fix renaming of parameters

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: HydeNet
 Type: Package
 Title: Hybrid Bayesian Networks Using R and JAGS
-Version: 0.10.7
+Version: 0.10.8
 Author: Jarrod E. Dalton <daltonj@ccf.org> and Benjamin Nutter
     <benjamin.nutter@gmail.com>
 Maintainer: Benjamin Nutter <benjamin.nutter@gmail.com>

R/Hyde-package.R

@@ -7,7 +7,7 @@
 #' probability distributions, where each node represents a random variable and 
 #' each edge represents conditionality. The full joint distribution is 
 #' therefore factorized as a product of conditional densities, where each node 
-#' is assumed to be independent of its non-desendents given information on its 
+#' is assumed to be independent of its non-descendants given information on its 
 #' parent nodes. Since exact, closed-form algorithms are computationally 
 #' burdensome for inference within hybrid networks that contain a combination 
 #' of continuous and discrete nodes, particle-based approximation techniques 

R/HydeNetwork.R

@@ -44,7 +44,7 @@
 #'       to fitter functions.
 #'   \item \code{nodeParams} A named list.  Each element is a vector of parameters 
 #'       that will be expected by JAGS.
-#'   \item \code{fromData} A named list with the logical value of wheather parameters
+#'   \item \code{fromData} A named list with the logical value of whether parameters
 #'       should be estimated from the data.
 #'   \item \code{nodeData} A named list with the data for each node.  If a node's 
 #'       entry in \code{fromData} is \code{TRUE} and \code{nodeData} is \code{NULL},

R/compileJagsModel.R

@@ -61,14 +61,15 @@ compileJagsModel <- function(network, data=NULL, ...)
 
   cpt_arrays <- makeCptArrays(network) #* The utilty function is in the 
                                        #* file for compileDecisionModel
- 
+
   jags <- 
     rjags::jags.model(
       file = textConnection(writeNetworkModel(network)), 
       data = 
         if (is.null(data) & length(cpt_arrays) == 0) 
         {
-          sys.frame(sys.parent()) 
+          sys.frame(sys.parent())
+          # .GlobalEnv
         }
         else 
         {

R/expectedVariables.R

@@ -87,3 +87,29 @@ expectedParameters <- function(network, node, returnVector=FALSE)
     )
   }
 }
+
+
+expectedParameters_ <- function(network, node, returnVector=FALSE)
+{
+  inputs <- network[["nodeType"]][[node]]
+
+  params <- jagsDists[["RParameter"]][jagsDists[["FnName"]] == inputs]
+
+  names(params) <- jagsDists[["Parameters"]][jagsDists[["FnName"]] == inputs]
+
+  if (returnVector)
+  {
+    return(params)
+  }
+  else 
+  {
+    cat(
+      paste(
+        paste(
+          paste0(params, "= "),
+          collapse=", "
+        )
+      )
+    )
+  }
+}

R/setNode.R

@@ -137,7 +137,7 @@
 #' The validation of parameters is performed by comparing the values provided with 
 #' the limits defined in the \code{jagsDists$paramLogic} variable. (look at 
 #' \code{data(jagsDists, data='HydeNet')}.  For most node types, validation will 
-#' be peformed for numeric variables.  For deterministic variables, the validation
+#' be performed for numeric variables.  For deterministic variables, the validation
 #' will only check that the parameter definition is a formula.  
 #' 
 #' It is possible to pass character strings as definitions, but when this is done, 

R/writeJagsModel.R

@@ -51,15 +51,12 @@ writeJagsModel <- function(network, node)
   node_params <- network[["nodeParams"]][[node_str]]
 
   params <- 
-    eval(
-      substitute(
-        expectedParameters(network = network, 
-                           node = node, 
-                           returnVector = TRUE
-        )
-      )
-    )
-
+    expectedParameters_(network = network, 
+                        node = node, 
+                        returnVector = TRUE)
+
+  names(node_params) <- names(params)
+
   switch(
     network[["nodeType"]][[node_str]],
     "dbern" =   writeJagsModel_dbern(network = network,

cran-comments.md

@@ -1,21 +1,13 @@
-This update fixes errors introduced with `DiagrammeR` 0.9.0
-
-This is a resubmission to address issues found regarding links in the vignettes.
-The links have been updated. The link to another package on CRAN now uses
-https.  The other problematic link does not have an https equivalent.  I did,
-however, write some tests to check that links to this page (rules for a card
-game) are valid so that I may catch this problem before submission in the future.
+This update provides fixes to design features that failed to meet the specification design. It permits the user to define distribution parameters using either the R distribution function argument, or the JAGS distribution function argument.
 
 ## Test environments
-* win-builder (release)
-* local windows install R 3.3.2
-* local windows install R-devel 2017-01-05 r71919
+* win-builder (devel 2017-09-12 r73242)
+* Local Linux install R 3.4.3 (Ubuntu 16.05.3 LTS)
+* Travis CI Linux install R 3.4.2 (Ubuntu 14.04.5 LTS)
 
 ## R CMD check results
 
-A NOTE was returned by win-builder (release and devel) regarding 
-potential spelling errors; all words in the DESCRIPTION file are 
-correctly spelled.
+There were no findings from the CHECK results
 
 ## Downstream dependencies
 There are no downstream dependencies for this package

vignettes/DecisionNetworks.Rmd

@@ -281,7 +281,7 @@ net <- setNodeModels(net, glm.hit1, glm.hit2, glm.hit3)
 
 Alternatively, decision nodes can be deterministic in nature. In this case, we interpret the function which sets the value of these nodes depending on the value(s) of its parent node(s) as a deterministic strategy that is chosen by the actor. Within the blackjack network, we might envision such a strategy by the following rule, which would be applicable to all three hit decisions in the network: choose 'hit' when the current point total is less than 15.
 
-**Utility nodes** are restricted to be deterministic nodes with no descendents. In the blackjack example, for instance, we would assign the payoff utility node as follows:
+**Utility nodes** are restricted to be deterministic nodes with no descendants. In the blackjack example, for instance, we would assign the payoff utility node as follows:
 
 ```{r}
 net <- setNode(net, payoff, "determ", define=fromFormula(),