From 4219e6c4ca90cb388a119de6b38c5bba77183f98 Mon Sep 17 00:00:00 2001
From: Danielle Callan <dcallan@upenn.edu>
Date: Thu, 22 Feb 2024 11:43:23 -0500
Subject: [PATCH] update documentation

---
 NAMESPACE                              | 12 +++++++---
 R/methods-Network.R                    |  8 +++----
 man/KPartiteNetwork-class.Rd           | 12 +++++++++-
 man/Link-class.Rd                      |  1 -
 man/Link.Rd                            | 22 ++++++++++++++++++
 man/LinkList-class.Rd                  |  1 -
 man/LinkList.Rd                        | 23 ++++++++++++++++++
 man/Network-class.Rd                   |  8 +++----
 man/Node-class.Rd                      |  3 ++-
 man/Node.Rd                            | 32 ++++++++++++++++++++++++++
 man/NodeId.Rd                          | 15 ------------
 man/NodeIdList.Rd                      |  8 ++++---
 man/NodeList-class.Rd                  |  1 -
 man/Partition-class.Rd                 |  4 ++--
 man/Partitions-class.Rd                |  2 +-
 man/Partitions.Rd                      |  2 +-
 man/getPartitionIndex.Rd               | 17 ++++++++++++++
 man/toJSON-KPartiteNetwork-method.Rd   | 16 +++++++++++++
 man/toJSON-Partitions-method.Rd        | 16 +++++++++++++
 man/writeJSON.Rd                       | 22 ++----------------
 man/writeNetworkJSON-Network-method.Rd | 22 ++++++++++++++++++
 man/writeNetworkJSON.Rd                | 20 ++++++++++++++++
 22 files changed, 209 insertions(+), 58 deletions(-)
 create mode 100644 man/Link.Rd
 create mode 100644 man/LinkList.Rd
 create mode 100644 man/Node.Rd
 delete mode 100644 man/NodeId.Rd
 create mode 100644 man/getPartitionIndex.Rd
 create mode 100644 man/toJSON-KPartiteNetwork-method.Rd
 create mode 100644 man/toJSON-Partitions-method.Rd
 create mode 100644 man/writeNetworkJSON-Network-method.Rd
 create mode 100644 man/writeNetworkJSON.Rd

diff --git a/NAMESPACE b/NAMESPACE
index e9bab982..03e79f22 100644
--- 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
index 93051867..ad06098e 100644
--- a/R/methods-Network.R
+++ b/R/methods-Network.R
@@ -193,7 +193,7 @@ 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.
@@ -201,9 +201,9 @@ setMethod(toJSONGeneric, "Network", function(object, named = c(TRUE, FALSE)) {
 #' @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
index c998bddc..021a0051 100644
--- a/man/KPartiteNetwork-class.Rd
+++ b/man/KPartiteNetwork-class.Rd
@@ -1,10 +1,20 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/class-KPartiteNetwork.R
-\docType{class}
 \name{KPartiteNetwork-class}
 \alias{KPartiteNetwork-class}
 \alias{KPartiteNetwork}
 \title{k-Partite Network}
+\usage{
+KPartiteNetwork(
+  object,
+  links,
+  nodes,
+  partitions = Partitions(),
+  linkColorScheme = "none",
+  variables = VariableMetadataList(),
+  ...
+)
+}
 \description{
 The k-partite network class represents data in the form of a network with k distinct groups of nodes
 in which nodes connect only with nodes from the other groups. In other words, there are only inter-group
diff --git a/man/Link-class.Rd b/man/Link-class.Rd
index 78c8efa9..d1b742ed 100644
--- a/man/Link-class.Rd
+++ b/man/Link-class.Rd
@@ -3,7 +3,6 @@
 \docType{class}
 \name{Link-class}
 \alias{Link-class}
-\alias{Link}
 \title{Link}
 \description{
 Represent one singular link. A link has a source, and a target. It may be directed or undirected.
diff --git a/man/Link.Rd b/man/Link.Rd
new file mode 100644
index 00000000..9342f273
--- /dev/null
+++ b/man/Link.Rd
@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/class-Link.R
+\name{Link}
+\alias{Link}
+\title{Link constructor}
+\usage{
+Link(source, target, weight = 1, color = NULL, isDirected = FALSE)
+}
+\arguments{
+\item{source}{The source node identifier}
+
+\item{target}{The target node identifier}
+
+\item{weight}{The weight of the link}
+
+\item{color}{The color of the link}
+
+\item{isDirected}{Whether the link is directed}
+}
+\description{
+Link constructor
+}
diff --git a/man/LinkList-class.Rd b/man/LinkList-class.Rd
index e5b8502d..efca0454 100644
--- a/man/LinkList-class.Rd
+++ b/man/LinkList-class.Rd
@@ -3,7 +3,6 @@
 \docType{class}
 \name{LinkList-class}
 \alias{LinkList-class}
-\alias{LinkList}
 \title{Link List}
 \description{
 A class for representing links in a network
diff --git a/man/LinkList.Rd b/man/LinkList.Rd
new file mode 100644
index 00000000..ca7762ef
--- /dev/null
+++ b/man/LinkList.Rd
@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/class-Link.R
+\name{LinkList}
+\alias{LinkList}
+\title{Generate a LinkList}
+\usage{
+LinkList(object, linkColorScheme = c("none", "posneg"))
+}
+\arguments{
+\item{object}{Object containing data to be converted to a LinkList. Could be a SimpleList of Links or a data.frame
+with columns source, target, and optionally weight and color.}
+
+\item{linkColorScheme}{Either 'none' or 'posneg'. If 'posneg', the link color will be based on the sign of the weight.}
+}
+\value{
+LinkList
+}
+\description{
+Generate a LinkList from an edgeList
+}
+\examples{
+LinkList(data.frame(source='a',target='b'))
+}
diff --git a/man/Network-class.Rd b/man/Network-class.Rd
index ab773093..da6de68e 100644
--- a/man/Network-class.Rd
+++ b/man/Network-class.Rd
@@ -3,7 +3,6 @@
 \docType{class}
 \name{Network-class}
 \alias{Network-class}
-\alias{Network}
 \title{Network}
 \description{
 A class for representing networks. A network is composed of nodes and links (edges, connections, etc.). A link is represented
@@ -17,9 +16,10 @@ in case some nodes have no links. A network can also have properties such as dir
 
