From 53bae463978f4d642eca36d23cffac442e205931 Mon Sep 17 00:00:00 2001
From: Waldir Leoncio <w.l.netto@medisin.uio.no>
Date: Thu, 15 Sep 2022 13:02:32 +0200
Subject: [PATCH] Translated `checkLogml()` (#3)

---
 NAMESPACE         |  1 +
 R/checkLogml.R    | 27 +++++++++++++++++++++++++++
 R/rBAPS-package.R |  2 +-
 3 files changed, 29 insertions(+), 1 deletion(-)
 create mode 100644 R/checkLogml.R

diff --git a/NAMESPACE b/NAMESPACE
index a7ddd55..aff9bfb 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -48,6 +48,7 @@ importFrom(ape,read.FASTA)
 importFrom(matlab2r,blanks)
 importFrom(matlab2r,cell)
 importFrom(matlab2r,colon)
+importFrom(matlab2r,disp)
 importFrom(matlab2r,find)
 importFrom(matlab2r,inputdlg)
 importFrom(matlab2r,isempty)
diff --git a/R/checkLogml.R b/R/checkLogml.R
new file mode 100644
index 0000000..ff7435c
--- /dev/null
+++ b/R/checkLogml.R
@@ -0,0 +1,27 @@
+checkLogml <- function(priorTerm, adjprior, cliques, separators) {
+  # tarkistaa logml:n
+
+  # global CLIQCOUNTS
+  # global SEPCOUNTS
+  # global PARTITION
+
+  npops <- length(unique(PARTITION))
+  cliqcounts <- computeCounts(cliques, separators, npops)$cliqcounts
+  sepcounts <- computeCounts(cliques, separators, npops)$sepcounts
+
+  CLIQCOUNTS <- cliqcounts
+  SEPCOUNTS <- sepcounts
+
+  logml <- computeLogml(adjprior, priorTerm)$logml
+  spatialPrior <- computeLogml(adjprior, priorTerm)$spatialPrior
+
+  disp(
+    c(
+      'logml: ',
+      logml2String(logml),
+      ', spatial prior: ',
+      logml2String(spatialPrior)
+    )
+  )
+  return(logml)
+}
diff --git a/R/rBAPS-package.R b/R/rBAPS-package.R
index c9fde26..3867ba3 100644
--- a/R/rBAPS-package.R
+++ b/R/rBAPS-package.R
@@ -7,6 +7,6 @@
 #' Check the "BugReports" field on the package description for the URL.
 #' @importFrom matlab2r blanks cell colon find inputdlg
 #' isempty isfield isspace max min ones questdlg rand repmat reshape
-#' size sortrows squeeze strcmp times zeros
+#' size sortrows squeeze strcmp times zeros disp
 #' @importFrom stats runif
 NULL