EcoNetWeb               ### MKLau 31Mar2016 Access example EcoNet
                        models from the EcoNet website.
ShannonDiversity        Shannon Diversity Metrics These are based on
                        entropy and build Shannon and Weaver 1949
TES                     TES.R - TOTAL ENVIRON STORAGE INPUT = network
                        model OUTPUT = total environ throughput - unit
                        and scaled
TET                     TET.R - TOTAL ENVIRON THROUGHFLOW INPUT =
                        network model OUTPUT = total environ throughput
                        - unit and scaled
as.bipartite            as.bipartite - convert a network object to a
                        matrix for analysis with the bipartite package
                        INPUT = network model OUTPUT = matrix
                        representation M. Lau July 2015 ------------
                        as.bipartite - convert a network object to a
                        matrix for analysis with the bipartite package
                        INPUT = network model OUTPUT = matrix
                        representation M. Lau July 2015 ------------
                        as.bipartite - convert a network object to a
                        matrix for analysis with the bipartite package
                        INPUT = network model OUTPUT = matrix
                        representation M. Lau July 2015 ------------
                        Create a bipartite network.
as.extended             as.extended - convert a network object to
                        extended format in Allesina and Bondavalli 2003
                        INPUT = network model OUTPUT = the same model
                        in extended format with inputs and
                        exports/respiration in the same matrix
                        REFERENCE: Allesina, S., Bondavalli, C., 2003.
                        Steady state of ecosystem flow networks: a
                        comparison between balancing procedures.
                        Ecological Modelling 165(2-3): 231-239. M. Lau
                        July 2011 ------------ as.extended - convert a
                        network object to extended format in Allesina
                        and Bondavalli 2003 INPUT = network model
                        OUTPUT = the same model in extended format with
                        inputs and exports/respiration in the same
                        matrix REFERENCE: Allesina, S., Bondavalli, C.,
                        2003. Steady state of ecosystem flow networks:
                        a comparison between balancing procedures.
                        Ecological Modelling 165(2-3): 231-239. M. Lau
                        July 2011 ------------ as.extended - convert a
                        network object to extended format in Allesina
                        and Bondavalli 2003 INPUT = network model
                        OUTPUT = the same model in extended format with
                        inputs and exports/respiration in the same
                        matrix REFERENCE: Allesina, S., Bondavalli, C.,
                        2003. Steady state of ecosystem flow networks:
                        a comparison between balancing procedures.
                        Ecological Modelling 165(2-3): 231-239. M. Lau
                        July 2011 ------------ Create an Extended
                        Format Matrix
bal                     bal - balances a flow model INPUT = network
                        model in extended format OUTPUT = balanced
                        model in extended format NOTE: this is the work
                        horse for balance.R Original: M. Lau | July
                        2011 Re-written: M. Lau | 17Oct2013
                        ------------ bal - balances a flow model INPUT
                        = network model in extended format OUTPUT =
                        balanced model in extended format NOTE: this is
                        the work horse for balance.R Original: M. Lau |
                        July 2011 Re-written: M. Lau | 17Oct2013
                        ------------ bal - balances a flow model INPUT
                        = network model in extended format OUTPUT =
                        balanced model in extended format NOTE: this is
                        the work horse for balance.R Original: M. Lau |
                        July 2011 Re-written: M. Lau | 17Oct2013
                        ------------ Subfunction for Balancing by
                        Either Inputs or Outputs
balance                 Balance Flow Network Models
bcratio                 Calculates the Ratio of Positive to Negative
                        Elements in a Network
bgcModels               Bigeochemical Cycling Models
cycliv                  ## Cycle Analysis for Feeding Cycles ## Singh
                        P.  | July 2014 ## Algorithm Source : Ulanowicz
                        1991: A package for the Analysis of Ecosystem
                        Flow Networks ## ---------- ## Cycle Analysis
                        for Feeding Cycles ## Singh P.  | July 2014 ##
                        Algorithm Source : Ulanowicz 1991: A package
                        for the Analysis of Ecosystem Flow Networks ##
                        ---------- ## Cycle Analysis for Feeding Cycles
                        ## Singh P.  | July 2014 ## Algorithm Source :
                        Ulanowicz 1991: A package for the Analysis of
                        Ecosystem Flow Networks ## ---------- Analysis
                        of Feeding Cycles in a Network
eigenCentrality         Calculates the Eigen Centrality of a Network
enaAll                  enaAll - Conduct all ecological network
                        analyses INPUT = network object OUTPUT = list
                        of analytical output
enaAscendency           enaAscendency - calculates the ascendency
                        statistics of Ulanowicz INPUT = network object
                        OUTPUT = matrix of ascendency statistics
enaControl              enaControl - control analyses INPUT = network
                        object OUTPUT = list of control statistics M.
