Closed xec-cm closed 1 year ago
The corncob
dependence detectseparation
has a new version for 5 days in cran (v0.3). In this new version the way to obtain the separation value is different from v0.2. Therefore these lines of code from the bbdm function fail:
https://github.com/bryandmartin/corncob/blob/7f146f2afcec703d3f21958ef55f48c4fd50a751/R/bbdml.R#L121 https://github.com/bryandmartin/corncob/blob/7f146f2afcec703d3f21958ef55f48c4fd50a751/R/bbdml.R#L129 https://github.com/bryandmartin/corncob/blob/7f146f2afcec703d3f21958ef55f48c4fd50a751/R/bbdml.R#L141 https://github.com/bryandmartin/corncob/blob/7f146f2afcec703d3f21958ef55f48c4fd50a751/R/bbdml.R#L149
In my opinion there are two solutions. The first is to indicate the version of detectseparation
as v0.2 in the DESCRIPTION. The other is to adapt the code to the new version of the detectseparation
package.
I hope you can resolve this issue early.
Thanks
Hi, I am having a similar problem with the vignette data:
> corncob1_da <- bbdml(formula = OTU.1 ~ DayAmdmt,
+ phi.formula = ~ DayAmdmt,
+ data = soil)
Error in if (detectseparation::detect_separation(y = cbind(W, M - W), :
argument is of length zero
I am using the demo script that was presented at STAMPS https://raw.githubusercontent.com/statdivlab/stamps2022/main/Sunday-afternoon/labs/corncob_tutorial/corncob_tutorial.R
You seem to have fixed something yesterday, I made sure I had the most recent version of corncob but that doesn't seem to work either.
@jorondo1 I am not the maintainer of this repository... My workaround (as long as Corncob is not updated) was to force installion of the version 0.2 of the detectseparation
package. You can do this easily with devtools
or remotes
:
## Using remotes
remotes::install_version("detectseparation", version = 0.2)
## Using devtools
devtools::install_version("detectseparation", version = 0.2)
After installation, you just need to restart R and run the code normally.
Thanks for posting this issue and your workaround @xec-cm, and for corroborating it, @jorondo1 ! Please note that the software authors have taken note of this issue and are working to come up with a long term solution soon. We will post updates here.
cc @bryandmartin
Thank you both, the workaround fixed it for me as well. Cheers !
Fixed in 365add6
Since a few days ago, code that runs
corncob
that used to work with the same data now returns an error. I think it could be some modification on somecorncob
dependency.I have reproduced the error with an example of the
corncob
vignette:Created on 2022-08-31 with reprex v2.0.2