CSOgroup · Arvindiyer · Apr 4, 2025 · Mar 19, 2025 · Mar 19, 2025 · Mar 21, 2025
diff --git a/._README.Rmd b/._README.Rmd
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,18 +1,16 @@
 Package: SelectSim
 Title: Selected Events Linked by Evolutionary Conditions across human Tumors
-Version: 0.0.1.3
+Version: 0.0.1.5
 Authors@R: 
     c(person("Arvind", "Iyer", , "ayalurarvind@gamil.com", role = c("aut", "cre"),comment = c(ORCID = "0000-0002-8247-700X")),
     person("Marco", "Mina", , "marco.mina.85@gmail.com", role = c("aut")),
+    person("Miljan", "Petrovic", , "miljanpet93@gmail.com", role = c("aut")),
     person("Giovanni", "Ciriello", , "givoanni.cirello@unil.ch", role = c("aut"),comment = c(ORCID ="0000-0003-2021-8683")))
-Description: This R package implements the SelectSim methodology to infer evolutionary dependencies between functional alterations in cancer.
+Description: This R package implements the SelectSim methodology to infer co-mutations between functional alterations in cancer.
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.0
-LinkingTo: 
-    Rcpp,
-    RcppArmadillo
+RoxygenNote: 7.3.2
 Imports: 
     doParallel,
     doRNG,
@@ -23,7 +21,6 @@ Imports:
     ggridges,
     Matrix,
     Rcpp,
-    RcppArmadillo,
     reshape2,
     Rfast,
     tictoc
@@ -33,7 +30,10 @@ Suggests:
     testthat (>= 3.0.0)
 Config/testthat/edition: 3
 Depends: 
-    R (>= 2.10)
+    R (>= 3.5)
 LazyData: true
 VignetteBuilder: knitr
 URL: https://csogroup.github.io/SelectSim/
+LinkingTo: 
+    Rcpp,
+    RcppArmadillo
diff --git a/INSTALLATION.md b/INSTALLATION.md
@@ -8,17 +8,20 @@
 devtools::install_github("CSOgroup/SelectSim",dependencies = TRUE, build_vignettes = TRUE)
 ```
 
-## Installation with micromamba enviorment
+## Installation with micromamba enviorment (prefered)
 
 
 `micromamba` is a tiny version of the mamba package manager (Like Conda). Refer [website](https://mamba.readthedocs.io/en/latest/installation/micromamba-installation.html) for it's installation guide.
 
 Steps to follow after installing micromamba in a terminal:
 
-`micromamba create -n r_env r-essentials r-base`\
+`micromamba create -n r_env`\
 `micromamba activate r_env`\
+`micromamba install conda-forge::r-base`\
+`micromamba install conda-forge::r-essentials`\
 `micromamba install conda-forge::r-devtools`\
-`micromamba install conda-forge::armadillo`\
+`micromamba install conda-forge::r-pak`\
+`micromamba install conda-forge::cmake`\
 `micromamba install conda-forge::r-rcppparallel`\
 `micromamba install conda-forge::r-rfast`
 
@@ -27,10 +30,15 @@ Steps to follow after installing micromamba in a terminal:
 # install.packages("devtools")
 devtools::install_github("CSOgroup/SelectSim",dependencies = TRUE, build_vignettes = TRUE)
 ```
+OR
+``` r
+library('pak')
+pak::pkg_install('CSOgroup/SelectSim')
+```
 
-Alternative way install with provided `enviorment.yml` file.
+Alternative way install with provided [`enviorment.yml`](enviorment.yml) file.
 
-`micromamba create -f env.yml`\
+`micromamba create -f enviorment.yml`\
 `micromamba activate r_env`
 - After this run R and install `SelectSim` R package as follows
 ``` r

diff --git a/LICENSE b/LICENSE
@@ -1,2 +1,2 @@
-YEAR: 2024
+YEAR: 2025
 COPYRIGHT HOLDER: SelectSim authors
diff --git a/LICENSE.md b/LICENSE.md
@@ -1,6 +1,6 @@
 # MIT License
 
-Copyright (c) 2024 SelectSim authors
+Copyright (c) 2025 SelectSim authors
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/NAMESPACE b/NAMESPACE
@@ -35,7 +35,6 @@ export(new.AL.general)
 export(new.ALS)
 export(new.AMS)
 export(null_model_parallel)
-export(null_model_parallel_debug)
 export(obs_exp_scatter)
 export(overlap_pair_extract)
 export(r.am.pairwise.alteration.overlap)
@@ -44,11 +43,11 @@ export(retrieveOutliers)
 export(ridge_plot_ed)
 export(ridge_plot_ed_compare)
 export(selectX)
-export(selectX_debug)
 export(stat_maf_column)
 export(stat_maf_gene)
 export(stat_maf_sample)
 export(templeate.obj.gen)
+export(theme_Publication)
 export(w.r.am.pairwise.alteration.overlap)
 import(doParallel)
 import(doRNG)
@@ -59,6 +58,8 @@ import(ggridges)
 import(graphics)
 import(parallel)
 importFrom(Matrix,Matrix)
+importFrom(Matrix,sparseMatrix)
+importFrom(Matrix,t)
 importFrom(Rcpp,sourceCpp)
 importFrom(Rfast,rowSort)
 importFrom(dplyr,"%>%")

diff --git a/NEWS.md b/NEWS.md
@@ -6,4 +6,16 @@
 * Added a `NEWS.md` file to track changes to the package.
 * Rename the pacakge SelectX to SelectSim by creating a new git folder.
 * Create CSO group repositroy and move the code there.
-* Created the website for github
+* Created the website for github
+
+# SelectX 0.0.1.4
+
+* Added Mijan in author's list
+* Remove C/C++ code dependecny to avoid installation diffculties in different systems.
+  * Hence move to using `Matrix` library functions and removed `RCpp` functions and code.
+* Update the website and vignette accordingly. 
+
+# SelectX 0.0.1.5
+
+* Fixed bug of outlier functions and added C/C++ code back.
+* More description in functions
diff --git a/R/._selectX_run.R b/R/._selectX_run.R
diff --git a/R/.gitignore b/R/.gitignore
@@ -8,3 +8,4 @@
 inst/doc
 .*
 !/.gitignore
+._*
diff --git a/R/gam_utils.r b/R/gam_utils.r
@@ -3,7 +3,7 @@
 # Email   : ayalurarvind@gmail.com
 # Project : SelectX
 # Desc    : Functions to process the maf to gam
-# Version : 0.1
+# Version : 0.1.5
 # Updates : 
 # Todo:
 ###
-Original file line number
+Diff line change
@@ Expand Up / @@ -8,3 +8,4 @@ @@
     inst/doc
     .*
     !/.gitignore
+    ._*