                        Lau | July 2011 P. Singh | Update Summer 2013
                        S.R. Borrett | Update March 2016 ------------
                        enaControl - control analyses INPUT = network
                        object OUTPUT = list of control statistics M.
                        Lau | July 2011 P. Singh | Update Summer 2013
                        S.R. Borrett | Update March 2016 ------------
                        enaControl - control analyses INPUT = network
                        object OUTPUT = list of control statistics M.
                        Lau | July 2011 P. Singh | Update Summer 2013
                        S.R. Borrett | Update March 2016 ------------
                        Control Analyses of Ecological Networks
enaCycle                ## NETWRK's Full Cycle Analysis ## Singh P. |
                        July 2014 ## Algorithm Source : Ulanowicz 1991:
                        A package for the Analysis of Ecosystem Flow
                        Networks ## ----------- ## NETWRK's Full Cycle
                        Analysis ## Singh P. | July 2014 ## Algorithm
                        Source : Ulanowicz 1991: A package for the
                        Analysis of Ecosystem Flow Networks ##
                        ----------- ## NETWRK's Full Cycle Analysis ##
                        Singh P. | July 2014 ## Algorithm Source :
                        Ulanowicz 1991: A package for the Analysis of
                        Ecosystem Flow Networks ## ----------- Full
                        Cycle Analysis of Ecological Networks
enaEnviron              environ - conducts environ analysis INPUT =
                        network object OUTPUT = input and/or output
                        environs
enaFlow                 enaFlow - flow analysis INPUT = network object
                        OUTPUT = list of flow statistics
enaMTI                  enaMTI - Mixed Trophic Impacts Analysis follows
                        Ulanowicz and Puccia, 1990. INPUT = network
                        object OUTPUT = list of trophic impact
                        statistics Borrett | June 2012, MKL | July 2013
                        -------- enaMTI - Mixed Trophic Impacts
                        Analysis follows Ulanowicz and Puccia, 1990.
                        INPUT = network object OUTPUT = list of trophic
                        impact statistics Borrett | June 2012, MKL |
                        July 2013 -------- enaMTI - Mixed Trophic
                        Impacts Analysis follows Ulanowicz and Puccia,
                        1990. INPUT = network object OUTPUT = list of
                        trophic impact statistics Borrett | June 2012,
                        MKL | July 2013 -------- Mixed Trophic Impacts
                        (MTI) Analysis
enaModelInfo            Ecosystem Model Information
enaModels               Ecosystem Models
enaR-package            Tools for Ecological Network Analysis (ena)
enaStorage              enaStorage - storage analysis INPUT = network
                        object OUTPUT = list of storage statistics
enaStructure            enaStructure - performes strucutral analysis of
                        the network graph (see Borrett et al. 2007)
                        INPUT = network object OUTPUT = list of
                        structure statistics
enaTroAgg               Trophic Aggregations (TroAgg) Analysis
enaUtility              enautility - utility analysis of a flow network
                        INPUT = network object OUTPUT = list of utility
                        statistics
environCentrality       environCentrality - calculates the centrality
                        of flow network environs INPUT = environ matrix
                        OUTPUT = in-going, out-going and average
                        centralities
findPathLength          findPathLength - calculates the flows over a
                        sequence up to a maximum path length INPUT =
                        network object OUTPUT = a list of flow
                        statistics over paths
force.balance           force.balance - repeatedly applies balance
                        until sub-tolerance is reached INPUT = network
                        model OUTPUT = balanced model M. Lau 1 Oct 2012
                        ------------ force.balance - repeatedly applies
                        balance until sub-tolerance is reached INPUT =
                        network model OUTPUT = balanced model M. Lau 1
                        Oct 2012 ------------ force.balance -
                        repeatedly applies balance until sub-tolerance
                        is reached INPUT = network model OUTPUT =
                        balanced model M. Lau 1 Oct 2012 ------------
                        Repeated Application the Balance Function
get.ns                  get.ns.R Input = network model Output = a
                        vector of global network statistics from ena
get.orient              get.orient - returns the global orientation
