Rcompadre 1.3.0
- Minor performance enhancements, some of which speed up functions
while others improve code readability and stability.
- Added functions
mpm_sd
/mat_sd
and
mpm_median
/mat_median
which join the existing
mpm_mean
/mat_mean
functions to calculate
element-wise summary statistics across MPMs of the same dimension. Code
contributed by Darren Norris with modifications by Owen Jones. A future
version will include a generic “summarise matrix” function.
- Increased test coverage.
Rcompadre 1.2.2
- Fixed minor errors causing some tests to fail.
Rcompadre 1.2.1
- Fixed an error in
cdb_build_cdb
causing an error in the
construction of the A matrix when a C matrix was not provided.
- Fixed a technical issue with
as_tibble.CompadreDB
that
caused a build failure on some platforms.
Rcompadre 1.2.0
- Improvements to
cdb_fetch
. Can add a comment as an
attribute on import. Can download particular versions of the databases
by version number. Can force quiet running (no messages).
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
which checks whether the F (sexual
reproduction) matrix is 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).
- Updated Compadre and Comadre data samples with the new names for
AnnualPeriodicity (changed to ProjectionInterval) and DOI.ISBN (changed
to DOI_ISBN).
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.