added all sh (slurm) and R scripts outside scripts dir

GreysAnatomy/dkseries/generate_dk0_simulated_networks_slurm_script.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+
+#SBATCH --job-name="gensim_dk0"
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=1
+#SBATCH --cpus-per-task=1
+#SBATCH --time=0-0:10:00
+#SBATCH --output=gensim_dk0-%j.out
+#SBATCH --error=gensim_dk0-%j.err
+
+uname -a
+echo Started at `date`
+
+Rscript ../../scripts/generateSimulatedNetworksFromErdosRenyiModel.R greysanatomy_edgelist.txt simulated/dk0
+
+echo Ended at `date` 

GreysAnatomy/dkseries/generate_dkseries_simulated_networks_slurm_script.sh

@@ -0,0 +1,20 @@
+#!/bin/bash
+
+#SBATCH --job-name="gensim_dkseries"
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=1
+#SBATCH --cpus-per-task=1
+#SBATCH --time=0-0:10:00
+#SBATCH --output=gensim_dkseries-%j.out
+#SBATCH --error=gensim_dkseries-%j.err
+
+uname -a
+echo Started at `date`
+
+for dk in 0 1 2 2.1 2.5
+do
+    dk_no_period=`echo "${dk}" | sed 's/[.]//g'`
+    ../../scripts/generateSimulatedNetworksFromDKseries.sh $dk greysanatomy_edgelist.txt simulated/dk${dk_no_period}
+done
+
+echo Ended at `date` 

GreysAnatomy/dkseries/get_greysanatomy_data.R

@@ -0,0 +1,17 @@
+###
+### File:    get_greysanatomy_data.R
+### Author:  Alex Stivala
+### Created: May 2020
+###
+### Load the Greys Anataomyh network and convert to plain edgelist
+### (no attributes) for RandNetGen
+###
+
+library(statnet)
+
+source('../statnet_estimations/load_greysanatomy_data.R')
+
+grey.net <- load_greysanatomy_data()
+
+el <- as.edgelist(grey.net)-1 # convertt to 0-based not 1-based
+write.table(el, 'greysanatomy_edgelist.txt', col.names=F, row.names=F)

GreysAnatomy/dkseries/run_atomic_cyclelengdistribution_dkseries_slurm_script.sh

@@ -0,0 +1,42 @@
+#!/bin/bash
+
+#SBATCH --job-name="atomic_dkseries"
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=1
+#SBATCH --cpus-per-task=1
+#SBATCH --time=0-0:40:00
+#SBATCH --output=atomic_dkseries-%j.out
+#SBATCH --error=atomic_dkseries-%j.err
+
+uname -a
+echo Started at `date`
+
+SCRIPTDIR=../../scripts
+
+
+
+OBS_ATOMICCYCLETAB=greysanatomy_atomiccycletable.txt
+
+#
+# generate tables using  FindAtomicCycles
+# (only run if not exist; so to regneraet remove these files first)
+#
+
+if [ ! -f $OBS_ATOMICCYCLETAB ]; then 
+	time $SCRIPTDIR/makeSingleNetworkAtomicCycleLengthDistributionTable.sh greysanatomy_edgelist.txt > ${OBS_ATOMICCYCLETAB}
+fi
+
+
+for dk in 0 1 2 21 25
+do
+    ATOMICTAB=dk${dk}_atomiccycledisttable.txt
+    if [ ! -f $ATOMICTAB ]; then 
+    	time $SCRIPTDIR/makeAtomicCycleLengthDistributionTables.sh simulated/dk${dk}/ > ${ATOMICTAB}
+    fi
+    # generate plots from tables with R
+    dktitle=`echo $dk | sed 's/21/2.1/;s/25/2.5/'`
+    time Rscript $SCRIPTDIR/plotCycleLengthDistributionsFromTables.R "dk-series $dktitle k" 'geodesic cycle'  ${ATOMICTAB} ${OBS_ATOMICCYCLETAB}
+done
+
+
+echo Ended at `date` 

