| liste {simba} | R Documentation |
Transposes dist objects to database list format (where each line represents a similarity value calculated between two plots, so the list has three columns containing information on plot x, plot y and information on similarity/dissimilarity). This might be useful if further database processing is intended. If the given matrix is not of class dist, the whole matrix is converted. This might be handy if species matrices are to be converted to database format.
liste(obj, x="NBX", y="NBY", entry=NULL, factorize=TRUE, splist=FALSE)
obj |
A distance object as it is returned from sim, dist, vegdist or dist.binary or a similar matrix with class="dist". If the matrix is not of class dist a data.frame is expected and all entries are converted. Species matrices are assumed to contain sites (or plots) in rows and species in columns. |
x |
How the second column should be named, standard is that it contains "NBX" the neighbour X. Obsolete when splist = TRUE. |
y |
How the second column should be named, standard is that it contains "NBY" the neighbour Y. Obsolete when splist = TRUE. |
entry |
How the third column should be named. If there is nothing given, it is named "we" (whatever). Obsolete when splist = TRUE. |
factorize |
If naming (first two) columns should be given as factors. Defaults to TRUE. |
splist |
Set to TRUE if a species matrix is transformed to a database list format. Automatically removes entries with zero occurrence of the species' and names columns correspondingly (see Value). |
Column x represents the column names of the input matrix. So if you want to reshape a species matrix, x will be the species names and y will be the plot names. If it is needed vice versa, you have to change column order. For convenience you can set splist = TRUE and you will get a species list in database format with columns representing the plot, species and occurrence information. Furthermore zero occurrences are already omitted.
Returns a data.frame with three columns:
Col1 |
The column names of the input matrix. If it is a dist-object only the lower triangle is used. Named plot when a species matrix is transformed with splist = TRUE. |
Col2 |
The row names of the input matrix. Named spec when a species matrix is transformed with splist = TRUE. |
Col3 |
The respective matrix entries. Named occ when a species matrix is transformed with splist = TRUE. |
Gerald Jurasinski
reshape, data.frame. It resembles functionality of reshape - which is more flexible (but also more complex).
data(abis) ## there are empty species entries: sum(colSums(abis.spec)==0) ## remove empty species abis.spec <- abis.spec[,colSums(abis.spec)!=0] abis.spec.ls <- liste(abis.spec, splist=TRUE)