Changes in version 1.10.2 - Added helper functions to compute the exact moments, so that the user can characterise the systematic biases in the diffusion scores Changes in version 1.10.1 - 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 Changes in version 1.3.1 - Fixed vignette title and citation - Fixed vignette title and citation - Small changes to documentation - Version number not malformed anymore Changes in 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) Changes in version 0.103.4 - Fix bug Changes in version 0.103.3 - Fixing warnings in doc Changes in version 0.103.2 - Reversed changes in Rcpp Changes in version 0.103.1 - Changed defunct latex2 to latex - Fixed links in doc files - Checks on graph: must be undirected Changes in version 0.101.1 - Added CITATION to the manuscript Changes in 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 Changes in version 0.99.12 - Small changes in vignette - Pushing to see if bot notices Changes in version 0.99.11 - No changes Changes in 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 Changes in 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) Changes in version 0.99.8 - Fixed check NOTE in vignette Changes in version 0.99.7 - Same as 0.99.4 Changes in version 0.99.6 - Same as 0.99.4 Changes in version 0.99.5 - Same as 0.99.4 Changes in version 0.99.4 - Changed the package name to diffuStats - More detailed package description in the DESCRIPTION file Changes in version 0.99.3 - Same as 0.99.1 Changes in version 0.99.2 - Same as 0.99.1 Changes in version 0.99.1 - Fixed eps that was a symlink - Main figure now with the right size Changes in version 0.99.0 - Changes in both vignettes, using Bioconductor style - Submitting to Bioconductor Changes in version 0.97.0 - Changes in main vignette - Ready to submit to Bioconductor Changes in version 0.5.5 - Final adjustments in main vignette - Added example to quickstart vignette - First internal review version Changes in version 0.5.4 - Changes in vignette - Temporarily depends on R>=3.2 to build a zip for iPsych Changes in version 0.5.3 - Modified main vignette: more proper introduction, more cites - Added code chunk to generate the figure in the paper Changes in 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 Changes in version 0.5.1 - Vignette has been added a "proper" introduction - Now main vignette is in sweave Changes in 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 Changes in 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 Changes in 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 Changes in 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 Changes in 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 Changes in 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(?) Changes in 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) Changes in 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 Changes in 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 Changes in 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)