GreysAnatomy/dkseries/run_combined2_max_geodesic_cycle_plots_slurm_script.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+
+#SBATCH --job-name="plot_max_geodesic_cycle2"
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=1
+#SBATCH --cpus-per-task=1
+#SBATCH --mem-per-cpu=4GB
+#SBATCH --time=0-0:10:00
+#SBATCH --output=plot_max_geodesic_cycle2-%j.out
+#SBATCH --error=plot_max_geodesic_cycle2-%j.err
+
+uname -a
+echo Started at `date`
+
+module load r
+
+SCRIPTDIR=../../scripts
+
+
+Rscript $SCRIPTDIR/plotCombinedMaxCycleLengthDistributionsFromTables.R 'geodesic cycle' ../statnet_estimations/model5_geodesiccycledisttable.txt "dk*_geodesiccycledisttable.txt" greysanatomy_geodesiccycletable.txt greysanatomy_combined2_max_geodesic.eps
+
+echo Ended at `date` 

GreysAnatomy/dkseries/run_combined_max_geodesic_cycle_plots_slurm_script.sh

@@ -0,0 +1,20 @@
+#!/bin/bash
+
+#SBATCH --job-name="plot_max_geodesic_cycle"
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=1
+#SBATCH --cpus-per-task=1
+#SBATCH --mem-per-cpu=4GB
+#SBATCH --time=0-0:10:00
+#SBATCH --output=plot_max_geodesic_cycle-%j.out
+#SBATCH --error=plot_max_geodesic_cycle-%j.err
+
+uname -a
+echo Started at `date`
+
+SCRIPTDIR=../../scripts
+
+
+Rscript $SCRIPTDIR/plotCombinedMaxCycleLengthDistributionsFromTables.R 'geodesic cycle' ../statnet_estimations/model5_atomiccycledisttable.txt "dk*_atomiccycledisttable.txt" greysanatomy_atomiccycletable.txt greysanatomy_combined_max_geodesic.eps
+
+echo Ended at `date` 

GreysAnatomy/dkseries/run_geodesic_cyclelengdistribution_dkseries_slurm_script.sh

@@ -0,0 +1,42 @@
+#!/bin/bash
+
+#SBATCH --job-name="geodesic_dkseries"
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=1
+#SBATCH --cpus-per-task=1
+#SBATCH --time=0-0:40:00
+#SBATCH --output=geodesic_dkseries-%j.out
+#SBATCH --error=geodesic_dkseries-%j.err
+
+uname -a
+echo Started at `date`
+
+SCRIPTDIR=../../scripts
+
+module load r
+
+OBS_GEODESICCYCLETAB=greysanatomy_geodesiccycletable.txt
+
+#
+# generate tables using  FindGeodesicCycles
+# (only run if not exist; so to regneraet remove these files first)
+#
+
+if [ ! -f $OBS_GEODESICCYCLETAB ]; then 
+	time $SCRIPTDIR/makeSingleNetworkGeodesicCycleLengthDistributionTable.sh greysanatomy_edgelist.txt > ${OBS_GEODESICCYCLETAB}
+fi
+
+
+for dk in 0 1 2 21 25
+do
+    GEODESICTAB=dk${dk}_geodesiccycledisttable.txt
+    if [ ! -f $GEODESICTAB ]; then 
+    	time $SCRIPTDIR/makeGeodesicCycleLengthDistributionTables.sh simulated/dk${dk}/ > ${GEODESICTAB}
+    fi
+    # generate plots from tables with R
+    dktitle=`echo $dk | sed 's/21/2.1/;s/25/2.5/'`
+    time Rscript $SCRIPTDIR/plotCycleLengthDistributionsFromTables.R "dk-series $dktitle k" 'geodesic cycle'  ${GEODESICTAB} ${OBS_GEODESICCYCLETAB}
+done
+
+
+echo Ended at `date` 