                        INPUT = none OUTPUT = returns the current
                        orientation of matrices
m.list                  Sub-set of the Larger Ecosystem Models
mExp                    # mExp - calculate the exponent of a given
                        matrix # INPUT = a matrix (x) and the exponent
                        (n) # OUTPUT = the resulting exponentiated
                        matrix # # Alberto Monteiro
                        (https://stat.ethz.ch/pipermail/ #
                        r-help/2007-May/131330.html) #
                        ___________________________________________________
                        # mExp - calculate the exponent of a given
                        matrix # INPUT = a matrix (x) and the exponent
                        (n) # OUTPUT = the resulting exponentiated
                        matrix # # Alberto Monteiro
                        (https://stat.ethz.ch/pipermail/ #
                        r-help/2007-May/131330.html) #
                        ___________________________________________________
                        # mExp - calculate the exponent of a given
                        matrix # INPUT = a matrix (x) and the exponent
                        (n) # OUTPUT = the resulting exponentiated
                        matrix # # Alberto Monteiro
                        (https://stat.ethz.ch/pipermail/ #
                        r-help/2007-May/131330.html) #
                        ___________________________________________________
                        Calculates the Exponent of a Matrix
netOrder                ## Function to order the nodes in a Network in
                        enaR ## Singh P. | July 2014 ## ---------- ##
                        Function to order the nodes in a Network in
                        enaR ## Singh P. | July 2014 ## ---------- ##
                        Function to order the nodes in a Network in
                        enaR ## Singh P. | July 2014 ## ----------
                        Reorder Nodes in a Network in enaR
oyster                  Intertidal Oyster Reef Ecosystem Model
pack                    Compile Network Information into a Network
                        Class
read.EcoNet             ### MKLau 1Mar2016 Read an EcoNet model.
read.enam               R function to read in a matrix formatted as
                        Mdloti (Ursula Sharler) Borrett | Sept. 12,
                        2012, MKL July 2013 Updated - Borrett, May 2016
                        - to use pack() to create the network data
                        object. ------ R function to read in a matrix
                        formatted as Mdloti (Ursula Sharler) Borrett |
                        Sept. 12, 2012, MKL July 2013 Updated -
                        Borrett, May 2016 - to use pack() to create the
                        network data object. ------ R function to read
                        in a matrix formatted as Mdloti (Ursula
                        Sharler) Borrett | Sept. 12, 2012, MKL July
                        2013 Updated - Borrett, May 2016 - to use
                        pack() to create the network data object.
                        ------ Read ENA Model from an Mdloti Formatted
                        Excel File
read.nea                read.nea.RData INPUT = Model Data (flows,
                        inputs, outputs, storage) formatted as for
                        NEA.m, saved as CSV file S= |[F][z][X]|
                        |[y][0][0]| OUPUT = R Network data object for
                        use with enaR
read.scor               read.scor - SCOR formatted file into R in
                        multiple formats INPUT = file path OUTPUT =
                        network model in chosen format S. Borrett and
                        M. Lau | July 2011 -------- read.scor - SCOR
                        formatted file into R in multiple formats INPUT
                        = file path OUTPUT = network model in chosen
                        format S. Borrett and M. Lau | July 2011
                        -------- read.scor - SCOR formatted file into R
                        in multiple formats INPUT = file path OUTPUT =
                        network model in chosen format S. Borrett and
                        M. Lau | July 2011 -------- Read SCOR Formatted
                        Model
read.wand               read.wand - WAND formatted file into R INPUT =
                        file path OUTPUT = network object S. Borrett |
                        May 2012 -------- read.wand - WAND formatted
                        file into R INPUT = file path OUTPUT = network
                        object S. Borrett | May 2012 -------- read.wand
                        - WAND formatted file into R INPUT = file path
                        OUTPUT = network object S. Borrett | May 2012
                        -------- Read WAND Formatted Model
relationalChange        Relational change compared between two
                        matrices.
