NEWS

Version 0.0.2

2022-03-11

1. Created package version 0.0.2 from 0.0.1.1.

Version 0.0.1.1 (not publicly released)

2022-03-10

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.

2022-02-10

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".

2022-01-20

1. Created package version 0.0.1.1 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

2022-01-17

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

2021-12-12

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

2021-12-11

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

2021-12-01

1. TreeDimensionTest version 1.0 created.