GreysAnatomy/dkseries/run_simfit_plots_slurm_script.sh

@@ -0,0 +1,27 @@
+#!/bin/bash
+
+#SBATCH --job-name="gof"
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=1
+#SBATCH --cpus-per-task=1
+#SBATCH --mem-per-cpu=4GB
+#SBATCH --time=0-0:10:00
+#SBATCH --output=gof_simfit-%j.out
+#SBATCH --error=gof_simfit-%j.err
+
+uname -a
+echo Started at `date`
+
+SCRIPTDIR=../../scripts
+
+
+OBS_EDGELIST=greysanatomy_edgelist.txt
+
+time Rscript $SCRIPTDIR/plotUndirectedSimFit.R $OBS_EDGELIST "../statnet_estimations/simulated/model5/sim_model5_*_edgelist.txt" statnet_model5_simfit_gof.pdf
+
+for dk in 0 1 2 21 25
+do
+  time Rscript $SCRIPTDIR/plotUndirectedSimFit.R $OBS_EDGELIST "simulated/dk${dk}/sim_modeldk${dk}_*_edgelist.txt" dk${dk}_simfit_gof.pdf
+done
+
+echo Ended at `date` 

GreysAnatomy/statnet_estimations/generate_simulated_networks_mode11_slurm_script.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+
+#SBATCH --job-name="gensim_model1"
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=1
+#SBATCH --cpus-per-task=1
+#SBATCH --time=0-0:10:00
+#SBATCH --output=gensim_model1-%j.out
+#SBATCH --error=gensim_model1-%j.err
+
+uname -a
+echo Started at `date`
+
+/usr/bin/time Rscript ../../scripts/generateSimulatedNetworksFromStatnetModel.R  model1.RData simulated/model1
+
+echo Ended at `date` 

GreysAnatomy/statnet_estimations/generate_simulated_networks_mode15_slurm_script.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+
+#SBATCH --job-name="gensim_model5"
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=1
+#SBATCH --cpus-per-task=1
+#SBATCH --time=0-0:10:00
+#SBATCH --output=gensim_model5-%j.out
+#SBATCH --error=gensim_model5-%j.err
+
+uname -a
+echo Started at `date`
+
+/usr/bin/time Rscript ../../scripts/generateSimulatedNetworksFromStatnetModel.R  model5.RData simulated/model5
+
+echo Ended at `date` 

GreysAnatomy/statnet_estimations/load_greysanatomy_data.R

@@ -0,0 +1,30 @@
+###
+### File:    load_greysanatomy_data.R
+### Author:  Alex Stivala
+### Created: August 2019
+###
+### Load the Grey's Anatomy Hookups data and return statnet network object.
+### Code taken from 
+###  SNA in R Workshop
+###  Administered at the University of Southern California
+###  by Alex Leavitt & Joshua Clark
+###  PhD students at the Annenberg School for Communication & Journalism
+###   adapted from materials by Katya Ognyanova and the BadHessian blog
+### https://github.com/alexleavitt/SNAinRworkshop
+###
+
+library(statnet)
+
+
+load_greysanatomy_data <- function() {
+  ga.el<-read.table('../data/grey_edgelist.tsv', sep="\t", header=T, quote="\"",
+                    stringsAsFactors=F, strip.white=T, as.is=T)
+
+  ga.atts<-read.table('../data/grey_nodes.tsv', sep="\t", header=T, quote="\"",
+                       stringsAsFactors=F, strip.white=T, as.is=T)
+  grey.net<-network(ga.el, vertex.attr=ga.atts,
+                    vertex.attrnames=colnames(ga.atts), directed=F, hyper=F,
+                    loops=F, multiple=F, bipartite=F)
+return(grey.net)
+}
+