scc                     scc - find the strongly connected component
                        INPUT = an adjacency matrix OUTPUT = list of
                        membership and values S. Borrett | July 2011
                        -------- scc - find the strongly connected
                        component INPUT = an adjacency matrix OUTPUT =
                        list of membership and values S. Borrett | July
                        2011 -------- scc - find the strongly connected
                        component INPUT = an adjacency matrix OUTPUT =
                        list of membership and values S. Borrett | July
                        2011 -------- Find the Strongly Connected
                        Component (SCC) in a Graph
scifix                  scifix - corrects missing e or E in scientific
                        notation INPUT = scalar either in or not in
                        scientific notation OUTPUT = corrected numeric
                        value M. Lau | July 2012 -------- scifix -
                        corrects missing e or E in scientific notation
                        INPUT = scalar either in or not in scientific
                        notation OUTPUT = corrected numeric value M.
                        Lau | July 2012 -------- scifix - corrects
                        missing e or E in scientific notation INPUT =
                        scalar either in or not in scientific notation
                        OUTPUT = corrected numeric value M. Lau | July
                        2012 -------- Standardizes Scientific Notation
                        from SCOR Formatted Files
set.orient              set.orient - globally reorients matrices INPUT
                        = matrix orientation (rc or cr) OUTPUT = sets
                        the expected orientation of matrices
signs                   Signs and summary of input matrix
ssCheck                 ssCheck - checks if the given network is out of
                        balance by a given tolerance threshold INPUT =
                        network object OUTPUT = logical indicating
                        violation of tolerance NOTE: used in the
                        balancing process M. Lau | July 2011 --------
                        ssCheck - checks if the given network is out of
                        balance by a given tolerance threshold INPUT =
                        network object OUTPUT = logical indicating
                        violation of tolerance NOTE: used in the
                        balancing process M. Lau | July 2011 --------
                        ssCheck - checks if the given network is out of
                        balance by a given tolerance threshold INPUT =
                        network object OUTPUT = logical indicating
                        violation of tolerance NOTE: used in the
                        balancing process M. Lau | July 2011 --------
                        Checks the Balance of Inputs and Outputs from a
                        Network
structure.statistics    structure.statistics - calculates structural
                        statistics INPUT = an adjacency matrix OUTPUT =
                        list of structural statistics S. Borrett | July
                        2011 -------- structure.statistics - calculates
                        structural statistics INPUT = an adjacency
                        matrix OUTPUT = list of structural statistics
                        S. Borrett | July 2011 --------
                        structure.statistics - calculates structural
                        statistics INPUT = an adjacency matrix OUTPUT =
                        list of structural statistics S. Borrett | July
                        2011 -------- Structural Statistics of an
                        Ecological Network
troModels               Trophic Models
unpack                  unpack - extracts network object into a list
                        INPUT = network object OUTPUT = list of network
                        model components S. Borrett and M. Lau | July
                        2011 -------- unpack - extracts network object
                        into a list INPUT = network object OUTPUT =
                        list of network model components S. Borrett and
                        M. Lau | July 2011 -------- unpack - extracts
                        network object into a list INPUT = network
                        object OUTPUT = list of network model
                        components S. Borrett and M. Lau | July 2011
                        -------- "Unpacks" the Network Object into
                        Separate Objects
write.EcoNet            ### MKLau 17nov2014 Write enaR models to an
                        EcoNet formatted file.
write.nea               ' write.nea.R INPUT = enaR network data object
                        Ouput = CSV formatted file with data arranged
                        as expected input for NEA.m