 \item{\code{nodes}}{NodeList object defining the nodes in the network. Some nodes may not have any links.}
 
-\item{\code{linkColorScheme}}{string defining the type of coloring scheme the links follow. Options are 'none' (default) and 'posneg'.}
-
-\item{\code{variableMapping}}{veupathUtils::VariableMetadataList object defining the variable mappings in the network.
+\item{\code{linkColorScheme}}{string defining the type of coloring scheme the links follow. Options are 'none' (default) and 'posneg'.
+In the case of 'posneg', the links color slot will be set to 1 if the link is positive, and -1 if the link is negative.
 Use a method assignLinkColors() to assign colors to links and set this slot's value.}
+
+\item{\code{variableMapping}}{veupathUtils::VariableMetadataList object defining the variable mappings in the network.}
 }}
 
diff --git a/man/Node-class.Rd b/man/Node-class.Rd
index f62ec593..6a7727f1 100644
--- a/man/Node-class.Rd
+++ b/man/Node-class.Rd
@@ -3,7 +3,6 @@
 \docType{class}
 \name{Node-class}
 \alias{Node-class}
-\alias{Node}
 \title{Node}
 \description{
 A class for representing nodes in a network
@@ -20,5 +19,7 @@ A class for representing nodes in a network
 \item{\code{color}}{string or numeric that determines the color of the node. Optional.}
 
 \item{\code{weight}}{numeric value associated with the node, such as timestamp or other node-associated data. Optional.}
+
+\item{\code{degree}}{numeric value indicating the degree of the node}
 }}
 
