Move species count to analysis

man/optimal_weights.Rd

@@ -4,13 +4,7 @@
 \alias{optimal_weights}
 \title{Find the best weights to rank the results.}
 \usage{
-optimal_weights(
-  analysis,
-  methods,
-  reference_gene_ids,
-  target = "mean",
-  min_n_species = 10
-)
+optimal_weights(analysis, methods, reference_gene_ids, target = "mean")
 }
 \arguments{
 \item{analysis}{Results from \code{\link[=analyze]{analyze()}} or \code{\link[=ranking]{ranking()}}.}
@@ -21,10 +15,6 @@ optimal_weights(
 
 \item{target}{The optimization target. It may be one of "mean", "min" or
 "max" and results in the respective rank being optimized.}
-
-\item{min_n_species}{Minimum number of required species per gene. Genes that
-have fewer species will not be included in the rankings used to find the
-optimal weights.}
 }
 \value{
 Named list pairing method names with their optimal weights. This

man/preset.Rd

@@ -8,6 +8,7 @@ preset(
   methods = c("clusteriness", "correlation", "neural", "proximity"),
   species_ids = NULL,
   gene_ids = NULL,
+  min_n_species = 10,
   reference_gene_ids = NULL
 )
 }
@@ -18,6 +19,9 @@ preset(
 
 \item{gene_ids}{IDs of genes to screen.}
 
+\item{min_n_species}{Minimum number of orthologs that a gene should have to
+be included in the analysis.}
+
 \item{reference_gene_ids}{IDs of reference genes to compare to.}
 }
 \value{

man/ranking.Rd

@@ -4,16 +4,13 @@
 \alias{ranking}
 \title{Rank the results by computing a score.}
 \usage{
-ranking(analysis, weights, min_n_species = 10)
+ranking(analysis, weights)
 }
 \arguments{
 \item{analysis}{Analysis object resulting from \code{\link[=analyze]{analyze()}}.}
 
 \item{weights}{Named list pairing method names with weighting factors. Only
 methods that are contained within this list will be included.}
-
-\item{min_n_species}{Minimum number of required species per gene. Genes that
-have fewer species will not be included in the ranking.}
 }
 \value{
 A ranking object. The object extends the analysis result with