NEWS.md
Add the reexports function.
Update the documentation of the modified functions.
The syntax of the functions reexported from the igraph package are corrected.
The package version is updated.
The function comp_manipulate is optimized.
The function exir is optimized. Also, the local and online version of the ExIR shiny apps are updated according to this optimization (calculation of zscores from the raw data rather than range normalized data).
The argument ‘scaled’ of the functions ivi, spreading.score, and hubness_score is changed to ‘scale’ and its functionality is optimized. Also, the performance and documentations of these functions are updated accordingly. Additionally, the local and online version of the IVI shiny apps are updated according to these changes.
SIRIR function, sirir, is optimized by providing access to several cores. Also, its documentation is updated.
The function collective.influence is updated to match the current updates of the igraph package.
The package readr is added to the ‘Suggests’ section of the Description file.
The function runShinyApp is updated to require the readr package.
The IVI local shiny app is updated to use the readr package for loading the datasets.
The IVI local shiny app is debugged.
The README file is updated.
DESCRIPTION of the package is updated.
New packages including foreach, and doParallel are added to the Imports section of the DESCRIPTION.
ExIR function, exir, is optimized by providing access to several cores. Also, its documentation is updated.
IVI function, IVI, is optimized by providing access to several cores. Also, its documentation is updated.
LH-index function, clusterRank, is optimized by providing access to several cores. This also significantly speeds up the ivi function. Also, its documentation is updated.
LH-index function, lh_index, is optimized by providing access to several cores. This also significantly speeds up the ivi function. Also, its documentation is updated.
A verbose argument is added all centrality measure functions and their corresponding documentations are updated as well.
The fcor function, fcor, as well as its documentation are optimized and updated.
The documentation of the SIRIR function, sirir, is updated.
Hubness score function, hubness.score, is debugged and optimized.
Spreading score function and its documentation, spreading.score, is debugged and optimized.
IVI function, ivi, is debugged and optimized.
IVI from indices function, ivi.from.indices, is debugged and optimized.
Collective Influence function, collective.influence, is optimized.
The documentation of the Collective Influence function, collective.influence, is updated.
ExIR Shiny app is updated according to the ExIR function.
ExIR visualization function, exir.vis, is optimized.
The package vignettes are updated and the fcor function described and exemplified in the vignettes.
The ExIR function is optimized (corrected for proper Spearman correlation analysis and added Mutual rank as a measure for filtering top correlations) and speeded up (using the data.table package).
A function named fcor is added to the package for super-fast correlation analysis of large datasets and simultaneous P-value and Mutual Rank calculations.
The package vignettes are updated.
The betweenness function is corrected.
Documentation of some functions corrected.
Links to my personal website are corrected.
The package vignettes are updated.
The implementations of shiny apps are optimized.
Shiny apps are debugged.
A new argument, label.position, is added to the exir.vis function.
The exir.vis function is debugged and optimized.
The upload file size limit is removed from the local shiny apps.
The package website built with pkgdown is added to github.
The default correlation coefficient is changed from 0.3 to 0.5 in the ExIR function and its shiny app.
The ExIR shiny app is debugged and updated.
The ExIR function is debugged and updated.
The DESCRIPTION file is updated.
The function ExIR as well as the ExIR shiny app are debugged.
Documentations of some functions are updated.
The DESCRIPTION file is updated.
The name of the function for running shiny apps is changed to runShinyApp.
Shiny apps are updated in the package for local use.
Documentations of several functions are updated.
The Vignettes are updated.
The Read Me file is updated.
Update package Vignettes.
Documentation on how to access ExIR shiny app is added to the Read Me file, vignettes, and the corresponding functions’ documentations.
The ExIR shiny app is added to the package.
A Shiny app is developed for the running the ExIR model and visualization of its output.
Add the comp_manipulate function for the simulation of gene knockout and up-regulation.
Debug the function IVI.
Debug the function ExIR.
Add dependence to R package janitor for the correction of illegal characters in feature names.
Documentation on how to access IVI shiny app is added to the Read Me file, vignettes, and the corresponding functions’ documentations.
The IVI shiny app is added to the package.
A Shiny app is developed for the calculation of IVI as well as IVI-based network visualization.
The dependence of the function ExIR on the package reshape2 is removed.
The function ExIR is debugged.
The ReadMe file is updated.
The citation details of the package is updated.
Vignettes of the package are updated and extended.
A new function named exir.vis is added for the visualization of the results of the function exir.
A new function named cent_network.vis is added for the visualization of a network based on a centrality measure.
A new function named graph_from_incidence_matrix is added (imported from the igraph package) for the network reconstruction from an incidence matrix.
A new column named Type is added to the Biomarker table of the function ExIR.
The Z-score and statistical significance are added to the results of the function ExIR.
The function ExIR is updated so that the experimental data are ranked prior to correlation analysis. This will result in the assessment of the association based on the Spearman method, a more robust algorithm in variable conditions and/or non-parametric distributions.
The version of Roxygen2 is updated in the DESCRIPTION file.
The documentation of the ExIR function is updated.
The ExIR function is updated to prevent outputting NULL results.
The package logo is updated in accordance with the logo design of well-known R packages.
Some documentations in the Read Me file are corrected.
The NC function is improved.
The documentation of the exir function is updated.
The DESCRIPTION file is updated according to all of the modifications.
The citation details of the package is updated.
The function diff.data.assembly is added for assembling the differential/regression data required as an input for the exir function.
The function exir is added for the experimental-data-based classification and ranking of top candidate features.
The function clusterrank is upgraded to clusterRank in order to calculate the ClusterRank centrality internally.
The function neighborhood.connectivity is undergone minor modifications to enhance the performance speed.
The function sif2igraph is added for automatic importing and conversion of a SIF file from the users’ local hard drive, cloud space, or internet into a graph with an igraph class.
The thesis advisors are added to the DESCRIPTION file.
Some minor corrections are done in the documentation of functions and DESCRIPTION file.
The DESCRIPTION file is updated.
The Vignettes file is updated.
The function sirir is added for the unsupervised influence ranking of network nodes.
The function hubness.score is added for the calculation of the Hubness score.
The function spreading.score is added for the calculation of the Spreading score.
The function ivi is added for the influential node identification from a graph.
The function ivi.from.indices is added for the influential node identification from indices.
The function ihs is removed as a refined formula is added for influential node identification.
Updating the normality assessment results of association functions for vectors of length < 4
The function clusterrank is added for the calculation of ClusterRank.
The function collective.influence is added for the calculation of Collective Influence.
The function lh_index is added for the calculation of local H-index.
The function h_index is added for the calculation of H-index.
The function neighborhood.connectivity is updated so that it will not return any NA or NaN values and the output will be a numeric vector.
The formatting of return values in the documentation of each function is corrected.
The citation details of the package are updated according to its associated published paper.
The error regarding the use of NNS since the second use of association assessment functions including cond.prob.analysis and double.cent.assess.noRegression is now corrected.