NEWS.md

In diffuStats: Diffusion scores on biological networks

Version log

Version 1.10.2/1.11.2

• Added helper functions to compute the exact moments, so that the user can characterise the systematic biases in the diffusion scores

Version 1.10.1/1.11.1

• Fixed issue in Rcpp code, due to deprecation in arma, info here
• Updated some warnings and notes from BiocCheck()
• Updated readme to link to bioconductor and the journal publications

Version 1.3.1

• Fixed vignette title and citation

Version 1.3.1

• Fixed vignette title and citation
• Small changes to documentation
• Version number not malformed anymore

Version 1.0.0

Overall summary:

• Five diffusion kernels available, they can be computed from an 'igraph' object.

• Diffusion implementations divided between 'diffuse_raw' for deterministic scores and 'diffuse_mc' for permutation analysis, which is parallelised. In total, seven diffusion scores are accessible through the 'diffuse' function.

• Performance evaluation wrapped in the 'perf' function.

• Helper functions in helpers.R (to plot diffusion scores, to check if a kernel matrix is actually a kernel, to extract largest CC from a graph)

Version 0.103.4

• Fix bug

Version 0.103.3

• Fixing warnings in doc

Version 0.103.2

• Reversed changes in Rcpp

Version 0.103.1

• Changed defunct latex2 to latex
• Fixed links in doc files
• Checks on graph: must be undirected

Version 0.101.1

• Added CITATION to the manuscript

Version 0.101.0

This version includes the requests from the reviewers

• Documentation is more complete now, especially in diffuse.
  • Examples on more scores, not only raw
  • Illustration on binary/continuous, differences in unlabelled/negatives
  • Definition of the different scores not only in the vignette, but (briefly) in ?diffuse
  • Description of kernels in ?kernels
  • References to the original publications
• Added the following functions, along with documentation, examples and unit testing:
  • perf_wilcox: test metrics through Wilcox test
  • diffuse_grid: sweep parameters to compute diffusion scores
  • metric_auc, metric_fun: provide basic performance metrics
• Switched dependency from Metrics to precrec
• Added reshape2 as a dependency in Suggests, for its usefulness in cast
• Changes in main vignette, to comply with former points
• Small update on the main figure in the vignette

Version 0.99.12

• Small changes in vignette
• Pushing to see if bot notices

Version 0.99.11

• No changes

Version 0.99.10

• Modified diffuse_mc so that it accepts quantitative inputs (but still should better be sparse)
• Scores ml and gm now throw an error if fed with quantitative inputs
• This version will be proposed to Bioconductor

Version 0.99.9

This version addresses the first reviews from Bioconductor

• Changed the vignette name from yeast.Rnw to diffuStats.Rnw
• Fixed some references in vignette
• Remove commented out code lines
• Remove calls to gc()
• Remove commented calls to browser()
• Remove Cpp commented code
• Vectorised code in diffuse.R (gm method)

Version 0.99.8

• Fixed check NOTE in vignette

Version 0.99.7

• Same as 0.99.4

Version 0.99.6

• Same as 0.99.4

Version 0.99.5

• Same as 0.99.4

Version 0.99.4

• Changed the package name to diffuStats
• More detailed package description in the DESCRIPTION file

Version 0.99.3

• Same as 0.99.1

Version 0.99.2

• Same as 0.99.1

Version 0.99.1

• Fixed eps that was a symlink
• Main figure now with the right size

Version 0.99.0

• Changes in both vignettes, using Bioconductor style
• Submitting to Bioconductor

Version 0.97.0

• Changes in main vignette
• Ready to submit to Bioconductor

Version 0.5.5

• Final adjustments in main vignette
• Added example to quickstart vignette
• First internal review version

Version 0.5.4

• Changes in vignette
• Temporarily depends on R>=3.2 to build a zip for iPsych

Version 0.5.3

• Modified main vignette: more proper introduction, more cites
• Added code chunk to generate the figure in the paper

Version 0.5.2

• Added basic sanity checking
• Fixed small bug: ml could be wrongly codified
• Sanity also checks the variance in the input - useful to detect pathological cases
• Reduced n.perm in vignettes and examples - they should build faster
• Added unit testing for sanity checkers

