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serocalculator 1.4.0

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@d-morrison d-morrison released this 21 Jan 06:41
v1.4.0
a0cdca2

New features

  • Added chain_color option to graph.curve.params() to control MCMC line color (#455)

  • Made graph.curve.params() the default sub-method for autoplot.curve_params() (#450)

  • Added log_x and log_y options to graph.curve.params() sub-method for
    autoplot.curve_params() (#453)

  • Extended sim_pop_data_multi() to loop over multiple sample sizes (#444)

  • Added new functions analyze_sims() and autoplot.sim_results() (#444)

  • Rename estimate_scr() to est_seroincidence_by() (#439)

  • Rename estimate_scr() to est_seroincidence() (#432)

  • Rename argument curve_params to sr_params for estimation functions (#424)

  • added documentation for count_strata() (#431)

  • Rename as_curve_params() to as_sr_params() (#421)

  • Rename load_curve_params() to load_sr_params() (#421)

  • added default for xvar in "scatter" option for autoplot.seroincidence.by() (#417)

  • Extended autoplot.summary.seroincidence.by() to include types for either scatter or bar plots of stratified results (#397)

  • added option to add lines using group_var input to autoplot.summary.seroincidence.by() (#410)

  • autoplot.pop_data(type = "age-scatter") now shows legend at bottom (#407)

  • autoplot.pop_data(type = "age-scatter") now facets by antigen isotype (#406)

  • Rename est.incidence.by() to estimate_scr_by() (#389)

  • Rename est.incidence() to estimate_scr() (#389)

  • Improved warning messages for get_biomarker_names_var()

  • Added get_*() extractor functions to API (#380)

  • Added optional CI error bars to autoplot.summary.seroincidence.by() (#372)

  • Improved y-limit calculation in graph.curve.params() (#368)

  • Added option for graph.curve.params() to show all curves (#368)

  • Added color-coding for graph.curve.params() (#383)

  • Added quantiles parameter to graph.curve.params() and corresponding test in test-graph.curve.params.R (#434)

  • Removed warn.missing.strata() from API (#366)

  • Added more details about contributing PRs in Contributing.md (#280)

  • Added warnings for missing biomarker data (#168):

    • completely missing antigen-isotype in a stratum
    • uneven antigen-isotype counts in a stratum (likely from incomplete data)

  • Split dev and release websites into:

  • Fixed citations in methodology.qmd article (#360)

  • Added outline to pkgdown website (#353)

  • Added verbose option for summary.seroincidence() and
    summary.seroincidence.by() (#348)

  • Extended simulate_xsectionalData.Rmd article to explore
    renew_params = TRUE vs renew_params = FALSE (#348)

  • Renamed variables for consistency (#281, #373):

    • sim.cs() -> sim_pop_data()
    • sim.cs.multi() -> sim_pop_data_multi()

Bug fixes

  • Fixed CRAN errors (#464)
  • Fixed stratification issue in enteric fever vignette (#418)
  • Fixed issue in graph.curve.params() where MCMC samples
    with the same iteration number from different MCMC chains
    would get merged by ggplot2::aes(group = iter) (#382)

Internal changes

  • switched expect_snapshot_data() to an internal function due to CRAN errors (#464)

  • generalized ab1()

  • added codecov/test-results-action to test-coverage.yaml workflow

  • added test for censored data in f_dev() (#399)

  • added test for autoplot.curve_params()

  • added test for graph.curve.params() (#368)

  • reverted Readme source file from qmd to Rmd.

  • switched pkgdown GHA from any::pkgdown to r-lib/pkgdown (i.e., dev version) (#359)

  • added test for summary.seroincidence.by() (#352)

  • Started checking for use of base pipe instead of magrittr pipe
    by linter (#347)

  • Removed ldpar() from API (#345)

  • Added test for sim.cs() (#344)

  • Added test for internal function ab() (#342)

  • Reverted name change ldpar()-> row_longitudinal_parameter() (#343)

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