diff --git a/man/Node.Rd b/man/Node.Rd
new file mode 100644
index 00000000..6a7fbc0d
--- /dev/null
+++ b/man/Node.Rd
@@ -0,0 +1,32 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/constructors-Node.R
+\name{Node}
+\alias{Node}
+\title{Create a Node}
+\usage{
+Node(
+  id,
+  x = numeric(),
+  y = numeric(),
+  color = NULL,
+  weight = NULL,
+  degree = NULL
+)
+}
+\arguments{
+\item{id}{string, NodeId or numeric: a unique identifier for the node}
+
+\item{x}{numeric value indicating the x coordinate of the node. Optional.}
+
+\item{y}{numeric value indicating the y coordinate of the node. Optional.}
+
+\item{color}{string or numeric that determines the color of the node. Optional.}
+
+\item{weight}{numeric value associated with the node, such as timestamp or other node-associated data. Optional.}
+
+\item{degree}{numeric value indicating the degree of the node. This only makes sense in the context of a network,
+and should not be provided in other contexts like when working w an individual node.}
+}
+\description{
+Create a Node given a unique identifier as either string, NodeId or numeric.
+}
diff --git a/man/NodeId.Rd b/man/NodeId.Rd
deleted file mode 100644
index f8d1b16e..00000000
--- a/man/NodeId.Rd
+++ /dev/null
@@ -1,15 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/class-Node.R
-\name{NodeId}
-\alias{NodeId}
-\title{Create a Node Id}
-\usage{
-NodeId(value)
-}
-\arguments{
-\item{value}{string a unique identifier for the node}
-}
-\description{
-Because typing `NodeId(id = 'foo')` is annoying, this function is provided
-to make things easier. Now you can do `NodeId('foo')`
-}
diff --git a/man/NodeIdList.Rd b/man/NodeIdList.Rd
index 6ddb4a35..aa51c894 100644
--- a/man/NodeIdList.Rd
+++ b/man/NodeIdList.Rd
@@ -1,13 +1,15 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/class-Node.R
+% Please edit documentation in R/constructors-Node.R
 \name{NodeIdList}
 \alias{NodeIdList}
 \title{Create a NodeIdList}
 \usage{
-NodeIdList(nodeIds)
+NodeIdList(object, uniquifyIds = c(TRUE, FALSE))
 }
 \arguments{
-\item{nodeIds}{list of node ids}
+\item{object}{Object containing list of node ids}
+
+\item{uniquifyIds}{Logical indicating whether to uniquify the node ids}
 }
 \description{
 Create a NodeIdList
diff --git a/man/NodeList-class.Rd b/man/NodeList-class.Rd
index e02ead8e..76f945c9 100644
--- a/man/NodeList-class.Rd
+++ b/man/NodeList-class.Rd
@@ -3,7 +3,6 @@
 \docType{class}
 \name{NodeList-class}
 \alias{NodeList-class}
-\alias{NodeList}
 \title{NodeList}
 \description{
 A class for representing a list of nodes.
diff --git a/man/Partition-class.Rd b/man/Partition-class.Rd
index 9ad0e46c..22fc7ad6 100644
--- a/man/Partition-class.Rd
+++ b/man/Partition-class.Rd
@@ -1,11 +1,11 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/class-KPartiteNetwork.R
+% Please edit documentation in R/class-Partitions.R
 \name{Partition-class}
 \alias{Partition-class}
 \alias{Partition}
 \title{Create a Partition}
 \usage{
-Partition(nodeIds)
+NodeIdList(object, uniquifyIds = c(TRUE, FALSE))
 }
 \description{
 An alias to NodeIdList
diff --git a/man/Partitions-class.Rd b/man/Partitions-class.Rd
index 3745ab72..253448c7 100644
--- a/man/Partitions-class.Rd
+++ b/man/Partitions-class.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/class-KPartiteNetwork.R
+% Please edit documentation in R/class-Partitions.R
 \docType{class}
 \name{Partitions-class}
 \alias{Partitions-class}
diff --git a/man/Partitions.Rd b/man/Partitions.Rd
index 1d49f22c..542eb3e6 100644
--- a/man/Partitions.Rd
+++ b/man/Partitions.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/class-KPartiteNetwork.R
+% Please edit documentation in R/class-Partitions.R
 \name{Partitions}
 \alias{Partitions}
 \title{Create Partitions}
diff --git a/man/getPartitionIndex.Rd b/man/getPartitionIndex.Rd
new file mode 100644
index 00000000..d4c2200b
--- /dev/null
+++ b/man/getPartitionIndex.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/class-Partitions.R
+\name{getPartitionIndex}
+\alias{getPartitionIndex}
+\title{Get Partition index of a Node}
+\usage{
+getPartitionIndex(partitions, node)
+}
+\arguments{
+\item{partitions}{Partitions}
+
+\item{node}{character, NodeId or Node object}
+}
+\description{
+Given a list of partitions and a node id, return the index
+of the partition that the node belongs to.
+}
diff --git a/man/toJSON-KPartiteNetwork-method.Rd b/man/toJSON-KPartiteNetwork-method.Rd
new file mode 100644
index 00000000..8eebafcd
--- /dev/null
+++ b/man/toJSON-KPartiteNetwork-method.Rd
@@ -0,0 +1,16 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/methods-KPartiteNetwork.R
+\name{toJSON,KPartiteNetwork-method}
+\alias{toJSON,KPartiteNetwork-method}
+\title{Convert KPartiteNetwork object to JSON}
+\usage{
+\S4method{toJSON}{KPartiteNetwork}(object, named = c(TRUE, FALSE))
+}
+\arguments{
+\item{object}{A KPartiteNetwork object}
+
+\item{named}{boolean that declares if names should be included}
+}
+\description{
+Converts a KPartiteNetwork object to JSON
+}
diff --git a/man/toJSON-Partitions-method.Rd b/man/toJSON-Partitions-method.Rd
new file mode 100644
index 00000000..693c5e0c
--- /dev/null
+++ b/man/toJSON-Partitions-method.Rd
@@ -0,0 +1,16 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/methods-KPartiteNetwork.R
+\name{toJSON,Partitions-method}
+\alias{toJSON,Partitions-method}
+\title{Convert Partitions object to JSON}
+\usage{
+\S4method{toJSON}{Partitions}(object, named = c(TRUE, FALSE))
+}
+\arguments{
+\item{object}{A Partitions object}
+
+\item{named}{boolean that declares if names should be included}
+}
+\description{
+Converts a Partitions object to JSON
+}
diff --git a/man/writeJSON.Rd b/man/writeJSON.Rd
index 539bffa6..87b63f8c 100644
--- a/man/writeJSON.Rd
+++ b/man/writeJSON.Rd
@@ -1,38 +1,20 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/methods-Network.R, R/utils-json.R
+% Please edit documentation in R/utils-json.R
 \name{writeJSON}
 \alias{writeJSON}
-\title{Write json to tmp file}
+\title{Write json to local tmp file}
 \usage{
-writeJSON(.pd, evilMode, pattern = NULL, verbose = c(TRUE, FALSE))
-
-writeJSON(.pd, evilMode, pattern = NULL, verbose = c(TRUE, FALSE))
-
 writeJSON(.pd, evilMode, pattern = NULL, verbose = c(TRUE, FALSE))
 }
 \arguments{
 \item{.pd}{a data.table to convert to json and write to a tmp file}
 
