-
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):
- completely missing antigen-isotype in a stratum
- uneven antigen-isotype counts in a stratum (likely from incomplete data)
-
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()
andsummary.seroincidence.by()
(#348) -
Extended
simulate_xsectionalData.Rmd
article to explorerenew_params = TRUE
vsrenew_params = FALSE
(#348) -
Renamed variables for consistency (#281, #373):
sim.cs()
->sim_pop_data()
sim.cs.multi()
->sim_pop_data_multi()
- Fixed issue in
graph.curve.params()
where MCMC samples with the same iteration number from different MCMC chains would get merged byggplot2::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
tor-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
(#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 inlog_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)
-
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 currentr-lib
standard (#330) -
Change default pipe setting (#312)
-
Add test for missing strata in
est.incidence.by
(#227) -
Added
snapshot_value
test forest.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
withlintr::use_lint()
(#278) -
created unit test for
df_to_array()
(#276) -
fixed
dplyr::select()
deprecation warning indf_to_array()
(#276) -
Added
devtag
to package (usingdevtag::use_devtag()
) (#292) -
Added
@dev
tag to?df_to_array()
(#292) -
Generalized
get_()
andset_()
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)
- check that
-
Added
test-summary.pop_data
test -
Modified
test-est.incidence
test -
Added stratification to
summary.pop_data
-
Added
verbose
option forcheck_pop_data()
, changing default behavior to avoid printing an OK message.
-
Renamed
llik()
tolog_likelihood()
-
Renamed
fdev()
tof_dev()
-
Renamed
df.to.array()
todf_to_array()
-
Renamed
getAdditionalData()
toget_additional_data()
-
Removed
clean_pop_data()
function -
Remove
clean_pop_data()
dependency functions documentation examples -
Added
age
,value
,id
andstandardize
arguments toload_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()
toautoplot.pop_data()
to avoid log 0 -
Added
test-est.incidence-status.R
test to check output whenstandardize
option is FALSE onload_pop_data()
-
Replaced column name comparison on
check_pop_data()
to use attribute name onpop_data
class
- added
n_points
argument toplot_curve_params_one_ab()
- Added
type = "age-scatter"
option forautoplot.pop_data()
- Moved underlying methods to
serocalculator
vignette
-
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()
toautoplot.curve_params()
-
plot()
methods have been renamed toautoplot()
, matching general convention forggplot2
-based graphics. -
added visualization of curve parameters
-
sim.cs()
now hasformat
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
- Fixed stability and documentation-clarity issues after initial tester feedback.
- Added new vignettes.
Forking from the seroincidence package and adding Teunis et al 2020 approach.