix: hardcoded "age" variable.
Fix: ignore case in variable search.
In R/compute_apar.R:
Fix: ignore case in variable search.

Full Changelog: <https://github.com/mcanouil/eggla/compare/v0.5.2...v0.6.0>

eggla 0.5.2

Fix: renv::restore issue with renv.lock from GitHub.
Fix: Update pak install command.
Chore: Upgrade lock files.

Full Changelog: <https://github.com/mcanouil/eggla/compare/v0.5.1...v0.5.2>

eggla 0.5.1

No longer uses nlme::corCAR1(form = ~ 1 | ID) in models.
Add Kimberley Burrows (@burrowsk) and Anni Heiskala as authors.

Full Changelog: <https://github.com/mcanouil/eggla/compare/v0.5.0...v0.5.1>

eggla 0.5.0

Improve/Polish documentation,
Add title.
Add/tweak description.
Add code examples.
In R/egg_*.R,
Add random_complexity parameter.
Remove _var arguments.
In R/compute_apar.R,
New function to compute adiposity peak and adiposity rebound from a lme model object, such as egg_model.
In R/compute_aucs.R,
Rename function for consistency, previously known as compute_auc.
In R/compute_slopess.R,
Rename function for consistency, previously known as predict_average_slopes.
In vignettes/articles,
Add 01-models-diagnostics.Rmd, to describe models testing and diagnostics.
Add 02-models-selection.Rmd, to show how to perform models selection based on results from models-diagnostics.Rmd.
Add 03-run-cubic-splines.Rmd, to show how to run cubic splines models on the example dataset (previously in README.Rmd).
Add 04-adiposity-peak-rebound.Rmd, to identify/caracterise adiposity peak and adiposity rebound from models-diagnostics.Rmd.
Add 99-run-eggla.Rmd, to show how to run analysis interactively or not.
In R/plot_*.R,
New functions to plot area under the curves and slopes.
In pkgdown/_pkgdown.yml,
Polish website.

Full Changelog: <https://github.com/mcanouil/eggla/compare/v0.4.4...v0.5.0>

eggla 0.4.4

In R/egg_model.R,
Three cublic spline random effects formula are tested in the following order:
1. ~ gsp(age, knots = c(2, 8, 12), degree = rep(3, 4), smooth = rep(2, 3)) | ID
2. ~ gsp(age, knots = c(2, 8, 12), degree = rep(3, 4), smooth = rep(2, 3))[,1:3] | ID
3. ~ gsp(age, knots = c(2, 8, 12), degree = rep(1, 4), smooth = rep(2, 3)) | ID
Add message about which model is currently being computed.
Add pkgdown website.

Full Changelog: <https://github.com/mcanouil/eggla/compare/v0.4.3...v0.4.4>

eggla 0.4.3

In README.(R)md,
Disable renv caching.
In inst/model-diagnostics,
Remove ragg dependency, uses grDevices instead.
In inst/setup,
Add Dockerfile.
Use pak in addition to renv.
In R/run_eggla.R,
Remove ragg dependency, uses grDevices instead.

Full Changelog: <https://github.com/mcanouil/eggla/compare/v0.4.2...v0.4.3>

eggla 0.4.2

In README.(R)md,
Fix typo in renv::init calls.

Full Changelog: <https://github.com/mcanouil/eggla/compare/v0.4.1...v0.4.2>

eggla 0.4.1

In README.(R)md,
Add renv cleaning in bash example script.
Add setup for both interactive and non-interactive use.
In R/run_eggla.R,
Switch from svglite to ragg to avoid issues with high number of elements.
Fix id_var which was not set with id_var = "egg_id" internally.
In DESCRIPTION,
Switch from svglite to ragg to avoid issues with high number of elements.

