version 1.0.0

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: slfm
 Type: Package
 Title: Tools for Fitting Sparse Latent Factor Model
-Version: 0.2.3
+Version: 1.0.0
 Author: Joao Duarte and Vinicius Mayrink
 Maintainer: Joao Duarte <jdanielnd@gmail.com>
 Description: Set of tools to find coherent patterns in microarray data using a Bayesian Sparse Latent Factor Model - SLFM; see Duarte and Mayrink (2015) <DOI:10.1007/978-3-319-12454-4_15>. Considerable effort has been put into making slfm fast and memory efficient, turning it an interesting alternative to simpler methods in terms of execution time. It implements versions of the SLFM based on two type of mixtures priors for the loadings: one relying on a degenerate component at zero and the other using a small variance normal distribution for the spike part of the mixture. It also implements additional functions to allow pre-processing procedures for the data and to fit the model for a large number of probesets or genes.
@@ -12,7 +12,7 @@ Imports: Rcpp (>= 0.11.0), coda, lattice
 LinkingTo: Rcpp, RcppArmadillo
 License: GPL-2
 NeedsCompilation: yes
-Packaged: 2019-05-27 11:32:20 UTC; vinicius
+Packaged: 2019-07-26 12:34:39 UTC; vinicius
 Repository: CRAN
-Date/Publication: 2019-05-27 12:50:02 UTC
+Date/Publication: 2019-07-27 23:00:02 UTC
 RoxygenNote: 6.1.1

MD5

@@ -1,16 +1,17 @@
-3472f77079053b928e4091ea11f45715 *DESCRIPTION
+0bab77e50ded6c4f77ee31e10b880e60 *DESCRIPTION
 e6e80f3d5ac67cf4cfe94ed870e41982 *NAMESPACE
-62ac52592f8e650558b3980e03a4fa3d *NEWS
+88498bbb4922412b0fbc23f0c80daf48 *NEWS
 cb351d710987f23af12ef8fc13359267 *R/RcppExports.R
 32e909834a9fc4e509216e033d45c8f6 *R/class_interval.r
 c8c06899e377b821e401c51cc8a6985b *R/plot_matrix.r
 733d512903b3a3fdfb7f595f8d4ae6c7 *R/process_matrix.r
-075689b99e4a310a768fccb9265063a6 *R/slfm.r
+71e37e4d0b84496952819703c211c920 *R/slfm.r
 2c2c9fd2b39f9c0aa0054dd5c64c2f20 *R/slfm_list.r
 dbc88a51796d4e612d0dc5fb43578df7 *R/slfm_package.r
+1a3584021c44fb4e71425c4a3d062385 *inst/CITATION
 11bd797b7ce4e536eab2da4d9953b1cf *man/plot_matrix.Rd
 313518435170f34d9728f6037a8f8d6d *man/process_matrix.Rd
-a31630a45716be6acf5c943a3f4f8586 *man/slfm.Rd
+d6e501d0d7cf7bed6d47cab809ac8c96 *man/slfm.Rd
 75fcdfaac729cf07e44123024a028bfd *man/slfm_list.Rd
 1466593d2f4583309e6462512cc9a16a *man/slfm_package.Rd
 bcc42aaeb0a69ec1b279b42021751d66 *src/Makevars

NEWS

@@ -1,3 +1,9 @@
+slfm 1.0.0
+===========
+
+* including a reference for a publication related to the package in the Journal of Statistical Software. 
+
+
 slfm 0.2.3
 ===========
 

R/slfm.r

@@ -3,8 +3,9 @@
 #' This function is used to fit a Bayesian Sparse
 #' Latent Factor Model to evaluate patterns in gene expression data matrices.
 #' 
+#' @references DOI:10.18637/jss.v090.i09
 #' @references DOI:10.1007/978-3-319-12454-4_15
-#' 
+#'  
 #' @param x matrix with the pre-processed data.
 #' @param a positive shape parameter of the Inverse Gamma prior distribution (default = 2.1). 
 #' @param b positive scale parameter of the Inverse Gamma prior distribution (default = 1.1).

inst/CITATION

@@ -0,0 +1,18 @@
+bibentry(bibtype = "Article",
+  title        = "{slfm}: An {R} Package to Evaluate Coherent Patterns in Microarray Data via Factor Analysis",
+  author       = c(person(given = c("Jo{\\~a}o", "Daniel", "N."),
+                          family = "Duarte",
+                          email = "jdanielnd@gmail.com"),
+                   person(given = c("Vin{\\'\\i}cius", "D."),
+                          family = "Mayrink",
+                          email = "vdm@est.ufmg.br")),
+  journal      = "Journal of Statistical Software",
+  year         = "2019",
+  volume       = "90",
+  number       = "9",
+  pages        = "1--22",
+  doi          = "10.18637/jss.v090.i09",
+
+  header       = "To cite slfm in publications use:"
+)
+