Version 0.0.2


  1. Created package version 0.0.2 from

Version (not publicly released)


  1. Removed the method parameter in separability() function. Separability is computed using the formula presented in the paper
  2. Modified minSubtreeCover() function in tree_dim_src.cpp to represent a tree by an adjacency list.
  3. Included code to check for required parameters in separability() function.


  1. Added a method parameter to the separability() function. A value of "original" returns tissue specificity as used in the original paper. A value of "normalized" returns the normalized tissue specificity.
  2. Modified test.trajectory() and compute.stats() to return size of original dimension and number of PCA components.
  3. Modified test.trajectory() to return a class of type "treedim" and to return an additional component "mst" in the list.
  4. Modified separability() to return a class of type "treedim" and to return an additional component "mst" in the list.
  5. Created a function plot.treedim() that plots an MST for an object of type "treedim".


  1. Created package version from 0.0.1.
  2. License changed from GPL (>= 2) to LGPL (>= 3).
  3. Updated CITATION.
  4. Included “@importFrom Rdpack reprompt” to avoid NOTE to 0.0.1 on CRAN.

Version 0.0.1


  1. Replaced the “ComputeMST” function from emstreeR package with “emst” function from mlpack package to compute fast MST.

  2. Modified “getStatistics” function to accommodate output of “emst” function which is now a list. Output of “ComputeMST” was a dataframe.

  3. Removed ‘randomize’ function

  4. Removed ‘DFtoNM’ function


  1. Created inst/extdata to store data used by vignette. Added data files bifurcating_7.rds, calcium_pathway_data.rdata and ribosome_pathway_data.rdata.

  2. Created testcases using testthat package. Created test-testrajectory.R file, which contains test cases for functions ‘test.trajectory’ and ‘compute.stats’. Also created test-separability.R file which contains test cases for function ‘separability’.

  3. Modified function ‘plotTree’ to accept node colors as argument

  4. Modified vignette to improve visibility of separability plots


  1. TreeDimensionTest version 0.0.1 created from version 1.0.
  2. Replaced depreciated random_shuffle() by shuffle() in tree_dim_src.cpp.

Version 1.0


  1. TreeDimensionTest version 1.0 created.