GreysAnatomy/statnet_estimations/plotGreysAnatomyNetwork.R

@@ -0,0 +1,35 @@
+#!/usr/bin/env Rscript
+###
+### File:    plotGreysAnatomyNetwork.R
+### Author:  Alex Stivala
+### Created: August 2019
+###
+### Make visualization of Greys Anatomy 'hookups' social network.
+###
+### code adapted from 
+###  SNA in R Workshop
+###  Administered at the University of Southern California
+###  by Alex Leavitt & Joshua Clark
+###  PhD students at the Annenberg School for Communication & Journalism
+###   adapted from materials by Katya Ognyanova and the BadHessian blog
+### https://github.com/alexleavitt/SNAinRworkshop
+### https://badhessian.org/2012/09/lessons-on-exponential-random-graph-modeling-from-greys-anatomy-hook-ups/
+###
+### Usage: plotGreysAnatomyNetwork.R
+###
+###
+### Output is to file
+###   'greysanatomy_network.eps'
+### WARNING: overwrites output files if they exist
+###
+
+
+source('load_greysanatomy_data.R')
+
+
+grey.net <- load_greysanatomy_data()
+summary(grey.net)
+postscript('greysanatomy_network.eps')
+plot(grey.net, vertex.col=c("blue","pink")[1+(get.vertex.attribute(grey.net, "sex")=="F")], label=get.vertex.attribute(grey.net, "name"), label.cex=.75)
+dev.off()
+

GreysAnatomy/statnet_estimations/run_cyclelengdistribution_model1_slurm_script.sh

@@ -0,0 +1,62 @@
+#!/bin/bash
+
+#SBATCH --job-name="cypath_model1"
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=1
+#SBATCH --cpus-per-task=1
+#SBATCH --time=0-0:10:00
+#SBATCH --output=cypath_model1-%j.out
+#SBATCH --error=cypath_model1-%j.err
+
+uname -a
+echo Started at `date`
+
+SCRIPTDIR=../../scripts
+
+ATOMICTAB=model1_atomiccycledisttable.txt
+CHORDLESSTAB=model1_chordlesscycledisttable.txt
+CYCLETAB=model1_cycledisttable.txt
+
+
+OBS_ATOMICCYCLETAB=greysanatomy_atomiccycletable.txt
+OBS_CHORDLESSCYCLETAB=greysanatomy_chordlesscycletable.txt
+OBS_CYCLETAB=greysanatomy_cycletable.txt
+
+#
+# generate tables using CYPATH or FindAtomicCycles
+# (only run if not exist; so to regneraet remove these files first)
+#
+if [ ! -f $ATOMICTAB ]; then 
+	time $SCRIPTDIR/makeAtomicCycleLengthDistributionTables.sh simulated/model1/ > ${ATOMICTAB}
+fi
+
+if [ ! -f $CHORDLESSTAB ]; then 
+	time $SCRIPTDIR/makeCycleLengthDistributionTables.sh C simulated/model1/ > ${CHORDLESSTAB}
+fi
+
+if [ ! -f $CYCLETAB ]; then 
+	time $SCRIPTDIR/makeCycleLengthDistributionTables.sh c simulated/model1 > ${CYCLETAB}
+fi
+
+if [ ! -f $OBS_ATOMICCYCLETAB ]; then 
+	time $SCRIPTDIR/makeSingleNetworkAtomicCycleLengthDistributionTable.sh greysanatomy_edgelist.txt > ${OBS_ATOMICCYCLETAB}
+fi
+
+if [ ! -f $OBS_CHORDLESSCYCLETAB ]; then 
+	time $SCRIPTDIR/makeSingleNetworkCycleLengthDistributionTable.sh C greysanatomy_edgelist.txt > ${OBS_CHORDLESSCYCLETAB}
+fi
+
+if [ ! -f $OBS_CYCLETAB ]; then 
+	time $SCRIPTDIR/makeSingleNetworkCycleLengthDistributionTable.sh c greysanatomy_edgelist.txt > ${OBS_CYCLETAB}
+fi
+
+#
+# generate plots from tables with R
+#
+time Rscript $SCRIPTDIR/plotCycleLengthDistributionsFromTables.R 'ERGM' 'geodesic cycle'  ${ATOMICTAB} ${OBS_ATOMICCYCLETAB}
+
+time Rscript $SCRIPTDIR/plotCycleLengthDistributionsFromTables.R 'ERGM' 'chordless cycle'  ${CHORDLESSTAB} ${OBS_CHORDLESSCYCLETAB}
+
+time Rscript $SCRIPTDIR/plotCycleLengthDistributionsFromTables.R 'ERGM' 'cycle'  ${CYCLETAB} ${OBS_CYCLETAB}
+
+echo Ended at `date`