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NEWS.md

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serocalculator (development version)

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()
    • get_age()
    • get_value()
    • get_id()
    • get_age_var()
    • get_value_var()
    • get_id_var()

  • 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.