nmds_ecosite runs an NMDS using the vegan package. NMDS has numerous settings
that can be adjusted, not all of which can be manipulated through the arguments
of this function. This function is intended to be used as a quick way of producing
ordinations. If you are interested in optimizing your NMDS, please do your own
research. At a minimum, you should understand stress and evaluate the stress
report in the results.
Arguments
- veg_summary
veg_summary object where the
ecositer::veg_summary()function was saved.- ecosite
ecosite is the ecosite(s) you want to include in an ordination. If you are interested in ordinating multiple ecosites together, concatenate the ecosites of interest (e.g.,
c("a", "b"))- pres_abs
use TRUE to convert data to presence/absence. This is the more robust option. If you have missing abundance values, presence/absence should be used. If you have abundance data, use FALSE.
- nmds_dim
specify the number of dimensions you want in your NMDS. This value will affect stress considerably.
- reduce_species
NAif you do not want to remove species. A numeric value, interpretted as percent, specifying the minimum percentage of plots a species must be present in to remain in the dataset.
Examples
formatted_veg <- formatted_veg_df(static_location = "C:/Users/Nathan.Roe/Documents/SEKI/CA792_veg.sqlite")
#> Error in formatted_veg_df(static_location = "C:/Users/Nathan.Roe/Documents/SEKI/CA792_veg.sqlite"): could not find function "formatted_veg_df"
my_veg_summary <- ecositer::veg_summary(veg_df = formatted_veg)
my_nmds <- ecositer::nmds_ecosite(veg_summary = my_veg_summary, ecosite = "F022AK100CA", pres_abs = TRUE, nmds_dim = 2, reduce_species = NA)
#> Error in veg_df %>% dplyr::group_by(vegplotid, plantsciname) %>% dplyr::summarise(sum(akstratumcoverclasspct)) %>% dplyr::rename(pctcover = `sum(akstratumcoverclasspct)`): could not find function "%>%"