Big backfill & Doc cleanup.

DESCRIPTION

@@ -1,10 +1,11 @@
 Package: Peanut
-Version: 0.7-1
-Date: 2019/10/21
+Version: 0.8-2
+Date: 2019/12/11
 Title: Parameterized Bayesian Networks, Abstract Classes
 Author: Russell Almond
 Maintainer: Russell Almond <ralmond@fsu.edu>
-Depends: R (>= 3.0), CPTtools (>= 0.5), methods, shiny (>= 1.1), shinyjs, futile.logger
+Depends: R (>= 3.0), CPTtools (>= 0.5), methods, futile.logger
+Imports: shiny (>= 1.1), shinyjs, utils
 Description: This provides support of learning conditional probability tables parameterized using CPTtools
 License: Artistic-2.0 
 URL: http://pluto.coe.fsu.edu/RNetica

NAMESPACE

@@ -15,7 +15,9 @@ export(is.Pnet, as.Pnet, Pnet,
        BuildAllTables,
        is.Pnode, as.Pnode, Pnode, PnodeNet,
        PnodeQ, "PnodeQ<-",
+       PnodeProbs, "PnodeProbs<-",
        PnodePriorWeight, "PnodePriorWeight<-",
+       PnodePostWeight,
        PnodeRules, "PnodeRules<-",
        PnodeLink, "PnodeLink<-",
        PnodeLnAlphas, "PnodeLnAlphas<-",
@@ -52,6 +54,7 @@ S3method(PnodeParentTvals, default)
 
 
 ## BN generics.
+exportClasses(Pnet,Pnode)
 export(PnodeName, "PnodeName<-",
        PnodeTitle, "PnodeTitle<-",
        PnodeDescription, "PnodeDescription<-",
@@ -70,7 +73,7 @@ export(PnodeName, "PnodeName<-",
        PnetDescription, "PnetDescription<-",
        PnetFindNode,
        PnetMakeStubNodes, PnetRemoveStubNodes,PnetAdjoin,
-       PnetDetach,
+       PnetDetach, PnetCompile,
        PnetSerialize, PnetUnserialize, unserializePnet
        )
 exportMethods(PnodeName, "PnodeName<-",
@@ -84,20 +87,22 @@ exportMethods(PnodeName, "PnodeName<-",
        PnodeStateBounds, "PnodeStateBounds<-",
        PnodeParents, "PnodeParents<-", PnodeParentNames, PnodeNumParents,
        isPnodeContinuous,
+       PnodeEvidence,"PnodeEvidence<-",
        PnetName, "PnetName<-",
        PnetTitle, "PnetTitle<-",
        PnetHub, "PnetHub<-",
        PnetPathname, "PnetPathname<-",
        PnetDescription, "PnetDescription<-",
        PnetMakeStubNodes, PnetRemoveStubNodes,
-       PnetAdjoin, PnetDetach,
+       PnetAdjoin, PnetDetach, PnetCompile,
        PnetFindNode)
 
 ## Manifests
 
 export(BuildNetManifest,BuildNodeManifest)
 
 ## Warehouses
+exportClasses(PnetWarehouse,PnodeWarehouse)
 export(ClearWarehouse,WarehouseManifest,"WarehouseManifest<-",
        WarehouseData,WarehouseSupply,WarehouseFetch,
        WarehouseMake,WarehouseFree, WarehouseUnpack,

R/BNgenerics.R

@@ -1,3 +1,11 @@
+################################
+## Generic objects.  These are implemented as class unions, so that
+## they can added to by implementing classes.
+
+setClassUnion("Pnode","NULL")
+setClassUnion("Pnet","NULL")
+
+
 ###
 ## These are functions which it is pretty safe to assume that every
 ## Bayes net package has.  We can put them here to make generics so
@@ -89,6 +97,14 @@ isPnodeContinuous <- function (node)
   UseMethod("isPnodeContinuous")
 setGeneric("isPnodeContinuous")
 
+PnodeEvidence <- function (node)
+  UseMethod("PnodeEvidence")
+setGeneric("PnodeEvidence")
+
+"PnodeEvidence<-" <- function (node,value)
+  UseMethod("PnodeEvidence<-")
+setGeneric("PnodeEvidence<-")
+
 
 #### Parents
 
@@ -108,6 +124,8 @@ PnodeNumParents <- function (node)
   UseMethod("PnodeNumParents")
 setGeneric("PnodeNumParents")
 
+
+###############################################################
 ## Pnets
 PnetName <- function (net)
   UseMethod("PnetName")
@@ -178,5 +196,9 @@ PnetUnserialize <- function (serial) {
   unserializePnet(factory,serial)
 }
 