Version 0.5.1

• Vignette has been added a "proper" introduction
• Now main vignette is in sweave

Version 0.5.0

• Fixed devel version numbering x.y.z, y must be odd
• Added correct indentation, built indentation-fixing function for Rd files
• Fixed CRAN's NOTE on R 3.4 about the c++ code
• Added NEWS file

Version 0.4.3

• Fixed small bug in gm
• Added unit testing for inputs using kernels

TODO

• Some more unit testing (helpers...). Aim at 100% coverage
• Test installation on other systems
• Sanity check for inputs
• Optional: one kernel wrapper with abbreviations

Version 0.4.2

• Added examples to all functions. BiocCheck not complaining anymore!
• Fixed small bugs

TODO

• Some more unit testing (helpers...). Aim at 100% coverage
• Test installation on other systems
• Sanity check for inputs
• Optional: one kernel wrapper with abbreviations

Version 0.4.0

• Added all the kernels and respective helpers, unit testing.
• diffuse, perf now accept kernels as inputs as well. Also, the default Laplacian kernel is computed using kernel functions

TODO

• Some more unit testing (helpers...). Aim at 100% coverage
• Add examples to each function
• Test installation on other systems
• Sanity check for inputs
• Optional: one kernel wrapper with abbreviations

Version 0.2.0

• Added performance wrapper: perf (and its core perf_eval) Can apply diffusion over a grid of parameters and compute a metric using "target scores". Unit testing written as well.
• Dropped pROC dependency, added Metrics
• Helper functions to deal with the format of the files

TODO

• Some more unit testing (helpers...). Aim at 100% coverage
• Add kernels
• Add examples to each function
• Test installation on other systems
• Sanity check for inputs

Version 0.0.10

• Added first 'wrapper': input scores can be given as vector, matrix or list of matrices. Whatever format was given will be returned. Contains unit testing. This simplified vignettes a bit as well.
• Modified graph_toy to contain examples of input vector and matrix. Updated doc and first vignette.
• Dense Matrix objects converted to base matrix in diffusion output.

TODO

• Exhaustive unit testing
• Add kernels
• Add examples to each function
• Test installation on other systems
• Add wrappers for several scores screening, AUC, CV(?)

Version 0.0.8

• Added largest_cc helper
• First version of the yeast vignette. Takes 1:15 to build.

TODO

• Exhaustive unit testing
• Add kernels
• Add examples to each function
• Test installation on other systems
• Should we add wrappers? (cross-validation scores, AUC... We can use try to give NA as an AUC value for bad data splits)

Version 0.0.6

• Fixed bug in ber_s (both matrices are from Matrix)
• Fixed bug in gm (missed drop = FALSE for the single-column case)
• Started second vignette with a bio example: yeast ppi. Added suggests.
• Now using igraphdata, the example is perfect!
• raw and ber_s will coincide if the tested nodes do not belong to the background

TODO

• Exhaustive unit testing
• Add kernels
• End vignette

Version 0.0.4

• Added synthetic input generator
• Fixed a bug in z-score - sums were computed over the raw scores and not the input
• Changed internal representation of default values for graph generation
• Added more unit testing (still missing some)
• Started synthetic example, see data-raw

TODO

• Exhaustive unit testing
• Add kernels
• Add biological example - search for a Bioconductor package with a network in igraph format
• Add example
• Investigate: are raw and ber_s the same? They should be similar but not the same

Version 0.0.2

First version of the package. Includes:

• Synthetic network generation (igraph backend)
• Diffusion scores: raw, ml, gm, z, mc, ber_s, ber_p
• Monte carlo trials are in C++ and parallelised
• Support for diffusion in batchs with different backgrounds
• Unit testing of the majority of functions
• Example data
• Vignette
• Helper functions to plot colours and shapes

Results of devtools::check(): 1 NOTE (line SystemRequirements: GNU make in DESCRIPTION file)

diffuStats documentation built on Feb. 22, 2021, 10 a.m.