Rcompadre 1.1.0 Unreleased

  • 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 2021-04-30

  • Released on CRAN on 20210430

Rcompadre 0.3.0 Unreleased

  • 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 Unreleased

  • 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 Unreleased

  • 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.