Updated min_abundance manuals

biobakery · Jan 30, 2025 · 85ef9f9 · 85ef9f9
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diff --git a/README.md b/README.md
@@ -437,9 +437,9 @@ writing results, and displaying plots.
 
 #### Analysis options ####
 
-* `min_abundance` (default `0`): Features with abundances of at least
-`min_abundance` in `min_prevalence` of the samples will be included for
-analysis. The threshold is applied before normalization and
+* `min_abundance` (default `0`): Features with abundances of more than
+`min_abundance` in more than `min_prevalence` of the samples will be 
+included for analysis. The threshold is applied after normalization and before
 transformation.
 * `min_prevalence` (default `0`): See above.
 * `zero_threshold` (default `0`): Abundances less than or equal to

diff --git a/man/maaslin3.Rd b/man/maaslin3.Rd
@@ -126,8 +126,8 @@ maaslin3(input_data,
     feature-specific covariates in the outputs when calculating p-values,
     writing results, and displaying plots.}
     \item{min_abundance}{Features with abundances more than
-    \code{min_abundance} in \code{min_prevalence} of the samples will be
-    included for analysis. The threshold is applied after normalization and
+    \code{min_abundance} in more than \code{min_prevalence} of the samples will 
+    be included for analysis. The threshold is applied after normalization and
     before transformation.}
     \item{min_prevalence}{See \code{min_abundance}.}
     \item{zero_threshold}{Abundances less than or equal to

diff --git a/man/maaslin_filter.Rd b/man/maaslin_filter.Rd
@@ -24,8 +24,8 @@ maaslin_filter(normalized_data,
     respectively.}
     \item{output}{The output folder to write results.}
     \item{min_abundance}{Features with abundances more than
-    \code{min_abundance} in \code{min_prevalence} of the samples will be
-    included for analysis. The threshold is applied after normalization and
+    \code{min_abundance} in more than \code{min_prevalence} of the samples will 
+    be included for analysis. The threshold is applied after normalization and
     before transformation.}
     \item{min_prevalence}{See \code{min_abundance}.}
     \item{zero_threshold}{Abundances less than or equal to

diff --git a/man/maaslin_log_arguments.Rd b/man/maaslin_log_arguments.Rd
@@ -102,8 +102,8 @@ maaslin_log_arguments(input_data,
     feature-specific covariates in the outputs when calculating p-values,
     writing results, and displaying plots.}
     \item{min_abundance}{Features with abundances more than
-    \code{min_abundance} in \code{min_prevalence} of the samples will be
-    included for analysis. The threshold is applied after normalization and
+    \code{min_abundance} in more than \code{min_prevalence} of the samples will 
+    be included for analysis. The threshold is applied after normalization and
     before transformation.}
     \item{min_prevalence}{See \code{min_abundance}.}
     \item{zero_threshold}{Abundances less than or equal to

diff --git a/vignettes/maaslin3_manual.Rmd b/vignettes/maaslin3_manual.Rmd
@@ -675,9 +675,9 @@ writing results, and displaying plots.
 
 #### Analysis options ####
 
-* `min_abundance` (default `0`): Features with abundances of at least
-`min_abundance` in `min_prevalence` of the samples will be included for
-analysis. The threshold is applied before normalization and
+* `min_abundance` (default `0`): Features with abundances of more than
+`min_abundance` in more than `min_prevalence` of the samples will be 
+included for analysis. The threshold is applied after normalization and before
 transformation.
 * `min_prevalence` (default `0`): See above.
 * `zero_threshold` (default `0`): Abundances less than or equal to