`NEWS.md`

- Added a function
`mpm_elementwise_apply`

which can apply any function over elements in a matrix. For example,`mean`

,`min`

,`max`

,`sd`

,`var`

etc. to allow summaries to conveniently be made across matrices of the same dimension. Replaces some of the functionality of`mpm_sd`

/`mat_sd`

,`mpm_median`

/`mat_median`

and`mpm_mean`

/`mat_mean`

, which are retained for convenience.

- 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.

- 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.

- 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).

- 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).

- 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).

- 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.

- 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.

Developed by Patrick Barks, Danny Buss, Roberto Salguero-Gomez, Iain Stott, William K. Petry, Tamora James, Owen Jones, Julia Jones, Gesa Römer, Sam Levin.

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