reset github and fix bug bwselect

jmbh · Jun 29, 2017 · e1b0581 · e1b0581
1 parent 2eacc47
commit e1b0581
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Showing 13 changed files with 190 additions and 125 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: mgm
 Type: Package
 Title: Estimating Time-Varying k-Order Mixed Graphical Models
-Version: 1.2-0
-Date: 2017-05-26
+Version: 1.2-1
+Date: 2017-06-20
 Author: Jonas Haslbeck
 Maintainer: Jonas Haslbeck  <jonashaslbeck@gmail.com>
 Description: Estimation of k-Order time-varying Mixed Graphical Models and mixed VAR(p) models via elastic-net regularized neighborhood regression.
@@ -11,4 +11,4 @@ BugReports: https://github.com/jmbh/mgm/issues
 License: GPL (>= 2)
 Imports: matrixcalc, glmnet, stringr, Hmisc
 LazyData: true
-Packaged: 2017-05-25 19:13:23 UTC; jo
+Packaged: 2017-06-20 10:13:23 CET; jo
diff --git a/R/bwSelect.R b/R/bwSelect.R
@@ -44,8 +44,7 @@ bwSelect <- function(data,
 
   if(is.null(args$saveData)) args$saveData <- FALSE
 
-  if(modeltype == 'mgm') if(is.null(args$overparameterize)) args$overparameterize <- TRUE
-  if(modeltype == 'mgm') if(is.null(args$overparameterize)) args$overparameterize <- FALSE
+  if(is.null(args$overparameterize)) args$overparameterize <- TRUE
 
 
   # ----- Compute Aux Variables -----

diff --git a/R/lagData.R b/R/lagData.R
@@ -75,12 +75,17 @@ lagData <- function(data, lags, consec = NULL) {
 
 
   # ---------- Output ----------
-
+  
   outlist <- list()
   outlist$data_response <- data_response
   outlist$l_data_lags <- l_data_lags
 
-  if(!is.null(consec)) outlist$included <- v_check
+  if(!is.null(consec)) {
+    outlist$included <- v_check
+  } else {
+    outlist$included <- rep(TRUE, n)
+    outlist$included[lags_ext] <- FALSE
+  }
 
 
   return(outlist)

diff --git a/R/mgm.R b/R/mgm.R
@@ -258,6 +258,7 @@ mgm <- function(data,         # n x p data matrix
                             level = level[-v],
                             labels = colnames(data)[-v],
                             d = d)
+
       X <- X_over
     } else {
       X <- X_standard
@@ -682,13 +683,15 @@ mgm <- function(data,         # n x p data matrix
 
           # if(sum(pair == c(1,3))==2) browser()
 
+
           int_sign <- getSign(l_w_ind,
                               l_w_par,
                               type,
                               set_signdefined,
                               overparameterize,
                               ord)
 
+
         } else {
           int_sign <- 0 # if not defined (set_signdefined): 0
         }

diff --git a/R/mvar.R b/R/mvar.R
@@ -168,9 +168,12 @@ mvar <- function(data,         # n x p data matrix
 
 
   # ----- Split up predictor Sets by lags -----
+
 
   # Divide Data in several parts: one response set, and one set of each lag
-  data_lagged <- lagData(data, lags, consec)
+  data_lagged <- lagData(data = data, 
+                          lags = lags, 
+                         consec = consec)
 
   data_response <- data_lagged$data_response
   l_data_lags <- data_lagged$l_data_lags
@@ -253,6 +256,7 @@ mvar <- function(data,         # n x p data matrix
   npar_standard <- rep(NA, p)
 
   for(v in 1:p) {
+
 
     # ----- Create VAR Design Matrix -----
 
@@ -442,6 +446,7 @@ mvar <- function(data,         # n x p data matrix
 
     # Update Progress Bar
     if(pbar==TRUE) setTxtProgressBar(pb, v)
+
 
   } # end for: p
 
@@ -464,6 +469,8 @@ mvar <- function(data,         # n x p data matrix
   if(length(pred_names) != (no_lags * p)) stop('Length of predictor variable names does not match calculated number of predictor varibales')
 
 
+
+
   # Fill parameter list
 
   for(v in 1:p) {