Rcompadre 0.2.0

Released on GitHub on 16th January 2019

  • 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

Released on GitHub on 30th August 2018

  • 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.