Changelog

Source: NEWS.md

serocalculator 1.3.0

CRAN release: 2025-01-25

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.