jfiksel/codalm

The codalm R package

The codalm R package implements the methods as described in A Transformation-free Linear Regression for Compositional Outcomes and Predictors (Fiksel, Zeger, and Datta, 2020)

Installation

codalm is now available on CRAN and can be installed using

install.packages('codalm')

You can also install the development version of codalm for github using the remotes package.

remotes::install_github("jfiksel/codalm")

Example

View the vignette (https://jfiksel.github.io/codalm/articles/codalm_quickstart.html) for examples of how to use the codalm package

codalm's Issues

Report CIs on ternary diagram of B

This is probably a somewhat dumb question...
In the paper, you mention that the confidence regions for each row of the B matrix can also be plotted on the ternary diagram.
However, while I manage to have ggtern plot some confidence regions, I can't find a way to represent the CIs produced by codalm_ci() onto the ternary diagram of the coefficients in B. Is that possible at all? Or is it "better" to use the CIs from ggtern::geom_confidence_tern() ?
Thanks in advance for your help.

TESTS: expect_true(inherits(plan(), 'sequential')) -> expect_true(identical(plan(), oplan))

Hi, I'm running reverse package dependency checks on future. I do this with the default settings as well as with env var R_FUTURE_PLAN=multisession, which will force the default future plan to be multisession rather than sequential. This will further validate that all packages work when running in parallel, e.g. all global variables are properly exported, etc.

This results in errors when checking your package because some of your tests assert at the end that sequential is still set. You can reproduce this yourself by running:

export R_FUTURE_PLAN=multisession
R CMD check codalm_0.1.0.tar.gz
...
* checking tests ... ERROR
  Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(codalm)
  > 
  > test_check("codalm")
  ── 1. Failure: bootstrap CI works with sequential evaluation (@test-codalm_ci.R#
  inherits(plan(), "sequential") isn't true.
  
  ── 2. Failure: bootstrap CI works with multisession evaluation (@test-codalm_ci.
  inherits(plan(), "sequential") isn't true.
  
  ── 3. Failure: independence test works with sequential evaluation (@test-indepen
  inherits(plan(), "sequential") isn't true.
  
  ── 4. Failure: independence test works with multisession evaluation (@test-indep
  inherits(plan(), "sequential") isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 22 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 4 ]
  1. Failure: bootstrap CI works with sequential evaluation (@test-codalm_ci.R#20) 
  2. Failure: bootstrap CI works with multisession evaluation (@test-codalm_ci.R#42) 
  3. Failure: independence test works with sequential evaluation (@test-independence_test.R#9) 
  4. Failure: independence test works with multisession evaluation (@test-independence_test.R#19) 
  
  Error: testthat unit tests failed
  Execution halted

Could you please update to check something like:

oplan <- plan()
...
expect_true(identical(plan(), oplan))