select.axes | R Documentation |
Selects the axes required to explain a cumulative threshold amount of variance in an ordination (e.g. > 95%).
select.axes(data, group, threshold = 0.95, inc.threshold = TRUE)
data |
The trait space to analyse. This can be either a |
group |
Optional, either a |
threshold |
The arbitrary threshold amount of variance (by default this is |
inc.threshold |
Logical, whether to output the axes that contain the threshold value ( , i.e. the axes necessary to include at least the threshold value |
If inc.threshold = TRUE
, the returned axes are the ones that contains at least the threshold value (e.g. if the threshold is 0.95
, all the returned axes contain at least 0.95
of the variance, potentially more). If inc.threshold = FALSE
, the returned axes are the ones before reaching this threshold (e.g. the cumulative variance returned is strictly less or equal to 0.95
).
A "dispRity"
, "axes"
object that can be printed, summarised and plot through generic print
, summary
and plot
functions.
The object is a list containing:
$dimensions
: the maximum number of dimensions selected across all groups;
$dim.list
: the selected dimensions per group;
$var
: the variance per axes per group;
$scaled.var
: the variance scaled variance per axes per group;
$cumsum.var
: the cumulative scaled variance per axes per group;
$call
: a list containing the $threshold
value and the $inc.threshold
option used.
Thomas Guillerme
custom.subsets
## Ordinating the USArrests dataset ordination <- princomp(USArrests, cor = TRUE) ## Which dimensions to select? (selected <- select.axes(ordination)) ## The selected dimensions selected$dimensions ## Visualising the results plot(selected) ## Same but by grouping the data into three groups states_groups <- list("Group1" = c("Mississippi","North Carolina", "South Carolina", "Georgia", "Alabama", "Alaska", "Tennessee", "Louisiana"), "Group2" = c("Florida", "New Mexico", "Michigan", "Indiana", "Virginia", "Wyoming", "Montana", "Maine", "Idaho", "New Hampshire", "Iowa"), "Group3" = c("Rhode Island", "New Jersey", "Hawaii", "Massachusetts")) (selected <- select.axes(ordination, group = states_groups)) ## Note that the required number of axes is now 4 (instead of 3) plot(selected) ## Loading some example dispRity data data(demo_data) ## How many axes are required to explain 99% of the variance ## for each group in the Healy et al 2019 data? (how_many <- select.axes(demo_data$healy, threshold = 0.99)) summary(how_many) plot(how_many)
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