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Recent Releases of eggla

eggla - eggla v1.0.4

Documentation

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    • docs: remove outdated email address.

What's Changed

  • docs: update install instructions and rm outdated email by @mcanouil in https://github.com/mcanouil/eggla/pull/129

Full Changelog: https://github.com/mcanouil/eggla/compare/v1.0.3...v1.0.4

- R
Published by mcanouil about 1 year ago

eggla - eggla v1.0.3

Fixes

  • 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)

Tests

  • In tests/testthat,
    • test: update snapshots

What's Changed

  • fix: ID ordering differences *aucs() / *slopes() by @mcanouil in https://github.com/mcanouil/eggla/pull/128

Full Changelog: https://github.com/mcanouil/eggla/compare/v1.0.2...v1.0.3

- R
Published by mcanouil over 1 year ago

eggla - eggla v1.0.2

Fixes

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

Chores

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

Tests

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    • test: cleanup duplicated and outdated tests.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

What's Changed

  • build: growthcleanr from GitHub by @mcanouil in https://github.com/mcanouil/eggla/pull/125
  • fix: use ID as character and use merge to combine data.frames/matrices. by @mcanouil in https://github.com/mcanouil/eggla/pull/126

Full Changelog: https://github.com/mcanouil/eggla/compare/v1.0.0...v1.0.2

- R
Published by mcanouil over 1 year ago

eggla - eggla v1.0.1

Build

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

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

- R
Published by mcanouil almost 2 years ago

eggla - eggla v1.0.0

Build

  • 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.

Chores

  • 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.

What's Changed

  • chore: bump year license by @mcanouil in https://github.com/mcanouil/eggla/pull/119
  • chore: devcontainer update via dependabot by @mcanouil in https://github.com/mcanouil/eggla/pull/120
  • chore: update cff by @mcanouil in https://github.com/mcanouil/eggla/pull/121
  • ci: add dev devcontainer and tweak workflow by @mcanouil in https://github.com/mcanouil/eggla/pull/122
  • chore: 1.0.0-pre by @mcanouil in https://github.com/mcanouil/eggla/pull/123

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

- R
Published by mcanouil about 2 years ago

eggla - eggla v1.0.0

Build

  • 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.

Chores

  • 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.

What's Changed

  • build(deps): bump actions/checkout from 3 to 4 by @dependabot in https://github.com/mcanouil/eggla/pull/117
  • build(deps): bump docker/login-action from 2 to 3 by @dependabot in https://github.com/mcanouil/eggla/pull/118
  • chore: bump year license by @mcanouil in https://github.com/mcanouil/eggla/pull/119
  • chore: devcontainer update via dependabot by @mcanouil in https://github.com/mcanouil/eggla/pull/120
  • chore: update cff by @mcanouil in https://github.com/mcanouil/eggla/pull/121
  • ci: add dev devcontainer and tweak workflow by @mcanouil in https://github.com/mcanouil/eggla/pull/122
  • chore: 1.0.0-pre by @mcanouil in https://github.com/mcanouil/eggla/pull/123

Full Changelog: https://github.com/mcanouil/eggla/compare/v0.19.6...v1.0.0-rc

- R
Published by mcanouil about 2 years ago

eggla - eggla 0.20.0

Fixes

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

Chores

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

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

- R
Published by mcanouil over 2 years ago

eggla - eggla 0.19.6

Fixes

  • 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

- R
Published by mcanouil over 2 years ago

eggla - eggla 0.19.5

Fixes

  • 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

- R
Published by mcanouil almost 3 years ago

eggla - eggla 0.19.4

Fixes

  • 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

- R
Published by mcanouil almost 3 years ago

eggla - eggla 0.19.3

Fixes

  • 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

- R
Published by mcanouil almost 3 years ago

eggla - eggla 0.19.2

Build

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

Chores

  • In inst/CITATION,
    • chore: convert to bibentry.

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

- R
Published by mcanouil almost 3 years ago

eggla - eggla 0.19.1

Chores

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

Docs

  • 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

- R
Published by mcanouil almost 3 years ago

eggla - eggla 0.19.0

Fixes

  • 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)

Chores

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

Build

  • 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

- R
Published by mcanouil almost 3 years ago

eggla - 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

What's Changed

  • fix return in roxygen block by @Ning-L in https://github.com/mcanouil/eggla/pull/94
  • docs: roxygen2::roxygenise() by @mcanouil in https://github.com/mcanouil/eggla/pull/95

New Contributors

  • @Ning-L made their first contribution in https://github.com/mcanouil/eggla/pull/94

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

- R
Published by mcanouil about 3 years ago

eggla - eggla 0.18.4

Chores

  • In DESCRIPTION,
    • chore: update email address.

