Merge branch 'develop' into master

.Rbuildignore

@@ -1,8 +1,12 @@
 ^.*\.Rproj$
-^\.Rproj\.user$     # used for temporary files.
-^README\.Rmd$       # An Rmarkdown file used to generate README.md
-^cran-comments\.md$ # Comments for CRAN submission
-^NEWS\.md$          # A news file written in Markdown
+^\.Rproj\.user$
+^README\.Rmd$
+^cran-comments\.md$
 ^\.travis\.yml$
 ^appveyor\.yml$
-appveyor.yml
+
+^fig$
+^inst/localTests$
+^docs$
+^_pkgdown\.yml$
+

.gitignore

@@ -40,13 +40,14 @@ vignettes/*.pdf
 .RData
 .Ruserdata
 
-inst/doc
-fig/
-
 ## OS X
 .DS_Store
 *~
 
 ## compiled C/C++ files
 src/*.o
-src/*.so
+src/*.so
+
+fig
+inst/localTests/
+inst/doc/

DESCRIPTION

@@ -1,21 +1,41 @@
 Package: adjclust
-Maintainer: Pierre Neuvial <[email protected]>
-Author: Christophe Ambroise, Alia Dehman, Michel Koskas, Pierre Neuvial and Guillem Rigaill
-Date: 2017-02-13
-Version: 0.3.0
+Maintainer: Pierre Neuvial <[email protected]>
+Authors@R: c(person("Christophe", "Ambroise", role="aut"),
+             person("Shubham", "Chaturvedi", role="aut"),
+             person("Alia", "Dehman", role="aut"),
+             person("Michel", "Koskas", role="aut"),
+             person("Pierre", "Neuvial", role=c("aut", "cre"), 
+                 email="[email protected]"),
+             person("Guillem", "Rigaill", role="aut"),
+             person("Nathalie", "Villa-Vialaneix", role="aut"))
+Date: 2017-10-16
+Version: 0.5.2
 License: GPL-3
-Title: Adjacency-constrained clustering of a block-diagonal similarity matrix
-Description: Adjacency-constrained clustering of a block-diagonal similarity
-    matrix.
+Title: Adjacency-Constrained Clustering of a Block-Diagonal Similarity Matrix
+Description: Implements a constrained version of hierarchical agglomerative 
+    clustering, in which each observation is associated to a position, and 
+    only adjacent clusters can be merged. Typical application fields in 
+    bioinformatics include Genome-Wide Association Studies or Hi-C data 
+    analysis, where the similarity between items is a decreasing function of 
+    their genomic distance. Taking advantage of this feature, the implemented 
+    algorithm is time and memory efficient. This algorithm is described in 
+    Chapter 4 of Alia Dehman (2015) 
+    <https://hal.archives-ouvertes.fr/tel-01288568v1>.
+Depends: R(>= 2.10.0)
 Imports:
     Matrix,
     matrixStats,
-    Rcpp (>= 0.12.3)
-LinkingTo: Rcpp
-Suggests:
     snpStats,
+    methods,
+    utils,
+    HiTC,
+Suggests:
+    BiocStyle,
     knitr,
     testthat,
-    rmarkdown
+    rmarkdown,
+    rioja
 VignetteBuilder: knitr
-RoxygenNote: 5.0.1
+URL: https://github.com/pneuvial/adjclust
+BugReports: https://github.com/pneuvial/adjclust/issues
+RoxygenNote: 6.0.1.9000

NAMESPACE

@@ -1,7 +1,23 @@
 # Generated by roxygen2: do not edit by hand
 
-importFrom(Rcpp,evalCpp)
+S3method(as.hclust,chac)
+S3method(head,chac)
+S3method(plot,chac)
+S3method(print,chac)
+S3method(summary,chac)
+export(adjClust)
+export(hicClust)
+export(snpClust)
+exportClasses(chac)
+importFrom(HiTC,intdata)
+importFrom(graphics,plot)
 importFrom(matrixStats,colCumsums)
 importFrom(matrixStats,rowCumsums)
-useDynLib(adjclust)
+importFrom(methods,as)
+importFrom(snpStats,ld)
+importFrom(stats,as.dendrogram)
+importFrom(stats,as.hclust)
+importFrom(utils,head)
+importFrom(utils,read.table)
+useDynLib(adjclust, .registration = TRUE)
 useDynLib(adjclust,percDown)

NEWS.md

@@ -1,11 +1,57 @@
-# Package: adjclust
+# Version 0.5.2 [2017-10-17]
 
-## Version 0.3.0 [2017-02-13]
+* Added citation to Alia Dehman's PhD thesis to DESCRIPTION.
+
+# Version 0.5.1 [2017-10-16]
+
+* Added citation to Alia Dehman's PhD thesis to DESCRIPTION.
+* More informative 'Description' of the method in DESCRIPTION
+* Updates to test scripts to pass R CMD check on all windows platforms
+* Moved README-*.png files to man/figures
+
+# Version 0.5.0 [2017-10-13]
+
+* Bump version number for CRAN submission
+
+# Version 0.4.2 [2017-10-05]
+
+* Added 'chac' S3 class and corresponding 'plot' and 'summary' methods
+* Documentation cleanups
+* Removed objects "R2.100" and "Dprime.100" (can be obtained from the 
+  imported 'snpStats' package)
+* In 'snpClust': argument 'stat' is now passed to the 'snpStats::ld' function 
+  through '...'
+* Some code cleanups
+* Improved handling of default value for 'h' in 'adjclust' for 'dist' objects
+* Renamed 'prevfit' into the more explicit 'res_adjclust_0.3.0'
+* Dropped 'simmatrix' toy data set (now generated on the fly in tests)
+
+# Version 0.4.1 [2017-09-15]
+
+* Cleanups in Hi-C and LD vignettes and corresponding tests
+* Dropped outdated BALD test script
+* Added test script for NA values in LD
+* Renamed Hi-C data sets and updated corresponding documentation
+* Added package website generated by pkgdown
+
+# Version 0.4.0 [2017-08-29]
+
+* Implemented interface to handle standard and sparse matrices in adjClust
+* Implemented interface to handle either kernel or dissimilarities
+* Implemented wrapper for SNP and Hi-C data
+* Documented the package and created vignettes for the different use cases
+* Added scripts to increase package coverage and test the equivalence with 
+  rioja for the small dimensional case
+* Cleaned up code to improve efficiency and removed unnecessary scripts and functions
+
+# Version 0.3.0 [2017-02-13]
 
 * Removed 'adjClustBand': main entry points are now 'HeapHop' and 'adjClustBand_heap'.
 * Updated test scripts and LD vignette accordingly.
 * Added Travis CI and Appveyor support.
 
+# Version 0.2.*
+
 ## Version 0.2.3 [2017-02-02]
 
 * Updated LD vignette
@@ -27,7 +73,7 @@
 * 'adjClustBand' is now a wrapper to call either Alia's or Michel's
   implementation
 
-## Version 0.1.0 [2016-06-24]
+# Version 0.1.0 [2016-06-24]
 
 * Created from BALD
-* Added a test to check that we are reproducing the results of BALD::cWard
+* Added a test to check that we are reproducing the results of BALD::cWard