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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()
  • 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.

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.