#########################################################
# CoNet Cytoscape plugin settings file
#
# This setting file configures CoNet to compute the permutation random scores for
# the relative abundances of a biome.
#
# DATA
# QIIME DB preprocessed biome-specific matrices with relative abundances can be downloaded
# together with feature and metadata files at CoNet's web page:
# http://systemsbiology.vub.ac.be/conet (dataset section)
# Go to Datasets and download QIIME biome data.
#  
# CONFIGURATION
# Set matrix, features and metadata to their right locations using the Data menu and its metadata and features submenu.
# In the "Save" section of the Randomization menu, set the correct location for the randscorefile, into which random scores are saved.
# Alternatively, paths to all these files can be set to the correct locations in this settings file.
# Once you have run CoNet with this settings file, continue with the CoNetBiomeBootSettings.txt file to construct the final network.
#
# REPRODUCIBILITY
# Since network construction was run on the QIIME data, CoNet has been upgraded to beta status (which included a re-implementation of its core to make it faster).
# Networks constructed with CoNet beta reproduce previous networks with Jaccard indices around 0.5-0.6 (a perfect reproduction has a Jaccard index of 1).
# The R2 of positive edge percentages generated with CoNet beta versus CoNet alpha is 0.9.
# To better reproduce previous results, please use CoNet's alpha version available at http://systemsbiology.vub.ac.be/conet (download section).
# Note that the alpha version only runs on command line.
#
# WARNING
# Permutation with renormalization takes hours to compute for the bigger matrices (days with disabled speed-up). 
# For a quick test, you can reduce the iteration number.
# Set nantreatment to pairwise_omit if the biome features contain missing values. In such a case, also
# adjust the nantreatmentparam. The following number of missing-value free value pairs were
# set during biome-specific network construction:
# grasslands = 12
# coniferousforests = 32
# moistforests = 34
# tundra = 13
# intestine = 418
# oral cavity = 137
# skin = 486
# For EMP data, the following number of missing-value free pairs was set:
# canyon = 23
# cryocarb = 22
# volcano = 32
# For HMP data, the following number of missing-value free pairs was set:
# oral cavity houston = 534
# nasal cavity houston = 55
# intestine houston = 62
# skin houston = 151
# vagina houston = 76
# oral cavity stlouis = 268
# nasal cavity stlouis = 26
# intestine stlouis = 34
# skin stlouis = 111
# vagina stlouis = 38
#
# Author: Karoline Faust
#
# Date: 26/August/2013
#
#########################################################
matrixtype==abundance
input==tundra.txt
features==tundra-features.txt
metadata==tundra-metadata.txt
metadataattribs==kingdom/phylum/class/order/family/genus/species/lineage/taxon
delimiter==tab
lineage_separator==--
thresholdguessing==edgeNumber
guessingparam==1000.0
topbottom==true
method==ensemble
ensemblemethods==correl_pearson/correl_spearman/dist_bray/dist_kullbackleibler
networkmergestrategy==union
resamplemethod==shuffle_rows
randroutine==edgeScores
edgethreshold==0.05
randscorefile==tundra-permutations.txt
iterations==1000
filter==noinclusivetaxalinks/rand
renorm==true
multigraph==true
scoreexport==true
no_rserve==true
nantreatment==none
nantreatmentparam==1