 \item{pattern}{optional tmp file prefix}
-
-\item{verbose}{boolean that declares if logging is desired}
-
-\item{x}{a data.table to convert to json and write to a tmp file}
 }
 \value{
-character name of a tmp file w ext *.json
-
-character name of a tmp file w ext *.json
-
 character name of a tmp file w ext *.json
 }
 \description{
-This function returns the name of a json file which it has
-written an object out to.
-
-This function returns the name of a json file which it has
-written a Network object out to.
-
 This function returns the name of a json file which it has
 written a data.table object out to.
 }
diff --git a/man/writeNetworkJSON-Network-method.Rd b/man/writeNetworkJSON-Network-method.Rd
new file mode 100644
index 00000000..18724370
--- /dev/null
+++ b/man/writeNetworkJSON-Network-method.Rd
@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/methods-Network.R
+\name{writeNetworkJSON,Network-method}
+\alias{writeNetworkJSON,Network-method}
+\title{Write network json to local tmp file}
+\usage{
+\S4method{writeNetworkJSON}{Network}(x, pattern = NULL, verbose = c(TRUE, FALSE))
+}
+\arguments{
+\item{x}{a data.table to convert to json and write to a tmp file}
+
+\item{pattern}{optional tmp file prefix}
+
+\item{verbose}{boolean that declares if logging is desired}
+}
+\value{
+character name of a tmp file w ext *.json
+}
+\description{
+This function returns the name of a json file which it has
+written a Network object out to.
+}
diff --git a/man/writeNetworkJSON.Rd b/man/writeNetworkJSON.Rd
new file mode 100644
index 00000000..1f321277
--- /dev/null
+++ b/man/writeNetworkJSON.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/methods-Network.R
+\name{writeNetworkJSON}
+\alias{writeNetworkJSON}
+\title{Write network json to tmp file}
+\usage{
+writeNetworkJSON(x, pattern = NULL, verbose = c(TRUE, FALSE))
+}
+\arguments{
+\item{x}{an object to convert to json and write to a tmp file}
+
+\item{verbose}{boolean that declares if logging is desired}
+}
+\value{
+character name of a tmp file w ext *.json
+}
+\description{
+This function returns the name of a json file which it has
+written an object out to.
+}