+PnetCompile <- function(net)
+  UseMethod("PnetCompile")
+setGeneric("PnetCompile")
+
 
 

R/Manifest.R

@@ -101,7 +101,7 @@ BuildNodeManifest <- function (Pnodelist) {
       if (isPnodeContinuous(nd)) {
         StateValue <- c(StateValue,rep(NA_real_,k))
         bnds <- PnodeStateBounds(nd)
-        LowerBound <- c(UpperBound,bnds[,1L])
+        LowerBound <- c(LowerBound,bnds[,1L])
         UpperBound <- c(UpperBound,bnds[,2L])
       } else {
         if (!is.null(PnodeStateValues(nd))) {

R/Pnets.R

@@ -262,6 +262,21 @@ setGeneric("PnodePriorWeight")
 }
 setGeneric("PnodePriorWeight<-")
 
+PnodePostWeight <- function (node) {
+  UseMethod("PnodePostWeight")
+}
+setGeneric("PnodePostWeight")
+
+PnodeProbs <- function (node) {
+  UseMethod("PnodeProbs")
+}
+setGeneric("PnodeProbs")
+
+"PnodeProbs<-" <- function (node,value) {
+  UseMethod("PnodeProbs<-")
+}
+setGeneric("PnodeProbs<-")
+
 PnodeParentTvals <- function (node) {
   UseMethod("PnodeParentTvals")
 }

R/QOmegaMat.R

@@ -844,7 +844,7 @@ Omega2Pnet <- function(OmegaMat,pn,nodewarehouse,
       napar <- sapply(PnodeParentTvals(node),function(x) any(is.na(x)))
       if (any(napar)) {
         flog.error("Parents %s of node %s don't have levels set.",
-                   paste(parnames[napar],collapse=", "),nodename)
+                   paste(parnames[napar],collapse=", "),ndn)
         stop("Parent",paste(parnames[napar],collapse=", "),
              "of node", nodename, "don't have levels set.")
       }

R/Warehouses.R

@@ -1,3 +1,5 @@
+setClassUnion("PnodeWarehouse","NULL")
+setClassUnion("PnetWarehouse","NULL")
 
 
 ClearWarehouse <- function (warehouse)

R/shinyNode.R

@@ -767,6 +767,6 @@ DPCGadget <- function(pnode, color="steelblue") {
 }
 
 ##########################################
-## Shiny breaks the show command
+## Shinyjs breaks the show command
 
 show <- methods::show

TODO

@@ -1,13 +1,8 @@
 * checking for missing documentation entries ... WARNING
 Undocumented code objects:
-  ‘WarehouseInventory’ ‘WarehouseUnpack’
-  ‘flog.try’ ‘name’
-Undocumented S4 methods:
-  generic 'WarehouseSupply' and siglist 'ANY'
-Functions or methods with usage in documentation object 'Pnet' but not in code:
-  Pnet.ANY
-
+  PnodePostWeight ‘name’
 
+
 https://docs.google.com/spreadsheets/d/{key}/gviz/tq?tqx=out:csv&sheet={sheet_name}
 
 https://docs.google.com/spreadsheets/d/1UoIfFQn5TUwDBDWqxBEQxkwJbUHHjlo7WDCebvzx9j8/edit?usp=sharing

