update documentation

VEuPathDB · Feb 22, 2024 · 4219e6c · 4219e6c
1 parent 2799e0c
commit 4219e6c
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Showing 22 changed files with 209 additions and 58 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -16,11 +16,9 @@ export(KPartiteNetwork)
 export(Link)
 export(LinkList)
 export(Network)
-export(Node)
 export(NodeId)
 export(NodeIdList)
 export(NodeList)
-export(Partition)
 export(Partitions)
 export(TwoByTwoTable)
 export(adjustToViewport)
@@ -45,6 +43,7 @@ export(findViewport)
 export(fishersTest)
 export(getDuplicateLinks)
 export(getIsolatedNodes)
+export(getPartitionIndex)
 export(getQuadrantValues)
 export(heatmap)
 export(heatmap.dt)
@@ -76,8 +75,8 @@ export(sensitivity)
 export(smoothedMean)
 export(specificity)
 export(writeJSON)
+export(writeNetworkJSON)
 exportClasses(ContingencyTable)
-exportClasses(KPartiteNetwork)
 exportClasses(Link)
 exportClasses(LinkList)
 exportClasses(Network)
@@ -87,6 +86,12 @@ exportClasses(NodeIdList)
 exportClasses(NodeList)
 exportClasses(Partitions)
 exportClasses(TwoByTwoTable)
+exportMethods(KPartiteNetwork)
+exportMethods(Link)
+exportMethods(LinkList)
+exportMethods(Network)
+exportMethods(NodeIdList)
+exportMethods(NodeList)
 exportMethods(allStats)
 exportMethods(chiSqResults)
 exportMethods(fishersTest)
@@ -106,6 +111,7 @@ exportMethods(relativeRisk)
 exportMethods(sensitivity)
 exportMethods(specificity)
 exportMethods(toJSON)
+exportMethods(writeNetworkJSON)
 import(data.table)
 import(veupathUtils)
 importFrom(S4Vectors,SimpleList)

diff --git a/R/methods-Network.R b/R/methods-Network.R
@@ -193,17 +193,17 @@ setMethod(toJSONGeneric, "Network", function(object, named = c(TRUE, FALSE)) {
   return(tmp)
 })
 
-#' Write json to tmp file
+#' Write network json to tmp file
 #' 
 #' This function returns the name of a json file which it has
 #' written an object out to.
 #' @param x an object to convert to json and write to a tmp file
 #' @param verbose boolean that declares if logging is desired
 #' @return character name of a tmp file w ext *.json
 #' @export
-setGeneric("writeJSON", function(x, pattern = NULL, verbose = c(TRUE, FALSE)) standardGeneric("writeJSON"))
+setGeneric("writeNetworkJSON", function(x, pattern = NULL, verbose = c(TRUE, FALSE)) standardGeneric("writeNetworkJSON"))
 
-#' Write json to local tmp file
+#' Write network json to local tmp file
 #'
 #' This function returns the name of a json file which it has
 #' written a Network object out to.
@@ -213,7 +213,7 @@ setGeneric("writeJSON", function(x, pattern = NULL, verbose = c(TRUE, FALSE)) st
 #' @return character name of a tmp file w ext *.json
 #' @importFrom jsonlite toJSON
 #' @export
-setMethod("writeJSON", "Network", function(x, pattern=NULL, verbose = c(TRUE, FALSE)) {
+setMethod("writeNetworkJSON", "Network", function(x, pattern=NULL, verbose = c(TRUE, FALSE)) {
   net <- x
   verbose <- veupathUtils::matchArg(verbose)
 

diff --git a/man/KPartiteNetwork-class.Rd b/man/KPartiteNetwork-class.Rd
diff --git a/man/Link-class.Rd b/man/Link-class.Rd
diff --git a/man/Link.Rd b/man/Link.Rd
diff --git a/man/LinkList-class.Rd b/man/LinkList-class.Rd
diff --git a/man/LinkList.Rd b/man/LinkList.Rd
diff --git a/man/Network-class.Rd b/man/Network-class.Rd
diff --git a/man/Node-class.Rd b/man/Node-class.Rd
diff --git a/man/Node.Rd b/man/Node.Rd
diff --git a/man/NodeId.Rd b/man/NodeId.Rd
diff --git a/man/NodeIdList.Rd b/man/NodeIdList.Rd
diff --git a/man/NodeList-class.Rd b/man/NodeList-class.Rd
diff --git a/man/Partition-class.Rd b/man/Partition-class.Rd
diff --git a/man/Partitions-class.Rd b/man/Partitions-class.Rd
diff --git a/man/Partitions.Rd b/man/Partitions.Rd
diff --git a/man/getPartitionIndex.Rd b/man/getPartitionIndex.Rd
diff --git a/man/toJSON-KPartiteNetwork-method.Rd b/man/toJSON-KPartiteNetwork-method.Rd
diff --git a/man/toJSON-Partitions-method.Rd b/man/toJSON-Partitions-method.Rd