View source: R/Claddis.ordination.R
Claddis.ordination | R Documentation |
Takes Claddis data and computes both the distance and the ordination matrix
Claddis.ordination(data, distance = "mord", ..., k, add = TRUE, arg.cmdscale)
data |
Data from |
distance |
Distance type to be computed by |
... |
Any optional arguments to be passed to |
k |
The number of dimensions in the ordination. If left empty, the number of dimensions is set to number of rows - 1. |
add |
whether to use the Cailliez correction for negative eigen values ( |
arg.cmdscale |
Any optional arguments to be passed to |
If data
is a file path, the function will use a modified version of read.nexus.data
(that handles polymorphic and ambiguous characters). The file content will then be converted into a read_nexus_matrix
type list treating all characters as unordered.
If the distance
is set to NULL
, data
will be only converted into a read_nexus_matrix
type list.
Thomas Guillerme
calculate_morphological_distances
, read_nexus_matrix
, build_cladistic_matrix
, cmdscale
, custom.subsets
, chrono.subsets
, boot.matrix
, dispRity
.
## Not run: require(Claddis) ## Ordinating the distance matrix of Claddis example data Claddis.ordination(Claddis::michaux_1989) ## Creating simple discrete morphological matrix (with polymorphisms) cat( "#NEXUS BEGIN DATA; DIMENSIONS NTAX=5 NCHAR=5; FORMAT SYMBOLS= \" 0 1 2\" MISSING=? GAP=- ; MATRIX t1 {01}1010 t2 02120 t3 1210(01) t4 01111 t5 00101 ; END;", file = "morpho_matrix.nex") ## Ordinating the matrix (using a distance matrix) Claddis.ordination("morpho_matrix.nex") ## Only converting the nexus matrix into a Claddis format Claddis_data <- Claddis.ordination("morpho_matrix.nex", distance = NULL) file.remove("morpho_matrix.nex") ## End(Not run)
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