cdb_collapse.RdCollapses a CompadreDB object by averaging matrices over levels of one or more grouping variables (e.g. SpeciesAuthor, MatrixPopulation).
For a given study and species, a COM(P)ADRE database may contain multiple matrices, reflecting different combinations of population, year, and/or treatment. Collapsing allows a user to obtain a single 'grand mean matrix' for each group of interest (e.g. MatrixPopulation), and therefore limit pseudoreplication.
All members of a group must have the same matrix dimension (consider
adding MatrixDimension as a grouping variable). All members of a group
should have the same AnnualPeriodicity and matrix stage class
definitions (see cdb_id_stages). Note that Seasonal matrices
should not be collapsed using this method (they should be matrix-multiplied
rather than averaged).
cdb_collapse(cdb, columns)
| cdb | A CompadreDB object |
|---|---|
| columns | Vector of grouping variables to collapse over (corresponding
to columns within |
A CompadreDB object
Will give a warning if members of any group do not all share the same
AnnualPeriodicity or stage class definitions, or if cdb contains any
rows with a MatrixComposite value of "Seasonal".
Prior to collapsing, columns of class 'factor' will be coerced to
'character', and any list-column apart from mat will be removed.
Within a group, rows of a given column are collapsed as follows:
mat: matrices are averaged using mpm_mean, and stage
class definitions are taken from the first group member
MatrixComposite: return original value if N = 1, else return
"Collapsed"
Lat: re-calculated by averaging Lat column (if available)
Lon: re-calculated by averaging Lon column (if available)
SurvivalIssue: re-calculated from the collapsed mat
(max(colSums(matU)))
others: if all elements equal return that unique value, else
paste together all unique values separated by "; "
# filter out Seasonal matrices CompSub <- subset(Compadre, MatrixComposite != "Seasonal") # add column identifying unique stage class definitions CompSub$id_stage <- cdb_id_stages(CompSub, "MatrixClassOrganized") # collapse CompCollapse <- cdb_collapse(CompSub, columns = c("id_stage"))