taxa_rich()andtaxa_pct_rich()now require the.count_colargument to be specified. In previous versions, the user did not need to provide this value. This change ensures that zero counts will be excluded from the calculations.
- When using the
.filterargument totaxa_rich(), if the specified taxon was not observed, a value ofNAwas returned and subsequently counted as a count of 1. This had a downstream impact ontaxa_pct_rich(), which was sometimes producing values of 100. This issue has been resolved.
taxa_seq()has a new argument,.exclude_pattern. This argument allows the user to specify a character string pattern or a vector of patterns that will exclude taxonomic names that match the pattern(s) from the iterative metric calculation sequence. For example,.exclude_pattern = "unidentified"would remove any taxonomic name that contains "unidentified" from the iterative taxa sequence (i.e., no metrics will be returned for taxa that contain this pattern). Multiple patterns can be supplied within a character vector (e.g.,.exclude_pattern = c("unidentified", "hyallella").
taxa_seq(): when the argument.group_col = NULLand the.job = "pct""NULL" would appear in the metric name. Now "NULL" will be correctly filtered out of the name.
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Added a
NEWS.mdfile to track changes to the package. -
Added
taxa_fill()to replaceNAs in the taxonomic hierarchy with the nearest identified taxonomic rank. Note that the order the columns are presented is used to create the hierarchy that identifies the previous taxonomic rank. For example, you want your columns to be ordered as: Phylum, Class, Order, Family, Genus.