version 0.2.2

cran · Aug 10, 2015 · 4583826 · 4583826
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commit 4583826
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Showing 4 changed files with 17 additions and 11 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: slfm
 Type: Package
 Title: Tools for Fitting Sparse Latent Factor Model
-Version: 0.2.1
+Version: 0.2.2
 Author: Joao Duarte and Vinicius Mayrink
 Maintainer: Joao Duarte <jdanielnd@gmail.com>
 Description: Set of tools to find coherent patterns in microarray data
@@ -21,6 +21,6 @@ Imports: Rcpp (>= 0.11.0), coda, lattice
 LinkingTo: Rcpp, RcppArmadillo
 License: GPL-2
 NeedsCompilation: yes
-Packaged: 2015-08-08 15:03:06 UTC; jdanielnd
+Packaged: 2015-08-10 01:50:32 UTC; jdanielnd
 Repository: CRAN
-Date/Publication: 2015-08-08 17:41:43
+Date/Publication: 2015-08-10 09:09:59
diff --git a/MD5 b/MD5
@@ -1,12 +1,12 @@
-c63be246b93827f2e4574d3231acab25 *DESCRIPTION
+ce2efd977e304e8f1f7c028f0511e1a9 *DESCRIPTION
 87b17ef5c347ec4ca6d1641066700c30 *NAMESPACE
-c16341d14e28876570e5c0f0a6b1ff87 *NEWS
+41649bf0cc9c65822824ba54266a1111 *NEWS
 3e11a37d28ca0244100992886a82d3d5 *R/RcppExports.R
 32e909834a9fc4e509216e033d45c8f6 *R/class_interval.r
 baabf72d4bc884b4c1a64efa0ab6929f *R/plot_matrix.r
 87f7eeceee7273541541ba5c589103ec *R/process_matrix.r
 43023f17cf4534c205f467c51594dff3 *R/slfm-package.r
-ccef8b309606ef4d17db2c21c47019ea *R/slfm.r
+b5d2f894bb4bd9bb537c3fdcfbd399f0 *R/slfm.r
 58005212f9aba9f2f545e0f1a0630f3e *R/slfm_list.r
 540f05f21a09f459cc33f9d244ac919d *man/plot_matrix.Rd
 59958c4ef88f62f062a57ede17dd64c7 *man/process_matrix.Rd

diff --git a/NEWS b/NEWS
@@ -1,3 +1,8 @@
+slfm 0.2.2
+===========
+
+* changing chain indicator used in alpha estimator
+
 slfm 0.2.1
 ===========
 

diff --git a/R/slfm.r b/R/slfm.r
@@ -55,10 +55,13 @@ slfm <- function(
   alpha_clas <- format_classification(class_interval(hpds_q_star))
   alpha_clas_mean <- class_mean(stats_q_star)
 
+  z_matrix <- coda::as.mcmc(res[["z"]][after_burnin,])
+  z_matrix <- window(z_matrix, thin = lag)
+
   alpha_matrix <- coda::as.mcmc(res[["alpha"]][after_burnin,])
   alpha_matrix <- window(alpha_matrix, thin = lag)
 
-  table_alpha <- alpha_estimation(res[["alpha"]][after_burnin,], alpha_clas_mean, res[["qstar"]][after_burnin,])
+  table_alpha <- alpha_estimation(res[["alpha"]][after_burnin,], alpha_clas_mean, res[["z"]][after_burnin,])
 
   lambda_matrix <- coda::as.mcmc(res[["lambda"]][after_burnin,])
   lambda_matrix <- window(lambda_matrix, thin = lag)
@@ -74,8 +77,6 @@ slfm <- function(
   table_sigma <- cbind(stats_sigma, hpds_sigma)[,-4]
   colnames(table_sigma)[4:5] = c("Upper HPD", "Lower HPD")
 
-  z_matrix <- coda::as.mcmc(res[["z"]][after_burnin,])
-  z_matrix <- window(z_matrix, thin = lag)
 
   obj <- list(
     x = x,
@@ -103,9 +104,9 @@ print.slfm <- function(x) {
   print(x$classification)
 }
 
-alpha_estimation <- function(x, alpha_clas, q_star_matrix) {
+alpha_estimation <- function(x, alpha_clas, z_matrix) {
   table_list <- lapply(1:length(alpha_clas), function(i) {
-    chain_indicator <- q_star_matrix[, i] > 0.5
+    chain_indicator <- z_matrix[, i] == 1
     if(alpha_clas[i]) {
       chain <- x[chain_indicator, i]
     } else {