# Tools for Ecological Network Analysis

## Documentation for package ‘enaR’ version 2.10.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

enaR-package | Tools for Ecological Network Analysis (ena)
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
EcoNetWeb | ### MKLau 31Mar2016 Access example EcoNet models from the EcoNet website.
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
enaModelInfo | Ecosystem Model Information
enaModels | Ecosystem Models
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
enaR | 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
ShannonDiversity | Shannon Diversity Metrics These are based on entropy and build Shannon and Weaver 1949
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
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
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