inst/auxdata/Mini-PP-Nodes.csv

@@ -1,21 +1,21 @@
 "","Model","NodeName","ModelHub","NodeTitle","NodeDescription","NodeLabels","Continuous","Nstates","StateName","StateTitle","StateDescription","StateValue","LowerBound","UpperBound"
-"1","miniPP_CM","Physics","","Physics Understanding","General understanding of Newtonian mechanics.","pnodes,Proficiencies",FALSE,3,"High","Highest 1/3","Highest third of target population",0.967421566101701,NA,NA
+"1","miniPP_CM","Physics","","Physics Understanding","General understanding of Newtonian mechanics.","Proficiencies,pnodes",FALSE,3,"High","Highest 1/3","Highest third of target population",0.967421566101701,NA,NA
 "2","miniPP_CM","Physics","","","","",NA,NA,"Medium","Middle 1/3","Middle Third of target Population",0,NA,NA
 "3","miniPP_CM","Physics","","","","",NA,NA,"Low","Lowest 1/3","Lowest third of target population",-0.967421566101701,NA,NA
 "4","miniPP_CM","IterativeD","","Use iterative design to solve a problem","Mass and GPE are directly related
-Height and GPE are directly related","pnodes,LowLevel,Proficiencies",FALSE,3,"High","","Complete Mastery",0.967421566101701,NA,NA
+Height and GPE are directly related","Proficiencies,pnodes,LowLevel",FALSE,3,"High","","Complete Mastery",0.967421566101701,NA,NA
 "5","miniPP_CM","IterativeD","","","","",NA,NA,"Medium","","Partial Mastery",0,NA,NA
 "6","miniPP_CM","IterativeD","","","","",NA,NA,"Low","","No Mastery",-0.967421566101701,NA,NA
-"7","miniPP_CM","EnergyTransfer","","Energy can Transfer","Energy can transfer from one object to another.","pnodes,LowLevel,Proficiencies",FALSE,3,"High","","Can use to solve difficult problems",0.967421566101701,NA,NA
+"7","miniPP_CM","EnergyTransfer","","Energy can Transfer","Energy can transfer from one object to another.","Proficiencies,pnodes,LowLevel",FALSE,3,"High","","Can use to solve difficult problems",0.967421566101701,NA,NA
 "8","miniPP_CM","EnergyTransfer","","","","",NA,NA,"Medium","","Can use to solve simple but not difficult problems",0,NA,NA
 "9","miniPP_CM","EnergyTransfer","","","","",NA,NA,"Low","","Can not solve simple problems.",-0.967421566101701,NA,NA
 "10","miniPP_CM","NTL","","Newton's Third Law","Force pairs act in opposite directions
-Force pairs have equal magnitudes","pnodes,LowLevel,Proficiencies",FALSE,3,"High","","",0.967421566101701,NA,NA
+Force pairs have equal magnitudes","Proficiencies,pnodes,LowLevel",FALSE,3,"High","","",0.967421566101701,NA,NA
 "11","miniPP_CM","NTL","","","","",NA,NA,"Medium","","",0,NA,NA
 "12","miniPP_CM","NTL","","","","",NA,NA,"Low","","",-0.967421566101701,NA,NA
 "13","miniPP_CM","POfMom","","Properties of momentum","Momentum is directly related to mass
 Momentum is directly related to velocity
-Momentum is parallel to velocity","pnodes,LowLevel,Proficiencies",FALSE,3,"High","","",0.967421566101701,NA,NA
+Momentum is parallel to velocity","Proficiencies,pnodes,LowLevel",FALSE,3,"High","","",0.967421566101701,NA,NA
 "14","miniPP_CM","POfMom","","","","",NA,NA,"Medium","","",0,NA,NA
 "15","miniPP_CM","POfMom","","","","",NA,NA,"Low","","",-0.967421566101701,NA,NA
 "Right","PPcompEM","CompensatoryObs","miniPP_CM","Compensatory Observable","A binary response which requires both parent variables for high probability of success.","onodes,Observables,pnodes",FALSE,2,"Right","","",NA,NA,NA
@@ -25,11 +25,11 @@ Momentum is parallel to velocity","pnodes,LowLevel,Proficiencies",FALSE,3,"High"
 "Full","PPtwostepEM","TwoStepObs","miniPP_CM","Partial Credit observable","A partial credit response where each step requires different inputs.","onodes,Observables,pnodes",FALSE,3,"Full","Complete Solution","",NA,NA,NA
 "Partial","PPtwostepEM","TwoStepObs","","","","",NA,NA,"Partial","First step but not second","",NA,NA,NA
 "None","PPtwostepEM","TwoStepObs","","","","",NA,NA,"None","No attempt of failed first step","",NA,NA,NA
-"one","PPdurAttEM","Attempts","miniPP_CM","Number of Attempts","The number of times level was started or restarted","onodes,Observables,pnodes",TRUE,4,"one","1","",NA,0.5,1.5
-"two","PPdurAttEM","Attempts","","","","",NA,NA,"two","2","",NA,1.5,2.5
-"three","PPdurAttEM","Attempts","","","","",NA,NA,"three","3","",NA,2.5,3.5
-"fourPlus","PPdurAttEM","Attempts","","","","",NA,NA,"fourPlus","4 or more","",NA,3.5,Inf
-"Q1","PPdurAttEM","Duration","miniPP_CM","Time spent on level","Total time spent on level less time spent on learning supports","onodes,Observables,pnodes",TRUE,4,"Q1","0–30.190","",NA,0,30.19
+"one","PPdurAttEM","Attempts","miniPP_CM","Number of Attempts","The number of times level was started or restarted","pnodes,onodes,Observables",TRUE,4,"one","1","",NA,0.1,1.1
+"two","PPdurAttEM","Attempts","","","","",NA,NA,"two","2","",NA,1.1,2.1
+"three","PPdurAttEM","Attempts","","","","",NA,NA,"three","3","",NA,2.1,3.1
+"fourPlus","PPdurAttEM","Attempts","","","","",NA,NA,"fourPlus","4 or more","",NA,3.1,Inf
+"Q1","PPdurAttEM","Duration","miniPP_CM","Time spent on level","Total time spent on level less time spent on learning supports","pnodes,onodes,Observables",TRUE,4,"Q1","0–30.190","",NA,0,30.19
 "Q2","PPdurAttEM","Duration","","","","",NA,NA,"Q2","30.190–67.037","",NA,30.19,67.037
 "Q3","PPdurAttEM","Duration","","","","",NA,NA,"Q3","67.037–154.893","",NA,67.037,154.893
 "Q4","PPdurAttEM","Duration","","","","",NA,NA,"Q4","154.893—Inf","",NA,154.893,Inf