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

- R
Published by mcanouil about 3 years ago

eggla - eggla 0.18.3

Fixes

  • 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

- R
Published by mcanouil over 3 years ago

eggla - eggla 0.18.2

Fixes

  • 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

- R
Published by mcanouil over 3 years ago

eggla - eggla 0.18.1

Fixes

  • 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

- R
Published by mcanouil over 3 years ago

eggla - eggla 0.18.0

Features

  • 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

- R
Published by mcanouil over 3 years ago

eggla - eggla 0.17.5

Style

  • 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

- R
Published by mcanouil over 3 years ago

eggla - eggla 0.17.4

Fixes

  • 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.

Docs

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

Style

  • 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

- R
Published by mcanouil over 3 years ago

eggla - eggla 0.17.3

Fixes

  • 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

- R
Published by mcanouil over 3 years ago

eggla - eggla 0.17.2

Fixes

  • 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

- R
Published by mcanouil over 3 years ago

eggla - eggla 0.17.1

Fixes

  • 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

  • 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

- R
Published by mcanouil over 3 years ago

eggla - eggla 0.17.0

Features

  • 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.

Fixes

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

Tests

  • In tests,
    • test: no longer uses snapshots.

Chores

  • 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

- R
Published by mcanouil over 3 years ago

eggla - eggla 0.16.0

Features

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

Fixes

  • 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

- R
Published by mcanouil over 3 years ago

eggla - eggla 0.15.0

Features

  • 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

- R
Published by mcanouil over 3 years ago

eggla - eggla 0.14.0

Breaking changes

  • refactor!: no longer rely on renv.

Features/Fixes

  • 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

- R
Published by mcanouil over 3 years ago

eggla - eggla 0.13.1

Chores

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

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

- R
Published by mcanouil over 3 years ago

eggla - eggla 0.13.0

Breaking changes

  • 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().

Features

  • 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).

Fixes

  • 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.

Chores

  • 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.

What's Changed

  • test: add VCF files to test run_eggla_gwas() using CI by @mcanouil in https://github.com/mcanouil/eggla/pull/43
  • fix: object name in docker build test example by @mcanouil in https://github.com/mcanouil/eggla/pull/44
  • build: fix missing data.table by @mcanouil in https://github.com/mcanouil/eggla/pull/45
  • build: fix bmigrowth not a data.table by @mcanouil in https://github.com/mcanouil/eggla/pull/46
  • fix: Genotypes / Phenotypes with no matching IDs by @mcanouil in https://github.com/mcanouil/eggla/pull/53
  • fix: Update knots from 2,8,12 to 1,8,12 by @mcanouil in https://github.com/mcanouil/eggla/pull/56
  • fix: non unique ids by @mcanouil in https://github.com/mcanouil/eggla/pull/52
  • ci: add devcontainer and use it for eggla image by @mcanouil in https://github.com/mcanouil/eggla/pull/58
  • fix: consistent arg names with lmm function by @mcanouil in https://github.com/mcanouil/eggla/pull/59
  • refactor: docker build and devcontainer by @mcanouil in https://github.com/mcanouil/eggla/pull/60
  • chore: Docker container and dev by @mcanouil in https://github.com/mcanouil/eggla/pull/61
  • ci: refactor and tweak GHA by @mcanouil in https://github.com/mcanouil/eggla/pull/63
  • fix: Add AP and AR in LMM and GWAS by @mcanouil in https://github.com/mcanouil/eggla/pull/57
  • feat: use_info to use or not INFO from VCF by @mcanouil in https://github.com/mcanouil/eggla/pull/64
  • fix: dependencies import/suggest and use cran by @mcanouil in https://github.com/mcanouil/eggla/pull/65
  • fix: shell error printed to console by @mcanouil in https://github.com/mcanouil/eggla/pull/66
  • fix: plink binary copy by @mcanouil in https://github.com/mcanouil/eggla/pull/67
  • fix: update output results with AP/AR GWAS by @mcanouil in https://github.com/mcanouil/eggla/pull/68
  • fix: remove remotes and roxygenise() by @mcanouil in https://github.com/mcanouil/eggla/pull/69
  • feat: aggregate when multiple measures and/or use "filter" arg by @mcanouil in https://github.com/mcanouil/eggla/pull/70

Full Changelog: https://github.com/mcanouil/eggla/compare/v0.12.2...v0.13.0

- R
Published by mcanouil over 3 years ago

eggla - eggla 0.12.3

Breaking changes

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

Fixes

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

Chores

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

Tests

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

- R
Published by mcanouil over 3 years ago

eggla - eggla 0.12.2

Fixes

  • 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

- R
Published by mcanouil over 3 years ago

eggla - eggla 0.12.1

Fixes

  • 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

- R
Published by mcanouil over 3 years ago

eggla - eggla 0.12.0

Fixes

  • 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.