Full Changelog: <https://github.com/mcanouil/eggla/compare/v0.4.0...v0.4.1>

eggla 0.4.0

In README.(R)md,
Add table of content.
Add Bash script to run everything.
In inst/setup,
Add renv.lock file to list dependencies with version and help install or restore them.
In R/egg_model.R,
Mixed model selected inside a helper/wrapper function.
In R/run_eggla.R,
Compute quaility-control for BMI.
Compute modelling.
Write model object.
Write derived parameters.
Generate residuals plot.
In R/time_model.R,
Fix model specification where additional covariates were not properly added to the model formula.
In R/plot_residuals.R,
Fix hardcoded variable, i.e., "age".
In inst/models-diagnostics,
models-diagnostics.R, R script to compute different models and extract performance metrics.
models-best.R, R script to compare models performance from models-diagnostics.R.
models-adiposity.R, R script to compare predicted BMI values to check for the "adiposity peak".
In R,
Remove trailing spaces.
Comment code not used.
Add missing documentation.
In LICENSE,
Add Nicole Warrington.

Full Changelog: <https://github.com/mcanouil/eggla/compare/v0.3.0...v0.4.0>

eggla 0.3.0

In R/time_model.R,
Add fall back (simpler random effect) models for "cubic_splines", "cubic_slopes" and "linear_splines".
Fix typos in messages.
Model call is printed as message.
In inst/rmarkdown/templates/eggla/skeleton/skeleton.Rmd,
Add Daymont flag exclusion argument and control before modelling step.
Summary table and models use covariates parameter.
Uses "sex" coded as 1 for male and 0 for female.
Small code refactoring.
Use performance to compare models.
Add summary_variables parameter to show in the summary table.
Decrease font size in Daymont's QC summary table .
Fix numbers in the summary table.

Full Changelog: <https://github.com/mcanouil/eggla/compare/v0.2.0...v0.3.0>

eggla 0.2.0

In R/time_model.R,
Fix output when using as_text = TRUE.
Add cov to allow additional covariates.
In inst/rmarkdown/templates/eggla/skeleton/skeleton.Rmd,
Add cov to allow additional covariates.

Full Changelog: <https://github.com/mcanouil/eggla/compare/v0.1.0...v0.2.0>

eggla 0.1.0

Initial version.

mcanouil/eggla documentation built on April 5, 2025, 3:06 a.m.

rdrr.io home R language documentation Run R code online

CRAN packages Bioconductor packages R-Forge packages GitHub packages

Note that we can't provide technical support on individual packages. You should contact the package authors for that.

mcanouil/eggla Early Growth Genetics Longitudinal Analysis

NEWS.md In mcanouil/eggla: Early Growth Genetics Longitudinal Analysis

eggla 1.0.4

Documentation

eggla 1.0.3

Fixes

Tests

eggla 1.0.2

Fixes

Chores

Tests

eggla 1.0.1

Build

eggla 1.0.0

Build

Chores

eggla 0.20.0

Fixes

Chores

eggla 0.19.6

Fixes

eggla 0.19.5

Fixes

eggla 0.19.4

Fixes

eggla 0.19.3

Fixes

eggla 0.19.2

Build

Chores

eggla 0.19.1

Chores

Docs

eggla 0.19.0

Fixes

Chores

Build

eggla 0.18.5

eggla 0.18.4

Chores

eggla 0.18.3

Fixes

eggla 0.18.2

Fixes

eggla 0.18.1

Fixes

eggla 0.18.0

Features

eggla 0.17.5

Style

eggla 0.17.4

Fixes

Docs

Style

eggla 0.17.3

Fixes

eggla 0.17.2

Fixes

eggla 0.17.1

Fixes

Style

eggla 0.17.0

Features

Fixes

Tests

Chores

eggla 0.16.0

Features

Fixes

eggla 0.15.0

Features

eggla 0.14.0

Breaking changes

Features/Fixes

eggla 0.13.1

Chores

eggla 0.13.0

Breaking changes

Features

Fixes

mcanouil/eggla
Early Growth Genetics Longitudinal Analysis

NEWS.md
In mcanouil/eggla: Early Growth Genetics Longitudinal Analysis