Supported Versions

Source: vignettes/supported.Rmd
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Staying Up to Date

This page is a summary of which versions of concurve are currently supported and which we will provide support with depending on the context. We will mostly be supporting the most recent versions of the package, as these versions will also be using the latest version of R and other dependencies that are necessary. As such, those who continue to use older versions of the package may be out of the loop on new changes in arguments to functions, along with new functions. We urge users to consult and stay up to date with the documentation, and update their R packages as frequently as possible. An easy way to remain updated is to visit the package website, as the newest version of the package number will always be on the top left.

Previous Versions

However, we’d still like users to be able to access old versions of concurve for whatever, reason, and in addition to using GitHub, those can also be found on the CRAN archive. A page with the test results for the most recent package on CRAN can also be found here.

Another useful link will be the NEWS section, which will inform users of bugs that have been patched and new changes to old functions. However, checking CRAN is less than desirable, due to the fact that new changes (that may even be very important), will often quickly be pushed to GitHub, rather than CRAN. Thus, installing or upgrading to the newest version of concurve via the script,

install_github("zadrafi/concurve@master", dependencies = TRUE)

may be useful.

You can also directly download a tarball or zip of the most recent package version using the following link.

Supported Versions

Package Version Currently Supported Information About Version
3.0.5 ✔ Supported Updates and Information about version 3.0.5
3.0.4 ✔ Supported Updates and Information about version 3.0.4
3.0.3 ✔ Supported Updates and Information about version 3.0.3
3.0.2 ✔ Supported Updates and Information about version 3.0.2
3.0.1 ✘ Not Supported Updates and Information about version 3.0.1

What’s New in Version 3.0.x

The 3.0 series is a major update that includes new functionality, reduced dependencies, and improved compatibility.

New Functions

The 3.0 series adds 27 exported functions relative to 2.7.7, the last release before it. (Determined by comparing the function definitions in R/ at tag 2.7.7 against the current NAMESPACE, excluding the tidy-eval re-exports and the defunct stubs.)

Constructing curves from estimates and models

  • curve_analytic() - Analytic consonance functions from summary statistics, read straight off a closed-form quantile function
  • curve_from_ratio() - Construct a consonance function from a ratio estimate and its interval bounds
  • curve_from_se() - Construct a consonance function from an estimate and its standard error
  • curve_wrap() - Construct consonance functions from any CI-producing function
  • curve_model() - Construct consonance functions from fitted models
  • curve_region() - Confidence in a parameter region

Likelihood functions

  • as_curve_lik() - Package a log-likelihood grid as a concurve likelihood object, bridging any likelihood-producing tool
  • curve_lik_glm() - Profile likelihood function for a model coefficient
  • curve_lik_exact() - Exact likelihood functions for common designs
  • curve_mpl() - Modified profile likelihood functions
  • curve_rstar() - Second-order consonance functions via the r* statistic
  • curve_support() - Support (likelihood) intervals from a likelihood function
  • construct_likelihood() - Build likelihood functions for statistical models from scratch

Monte Carlo confidence distributions

  • curve_stan() - Consonance functions from Monte Carlo draws of a confidence distribution; needs no Stan installation
  • curve_stan_fit() - Sample a Stan model and build a consonance function from it
  • concurve_stan_file() - Locate the Stan programs bundled with the package

Databases and export

Plotting and reporting

Dependency Changes

  • Removed pbmcapply dependency - Replaced with base R parallel::mclapply() for parallel processing, reducing the package’s dependency footprint
  • Optional database dependencies - DBI and odbc are now in Suggests for Snowflake integration (install only if needed)

Bug Fixes and Improvements

  • Fixed scoping issues with subset() inside parallel processing calls
  • Improved roxygen2 documentation across all functions
  • Enhanced error messages and input validation
  • Updated vignettes with corrected examples

Dependencies

The package constructs interval estimates using a wide variety of functions that already exist within the R ecosystem, whether that is from base R or from community-contributed packages that are on CRAN. Here is a list of those packages. Those that are necessary to produce distributions of parameters are specified as Imports, while those that are optional and not necessary are specified as Suggests.

Those that are listed in the Suggests section are typically used for additional functionality such as database connectivity or testing.

Package Imports

Package Imports
Package Package Version
bcaboot 0.2.3
boot 1.3.32
colorspace 2.1.3
dplyr 1.2.1
flextable 0.10.0
ggplot2 4.0.3
knitr 1.52
lme4 2.0.6
metafor 5.0.1
methods 4.6.1
numDeriv 2016.8.1.1
parallel 4.6.1
rlang 1.3.0
scales 1.4.0
tibble 3.3.1
tidyr 1.3.2

Package Suggestions

Package Suggestions
Package Package Version
bayesplot 1.16.0
bbmle 1.0.26
bench 1.1.4
brms 2.23.0
carData 3.0.6
cond 1.2.4
covr 3.6.5
cowplot 1.2.0
daewr 1.2.11
data.table 1.18.6.1
DBI 1.3.0
ggtext 0.2.0
jsonlite 2.0.0
kableExtra 1.4.1
likelihoodAsy 0.51
Lock5Data 4.0.1
magick 2.9.1
MASS 7.3.65
maxLik 1.5.2.2
nlme 3.1.169
odbc 1.7.0
officer 0.7.6
openxlsx 4.2.9
patchwork 1.3.2
plotly 4.12.1
ProfileLikelihood 1.3
reprex 2.1.1
rmarkdown 2.32
rms 8.1.1
roxygen2 8.1.0
roxygen2md 1.0.1
rstan 2.32.7
rstanarm 2.32.2
simstudy 0.9.2
spelling 2.3.2
survival 3.8.6
survminer 0.5.2
svglite 2.2.2
testthat 3.3.2
vdiffr 1.0.9

Reporting Bugs, Vulnerabilities, and Issues

Please see here to report any vulnerabilities within the package, and to follow best practices for reporting any bugs, issues, or concerns. When submitting an issue, please try to submit a REPREX, so that the developers may quickly see the issue.

Session info 

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