Big backfill & Doc cleanup.

Author: ralmond

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