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serocalculator 1.4.0

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:

  • release: https://ucd-serg.github.io/serocalculator/
  • dev: https://ucd-serg.github.io/serocalculator/dev/

• 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)

serocalculator 1.3.0

New features

• Removed function ‘get_additional_data()’ (#332)

• Updated documentation examples to include csv files (#328)

• Added csv files for use in documentation examples (#329)

• Added serocalculator_example() function to help locate example data files (#329)

• Fixed a bug in computing the antibody response curve when \(r=1\) (#323)

• Added example datasets with documentation for examples and testing (#314)

• Improved error messaging for autoplot.pop_data() (#234).

• Clarified package installation instructions in scrub typhus vignette (#234).

• Add as_noise_params (#228)

• Updated simulate_xsectionalData.Rmd (linting, removing deprecated functions) (#289)

• Added default value for antigen_isos argument in log_likelihood() (#286)

• Updated enteric fever example article with upgraded code and visualizations (#290)

• Added Methodology vignette (#284, #302, #303)

• Added template for reporting Issues (from usethis::use_tidy_issue_template()) (#270)

• Added template for pull requests (from https://github.com/bcgov/ssdtools) (#265)

Internal changes

• Updated documentation to align with previous CRAN feedback (#328)

• Updated tests to use internal testing datasets instead of external links (#328)

• Updated test-coverage.yml GHA action to current r-lib standard (#330)

• Change default pipe setting (#312)

• Add test for missing strata in est.incidence.by (#227)

• Added snapshot_value test for est.incidence() (#315)

• Sped up lint-changed-files GitHub Action (#317)

• Added online preview builds for PRs that change the pkgdown website (#309)

• Added test-autoplot.pop_data test (#234)

• initialized lintr with lintr::use_lint() (#278)

• created unit test for df_to_array() (#276)

• fixed dplyr::select() deprecation warning in df_to_array() (#276)

• Added devtag to package (using devtag::use_devtag()) (#292)

• Added @dev tag to ?df_to_array() (#292)

• Generalized get_() and set_() methods to be general-purpose (no S3 class-specific methods needed yet) (#274).

• Updated GitHub Action files and reformatted DESCRIPTION (#268)

• Added .gitattributes file (https://git-scm.com/docs/gitattributes) copied from https://github.com/tidyverse/ggplot2

• Added QR code to README.qmd

• Added additional automated checks through GitHub actions, including:

  • check that README.qmd still compiles (advice from preventive-r-package-care) (#259)
  • check NEWS.md for updated change log (#257)
  • lint changed files (#256)

serocalculator 1.2.0

• Added test-summary.pop_data test

• Modified test-est.incidence test

• Added stratification to summary.pop_data

• Added verbose option for check_pop_data(), changing default behavior to avoid printing an OK message.

serocalculator 1.1.0

• Renamed llik() to log_likelihood()

• Renamed fdev() to f_dev()

• Renamed df.to.array() to df_to_array()

• Renamed getAdditionalData() to get_additional_data()

• Removed clean_pop_data() function

• Remove clean_pop_data() dependency functions documentation examples

• Added age, value, id and standardize arguments to load_pop_data()

• Added the following methods to pop_data class:

  • set_age()
  • set_value()
  • set_id_var()
  • get_age()
  • get_values()
  • ids()
  • get_age_var()
  • get_values_var()
  • ids_varname()

• Added additional warnings to load_pop_data()

• Added scales::pseudo_log_trans() to autoplot.pop_data() to avoid log 0

• Added test-est.incidence-status.R test to check output when standardize option is FALSE on load_pop_data()

• Replaced column name comparison on check_pop_data() to use attribute name on pop_data class

serocalculator 1.0.1

• added n_points argument to plot_curve_params_one_ab()
• Added type = "age-scatter" option for autoplot.pop_data()

serocalculator 1.0.0

• Moved underlying methods to serocalculator vignette

serocalculator 0.5.0

• Spell-checking of function documentation and tutorial articles.

• Added functions and methods:

  • load_pop_data()
  • check_pop_data()
  • summary.pop_data()
  • autoplot.pop_data()
  • load_curve_params()

• Renamed graph.decay.curves.by() to autoplot.curve_params()

serocalculator 0.4.0

• plot() methods have been renamed to autoplot(), matching general convention for ggplot2-based graphics.

• added visualization of curve parameters

• sim.cs() now has format argument to specify long or wide format for output.

serocalculator 0.3.2

Fixed bug in passing antigen_isos from est.incidence.by() to est.incidence().

serocalculator 0.3.1

Rolled back required R version from 4.2 to 4.1

serocalculator 0.3.0

• Fixed stability and documentation-clarity issues after initial tester feedback.

serocalculator 0.2.0 (never formally incremented in DESCRIPTION)

• Added new vignettes.

serocalculator 0.1.0

Forking from the seroincidence package and adding Teunis et al 2020 approach.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.