man/BuildNodeManifest.Rd

@@ -125,13 +125,13 @@ BuildNodeManifest(Pnodelist)
     are used instead.}
   \item{LowerBound}{This servers as the lower bound for each partition
     of the continuous variagle. \code{-Inf} is a legal value for the
-    first row.}
+    first or last row.}
   \item{UpperBound}{This is only used for continuous variables, and the
     value only is needed for one of the states.  This servers as the
     upper bound of range each state.  Note the upper
     bound needs to match the lower bounds of the next state. \code{Inf}
-    is a legal value for the last row.}
-  
+    is a legal value for the first or last row.}
+
 }
 \section{Continuous Variables}{
 
@@ -192,6 +192,8 @@ nodeman1 <- read.csv(file.path(library(help="Peanut")$path, "auxdata",
 
 \dontrun{
 library(PNetica) ## Requires PNetica
+sess <- NeticaSession()
+startSession(sess)
 
 netpath <- file.path(library(help="PNetica")$path, "testnets")
 netnames <- paste(c("miniPP-CM","PPcompEM","PPconjEM","PPtwostepEM",
@@ -210,13 +212,15 @@ for (n in 1:length(EMs)) {
                     BuildNodeManifest(lapply(NetworkAllNodes(EMs[[n]]),
                                              as.Pnode)))
 }
-## Exclude node labels from this test, as they could appear in arbitrary order
-stopifnot(all.equal(nodeman[,-6],nodeman1[,-6]))
-## Note:  This test might fail because of node order.  Need to improve it.
 
-nl <- strsplit(nodeman$NodeLabels,",")
-nl1 <- strsplit(nodeman1$NodeLabels,",")
-stopifnot(all(mapply(setequal,nl,nl1)))
+## Need to ensure that labels are in cannonical order only for the
+## purpose of testing
+nodeman[,6] <- sapply(strsplit(nodeman[,6],","),
+      function(l) paste(sort(l),collapse=","))
+nodeman1[,6] <- sapply(strsplit(nodeman1[,6],","),
+      function(l) paste(sort(l),collapse=","))
+
+stopifnot(all.equal(nodeman,nodeman1))
 
 ## This is the node warehouse for PNetica
 Nodehouse <- NNWarehouse(manifest=nodeman1,

man/BuildTable.Rd

@@ -73,12 +73,15 @@ BuildAllTables(net, debug=FALSE)
 }
 
 \seealso{
-  \code{\link{Pnode}}, \code{\link{PnodeQ}},
+  \code{\link{Pnode}}, \code{\link{PnodeProbs}}, \code{\link{PnodeQ}},
   \code{\link{PnodePriorWeight}}, \code{\link{PnodeRules}}, 
   \code{\link{PnodeLink}}, \code{\link{PnodeLnAlphas}}, 
   \code{\link{PnodeAlphas}}, \code{\link{PnodeBetas}}, 
   \code{\link{PnodeLinkScale}},\code{\link{GetPriorWeight}},
   \code{\link[CPTtools]{calcDPCTable}}
+
+  In many implementations, it will be necessary to run
+  \code{\link{PnetCompile}} after building the tables.
 }
 \examples{
 
@@ -88,7 +91,7 @@ BuildAllTables(net, debug=FALSE)
 ## NodeExperience functions are part of the RNetica implementation.
 
 BuildTable.NeticaNode <- function (node) {
-  node[] <- calcDPCFrame(ParentStates(node),NodeStates(node),
+  node[] <- calcDPCFrame(ParentStates(node),PnodeStates(node),
                           PnodeLnAlphas(node), PnodeBetas(node),
                           PnodeRules(node),PnodeLink(node),
                           PnodeLinkScale(node),PnodeQ(node),