NEWS.md
cdb_build_cdb
function, which allows users to build compadreDB
objects from their own dataflag
argument to cdb_fetch
. If this is set to TRUE
then the checks from cdb_flag
will be run on the database during the downloaded process thus streamlining coding.cdb_fetch
: check_zero_F
, check_zero_C
, which checks whether the F and C matrices (sexual and clonal reproduction respectively) are all zeros (TRUE if all zero) and check_zero_U_colsum
which checks whether there are any columns of the U matrix that are all zero (i.e. whether there are some stages where there is 100% mortality)check_surv_gte_1
) to cdb_check
to check matU
for elements greater than or equal to 1.cdb_metadata
function to provide easy access to metadata (without associated matrices).matA
, matU
etc.) now ensure that the matrices are provided with named columns and rows. Names are prefixed by matrix type (e.g. A1, A2, A3 or U1, U2, U3).codemeta.json
)CompadreDB
and CompadreM
.ClassUnionMethods
. e.g. functions matA
, matU
, matF
, and matC
output all A,U,F, or C matrices from a database.cdb_fetch
function to obtain the latest version of COMPADRE or COMADRE.dplyr
functions can be used with the database (e.g. filter).subset
, []
now work.magrittr
pipes.cdb_
prefix, followed by verb (e.g. dbCompare
becomes cdb_compare
and cleanDatabase
becomes cdb_flag
).cdb_unnest
unnests the DB by spreading the matrices into separate list columns.convert2flat
is replaced with cdb_flatten
, but works on an entire database rather than a single matrix. cdb_unflatten
reverses the procedure.collapseMatrix
, identifyReprodStages
, rearrangeMatrix
, splitMatrix
moved to the Rage
package.CompadreData
with definition and methods.CompadreM
with definition and methods.checkspecies
, check for matrix problems (cleanDatabase
),mergeDB
), compare database versions (dbCompare
), subset the database (subsetDB
).collapseMatrix
), convert matrix to a “flat” format (convert2flat
), calculate the mean F matrix (getMeanMatF
), segregate reproductive/non-reproductive stages rearrangeMatrix
, split the matrix into submatrices (splitMatrix
)stringtomatrix
.