doc, readme edits

CHANGELOG.md

@@ -1,7 +1,10 @@
 # Changelog
 
+## [1.1.2] - 2023 September 3
+* README changes, documentation changes
+
 ## [1.1.1] - 2023 August 31
-* Yichen Wang (U. Michigan) added function `find_partition_with_rep_rcpp()`
+* Yichen Wang (U. Michigan) added functions `find_partition_with_rep()` and `find_partition_with_rep_rcpp()`
 
 ## [1.1.0] - 2023 July 1
 * Fixed bugs due to release of igraph verison 1.5.0. Refer to https://github.com/kharchenkolab/leidenAlg/issues/13

DESCRIPTION

@@ -1,14 +1,14 @@
 Package: leidenAlg
 Type: Package
 Title: Implements the Leiden Algorithm via an R Interface
-Version: 1.1.1
+Version: 1.1.2
 Authors@R: c(person("Peter", "Kharchenko", email = "Peter_Kharchenko@hms.harvard.edu", role = c("aut")), 
              person("Viktor", "Petukhov", email = "viktor.s.petukhov@ya.ru", role = c("aut")), 
+             person("Yichen", "Wang", email = "wayichen@umich.edu", role=c("aut")),
              person("V.A.", "Traag", email = "v.a.traag@cwts.leidenuniv.nl", role = c("ctb")), 
              person("Gábor", "Csárdi", email = "sardi.gabor@gmail.com", role = c("ctb")), 
              person("Tamás", "Nepusz", email = "ntamas@gmail.com", role = c("ctb")), 
              person("Minh Van", "Nguyen", email = "nguyenminh2@gmail.com", role = c("ctb")), 
-             person("Yichen", "Wang", email = "wayichen@umich.edu", role=c("aut")),
              person("Evan", "Biederstedt", email = "evan.biederstedt@gmail.com", role=c("cre", "aut")))
 Description: An R interface to the Leiden algorithm, an iterative community detection algorithm on networks. The algorithm is designed to converge to a partition in which all subsets of all communities are locally optimally assigned, yielding communities guaranteed to be connected. The implementation proves to be fast, scales well, and can be run on graphs of millions of nodes (as long as they can fit in memory). The original implementation was constructed as a python interface "leidenalg" found here: <https://github.com/vtraag/leidenalg>. The algorithm was originally described in Traag, V.A., Waltman, L. & van Eck, N.J. "From Louvain to Leiden: guaranteeing well-connected communities". Sci Rep 9, 5233 (2019) <doi:10.1038/s41598-019-41695-z>.
 License: GPL-3 
@@ -34,5 +34,5 @@ RoxygenNote: 7.2.3
 URL: https://github.com/kharchenkolab/leidenAlg
 BugReports: https://github.com/kharchenkolab/leidenAlg/issues
 NeedsCompilation: yes
-Author: Peter Kharchenko [aut], Viktor Petukhov [aut], V.A. Traag [ctb], Gábor Csárdi [ctb], Tamás Nepusz [ctb], Minh Van Nguyen [ctb], Yichen Wang [aut], Evan Biederstedt [cre, aut]
+Author: Peter Kharchenko [aut], Viktor Petukhov [aut], Yichen Wang [aut], V.A. Traag [ctb], Gábor Csárdi [ctb], Tamás Nepusz [ctb], Minh Van Nguyen [ctb], Evan Biederstedt [cre, aut]
 Maintainer: Evan Biederstedt <evan.biederstedt@gmail.com>

R/communities.R

@@ -19,7 +19,7 @@ NULL
 
 
 #' Leiden algorithm community detection
-#' Detect communities using Leiden algorithm (implementation copied from https://github.com/vtraag/leidenalg)
+#' Detects communities using Leiden algorithm (implementation copied from https://github.com/vtraag/leidenalg)
 #'
 #' @param graph graph on which communities should be detected
 #' @param resolution resolution parameter (default=1.0) - higher numbers lead to more communities

README.md

@@ -70,19 +70,24 @@ brew install libxml2 glpk gmp
 
 ## Functions
 
-* `leiden.community()`: Detect communities using Leiden algorithm, output as `fakeCommunities` class for downstream use.
+* `find_partition()`: Finds the optimal partition using the Leiden algorithm.
+
+* `find_partition_with_rep()`: Finds the optimal partition using the Leiden algorithm with replicate starts
+
+* `leiden.community()`: Detects communities using Leiden algorithm, output as `fakeCommunities` class for downstream use.
 
 * `rleiden.community()`: Recursive leiden communities, constructs an n-step recursive clustering, using leiden.community.detection. Returns a `fakeCommunities` object that has methods membership(), without dendrogram.
 
 * `as.dendrogram()`: Returns pre-calculated dendrogram from `"fakeCommunities"` object
 
 * `membership()`: Returns pre-calculated membership factor from `"fakeCommunities"` object
 
+
 ## Citation
 If you find `leidenAlg` useful for your publication, please cite:
 
 ```
 Peter Kharchenko, Viktor Petukhov, Yichen Wang, and Evan Biederstedt (2023).
 leidenAlg: Implements the Leiden Algorithm via an R Interface. R
-package version 1.1.1. https://github.com/kharchenkolab/leidenAlg
+package version 1.1.2. https://github.com/kharchenkolab/leidenAlg
 ```