Features

  • 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).

Chores

  • chore: remove version from CFF file.

Style

  • style: remove break line in badges section.

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

- R
Published by mcanouil over 3 years ago

eggla - eggla 0.11.2

Fixes

  • fix: uses general Zenodo DOI.

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

- R
Published by mcanouil over 3 years ago

eggla - eggla 0.11.1

Chores

  • chore: add DOI and citation files.

Fixes

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

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

- R
Published by mcanouil over 3 years ago

eggla - eggla 0.11.0

Breaking changes

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

Fixes

  • 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.

Features

  • 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)

Tests

  • 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

- R
Published by mcanouil over 3 years ago

eggla - eggla 0.10.4

Fixes

  • 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 conssitency with code, i.e., replaced "AR1" with "CAR1" (#21).

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

- R
Published by mcanouil over 3 years ago

eggla - eggla 0.10.3

Fixes

  • 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

- R
Published by mcanouil over 3 years ago

eggla - eggla 0.10.2

Fixes

  • In R/egg_model.R,
    • Fix: try without AR1 before reducing random effect. (#18)

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

- R
Published by mcanouil over 3 years ago

eggla - eggla 0.10.1

Fixes

  • 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

- R
Published by mcanouil almost 4 years ago

eggla - eggla 0.10.0

Features

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

Improvements

  • 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).

Fixes

  • 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

- R
Published by mcanouil almost 4 years ago

eggla - eggla 0.9.1

Features

  • 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

- R
Published by mcanouil almost 4 years ago

eggla - eggla 0.9.0

Features

  • 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.

Fixes

  • 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.

Documents

  • 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

- R
Published by mcanouil almost 4 years ago

eggla - eggla 0.8.1

Features

  • In inst/setup/Dockerfile,
    • Feat: Docker image built automatically "devel" from "main" and "tag" from "releases".
    • ghcr.io/mcanouil/eggla:latest
    • docker.io/mcanouil/eggla:latest
    • docker.io/mcanouil/eggla:v0.8.1
    • docker.io/mcanouil/eggla:devel

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

- R
Published by mcanouil almost 4 years ago

eggla - eggla 0.8.0

Features

  • 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.

Bug Fixes

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

Build

  • 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

- R
Published by mcanouil almost 4 years ago

eggla - eggla 0.7.0

Features

  • 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.

Fixes

  • In vignettes/articles/run-eggla.Rmd, vignettes/articles/models-diagnostics.Rmd,
    • Fix: Uses AR1 by default in vignettes, only to speed-up computation.

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

- R
Published by mcanouil almost 4 years ago

eggla - eggla 0.6.1

Fixes

  • 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

- R
Published by mcanouil almost 4 years ago

eggla - eggla 0.6.0

New Feature

  • 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.

Fixes

  • 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

- R
Published by mcanouil almost 4 years ago

eggla - 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

- R
Published by mcanouil almost 4 years ago

eggla - 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

- R
Published by mcanouil almost 4 years ago

eggla - 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

- R
Published by mcanouil almost 4 years ago

eggla - eggla 0.4.4

  • In R/egg_model.R,
    • Three cublic spline random effects formula are tested in the following order:
    • ~ gsp(age, knots = c(2, 8, 12), degree = rep(3, 4), smooth = rep(2, 3)) | ID
    • ~ gsp(age, knots = c(2, 8, 12), degree = rep(3, 4), smooth = rep(2, 3))[,1:3] | ID
    • ~ 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

- R
Published by mcanouil almost 4 years ago

eggla - 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

- R
Published by mcanouil almost 4 years ago

eggla - 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

- R
Published by mcanouil about 4 years ago

eggla - 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

- R
Published by mcanouil about 4 years ago

eggla - 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

- R
Published by mcanouil over 4 years ago

eggla - eggla 0.3.0

  • In R/time_model.R,

    • Add fall back (simpler random effect) models for "cubicsplines", "cubicslopes" 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

- R
Published by mcanouil about 5 years ago

eggla - 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

- R
Published by mcanouil about 5 years ago

eggla - eggla 0.1.0

  • Initial version.

- R
Published by mcanouil about 5 years ago