Merge pull request #12 from biobakery/devel

Devel

README.md

@@ -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

man/maaslin3.Rd

@@ -120,7 +120,8 @@ maaslin3(input_data,
     names
     and sample names respectively.}
     \item{feature_specific_covariate_name}{The name for the feature-specific
-    covariates when fitting the models.}
+    covariates when fitting the models. This string must be parse-able
+    in a formula (e.g., no spaces).}
     \item{feature_specific_covariate_record}{Whether to keep the
     feature-specific covariates in the outputs when calculating p-values,
     writing results, and displaying plots.}