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)
Removed warn.missing.strata() from API (#366)
Added more details about contributing PRs in Contributing.md (#280)
Added warnings for missing biomarker data (#168):
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()graph.curve.params() where MCMC samples
with the same iteration number from different MCMC chains
would get merged by ggplot2::aes(group = iter) (#382)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)
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 template for reporting Issues
(from usethis::use_tidy_issue_template()) (#270)
Added template for pull requests (from https://github.com/bcgov/ssdtools) (#265)
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)
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:
README.qmd still compiles
(advice from preventive-r-package-care) (#259)NEWS.md for updated change log (#257)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.
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
n_points argument to plot_curve_params_one_ab()type = "age-scatter" option for autoplot.pop_data()serocalculator vignetteSpell-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()
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.
Fixed bug in passing antigen_isos from est.incidence.by() to est.incidence().
Rolled back required R version from 4.2 to 4.1
Forking from the seroincidence package and adding Teunis et al 2020 approach.