Rcompadre 1.1.0
- Added
cdb_build_cdb
function, which allows users to build compadreDB
objects from their own data
- Added
flag
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.
- Added additional flags to
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)
Rcompadre 1.0.0
- Released on CRAN on 20210430
Rcompadre 0.3.0
- Updated DESCRIPTION with new contributors.
- Improved documentation to ensure it is more understandable to less experienced users.
- Grouped functions by type in the documentation.
- Improved vignettes with a range of examples demonstrating the range of basic to complex features.
- Added an argument (
check_surv_gte_1
) to cdb_check
to check matU
for elements greater than or equal to 1.
- Added
cdb_metadata
function to provide easy access to metadata (without associated matrices).
- Matrix accessor functions (
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).
- Added machine-readable codemeta-data information (
codemeta.json
)
- Unit tests improved to increase coverage.
- Modified build checks via continuous integration on Travis, Appveyor and GitHub actions (including weekly checks).
Rcompadre 0.2.0
- Modifications to improve the class definitions, which are renamed to
CompadreDB
and CompadreM
.
- Added generic functionality with accessor methods via
ClassUnionMethods
. e.g. functions matA
, matU
, matF
, and matC
output all A,U,F, or C matrices from a database.
- Added
cdb_fetch
function to obtain the latest version of COMPADRE or COMADRE.
- The database object behaves more like a data frame than the complex hierarchical object it is.
- Added Tidyverse support so that most
dplyr
functions can be used with the database (e.g. filter).
- Generic subsetting methods including
subset
, []
now work.
- Database can be used with
magrittr
pipes.
- Most functions renamed with
cdb_
prefix, followed by verb (e.g. dbCompare
becomes cdb_compare
and cleanDatabase
becomes cdb_flag
).
- The function
cdb_unnest
unnests the DB by spreading the matrices into separate list columns.
- The function
convert2flat
is replaced with cdb_flatten
, but works on an entire database rather than a single matrix. cdb_unflatten
reverses the procedure.
- Other functions are also renamed with more intuitive names.
- Functions
collapseMatrix
, identifyReprodStages
, rearrangeMatrix
, splitMatrix
moved to the Rage
package.
- Added simple vignettes.
- Added unit tests for all functions.
Rcompadre 0.1.0
- First pre-release version!
- Established S4 class
CompadreData
with definition and methods.
- Established S4 class
CompadreM
with definition and methods.
- Functions to
checkspecies
, check for matrix problems (cleanDatabase
),
- Functions to manipulate the databases: merge databases (
mergeDB
), compare database versions (dbCompare
), subset the database (subsetDB
).
- Functions to manipulate matrices: to collapse matrix to a smaller number of stages (
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
)
- Function to produce a matrix from a string representation
stringtomatrix
.
- Added continuous integration.