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Update README.md
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WillNickols committed Jan 13, 2025
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Expand Up @@ -662,25 +662,6 @@ save them to an RData file.
`logging` package.
* `save_plots_rds` (default `FALSE`): Whether to save the plots as RDS files.

## Tool comparison ##

| Tool | Models differential abundance | \
Models differential prevalence | Models allowed | Accounts for\
compositionality | Can use experimental absolute abundance information |
|:---:|:---:|:---:|:---:|:---:|:---:|
| MaAsLin 3 | Yes | Yes, for any model type | Any lme4 model\
(general mixed models), level-vs-level differences, group-wise differences, \
feature-specific covariates, contrast tests | Yes | Yes |
| MaAsLin 2 | Yes | Only insofar as it affects abundance | Fixed and random \
effects (subset of general mixed models) | No | No |
| ANCOM-BC2 | Yes | Only when completely absent in a group | Any lme4 model \
(general mixed models), level-vs-level differences, group-wise differences, \
contrast tests | Yes | No |
| ALDEx2 | Yes | Only insofar as it affects abundance | Fixed \
effects | Yes | No |
| LinDA | Yes | Only insofar as it affects abundance | Any lme4 model \
(general mixed models), group-wise differences, contrast tests | Yes | No |

## Troubleshooting ##

1. Question: When I run from the command line I see the error
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