From 70328b4a1510e4051b9ca75991a9576b75396ab8 Mon Sep 17 00:00:00 2001 From: dhaw Date: Fri, 28 Feb 2020 16:07:52 +0000 Subject: [PATCH] Add files via upload --- Read me Sub Exp.rtf | 296 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 296 insertions(+) create mode 100644 Read me Sub Exp.rtf diff --git a/Read me Sub Exp.rtf b/Read me Sub Exp.rtf new file mode 100644 index 0000000..5ac33d8 --- /dev/null +++ b/Read me Sub Exp.rtf @@ -0,0 +1,296 @@ +{\rtf1\adeflang1025\ansi\ansicpg1252\uc1\adeff0\deff0\stshfdbch31505\stshfloch31506\stshfhich31506\stshfbi0\deflang2057\deflangfe2057\themelang2057\themelangfe0\themelangcs0{\fonttbl{\f0\fbidi \froman\fcharset0\fprq2{\*\panose 02020603050405020304}Times New Roman;}{\f34\fbidi \froman\fcharset0\fprq2{\*\panose 02040503050406030204}Cambria Math;} +{\f37\fbidi \fswiss\fcharset0\fprq2{\*\panose 020f0502020204030204}Calibri;}{\flomajor\f31500\fbidi \froman\fcharset0\fprq2{\*\panose 02020603050405020304}Times New Roman;} +{\fdbmajor\f31501\fbidi \froman\fcharset0\fprq2{\*\panose 02020603050405020304}Times New Roman;}{\fhimajor\f31502\fbidi \fswiss\fcharset0\fprq2{\*\panose 020f0302020204030204}Calibri Light;} +{\fbimajor\f31503\fbidi \froman\fcharset0\fprq2{\*\panose 02020603050405020304}Times New Roman;}{\flominor\f31504\fbidi \froman\fcharset0\fprq2{\*\panose 02020603050405020304}Times New Roman;} +{\fdbminor\f31505\fbidi \froman\fcharset0\fprq2{\*\panose 02020603050405020304}Times New Roman;}{\fhiminor\f31506\fbidi \fswiss\fcharset0\fprq2{\*\panose 020f0502020204030204}Calibri;} +{\fbiminor\f31507\fbidi \froman\fcharset0\fprq2{\*\panose 02020603050405020304}Times New Roman;}{\f461\fbidi \froman\fcharset238\fprq2 Times New Roman CE;}{\f462\fbidi \froman\fcharset204\fprq2 Times New Roman Cyr;} +{\f464\fbidi \froman\fcharset161\fprq2 Times New Roman Greek;}{\f465\fbidi \froman\fcharset162\fprq2 Times New Roman Tur;}{\f466\fbidi \froman\fcharset177\fprq2 Times New Roman (Hebrew);}{\f467\fbidi \froman\fcharset178\fprq2 Times New Roman (Arabic);} +{\f468\fbidi \froman\fcharset186\fprq2 Times New Roman Baltic;}{\f469\fbidi \froman\fcharset163\fprq2 Times New Roman (Vietnamese);}{\f801\fbidi \froman\fcharset238\fprq2 Cambria Math CE;}{\f802\fbidi \froman\fcharset204\fprq2 Cambria Math Cyr;} +{\f804\fbidi \froman\fcharset161\fprq2 Cambria Math Greek;}{\f805\fbidi \froman\fcharset162\fprq2 Cambria Math Tur;}{\f808\fbidi \froman\fcharset186\fprq2 Cambria Math Baltic;}{\f809\fbidi \froman\fcharset163\fprq2 Cambria Math (Vietnamese);} +{\f831\fbidi \fswiss\fcharset238\fprq2 Calibri CE;}{\f832\fbidi \fswiss\fcharset204\fprq2 Calibri Cyr;}{\f834\fbidi \fswiss\fcharset161\fprq2 Calibri Greek;}{\f835\fbidi \fswiss\fcharset162\fprq2 Calibri Tur;} +{\f836\fbidi \fswiss\fcharset177\fprq2 Calibri (Hebrew);}{\f837\fbidi \fswiss\fcharset178\fprq2 Calibri (Arabic);}{\f838\fbidi \fswiss\fcharset186\fprq2 Calibri Baltic;}{\f839\fbidi \fswiss\fcharset163\fprq2 Calibri (Vietnamese);} +{\flomajor\f31508\fbidi \froman\fcharset238\fprq2 Times New Roman CE;}{\flomajor\f31509\fbidi \froman\fcharset204\fprq2 Times New Roman Cyr;}{\flomajor\f31511\fbidi \froman\fcharset161\fprq2 Times New Roman Greek;} +{\flomajor\f31512\fbidi \froman\fcharset162\fprq2 Times New Roman Tur;}{\flomajor\f31513\fbidi \froman\fcharset177\fprq2 Times New Roman (Hebrew);}{\flomajor\f31514\fbidi \froman\fcharset178\fprq2 Times New Roman (Arabic);} +{\flomajor\f31515\fbidi \froman\fcharset186\fprq2 Times New Roman Baltic;}{\flomajor\f31516\fbidi \froman\fcharset163\fprq2 Times New Roman (Vietnamese);}{\fdbmajor\f31518\fbidi \froman\fcharset238\fprq2 Times New Roman CE;} +{\fdbmajor\f31519\fbidi \froman\fcharset204\fprq2 Times New Roman Cyr;}{\fdbmajor\f31521\fbidi \froman\fcharset161\fprq2 Times New Roman Greek;}{\fdbmajor\f31522\fbidi \froman\fcharset162\fprq2 Times New Roman Tur;} +{\fdbmajor\f31523\fbidi \froman\fcharset177\fprq2 Times New Roman (Hebrew);}{\fdbmajor\f31524\fbidi \froman\fcharset178\fprq2 Times New Roman (Arabic);}{\fdbmajor\f31525\fbidi \froman\fcharset186\fprq2 Times New Roman Baltic;} +{\fdbmajor\f31526\fbidi \froman\fcharset163\fprq2 Times New Roman (Vietnamese);}{\fhimajor\f31528\fbidi \fswiss\fcharset238\fprq2 Calibri Light CE;}{\fhimajor\f31529\fbidi \fswiss\fcharset204\fprq2 Calibri Light Cyr;} +{\fhimajor\f31531\fbidi \fswiss\fcharset161\fprq2 Calibri Light Greek;}{\fhimajor\f31532\fbidi \fswiss\fcharset162\fprq2 Calibri Light Tur;}{\fhimajor\f31533\fbidi \fswiss\fcharset177\fprq2 Calibri Light (Hebrew);} +{\fhimajor\f31534\fbidi \fswiss\fcharset178\fprq2 Calibri Light (Arabic);}{\fhimajor\f31535\fbidi \fswiss\fcharset186\fprq2 Calibri Light Baltic;}{\fhimajor\f31536\fbidi \fswiss\fcharset163\fprq2 Calibri Light (Vietnamese);} +{\fbimajor\f31538\fbidi \froman\fcharset238\fprq2 Times New Roman CE;}{\fbimajor\f31539\fbidi \froman\fcharset204\fprq2 Times New Roman Cyr;}{\fbimajor\f31541\fbidi \froman\fcharset161\fprq2 Times New Roman Greek;} +{\fbimajor\f31542\fbidi \froman\fcharset162\fprq2 Times New Roman Tur;}{\fbimajor\f31543\fbidi \froman\fcharset177\fprq2 Times New Roman (Hebrew);}{\fbimajor\f31544\fbidi \froman\fcharset178\fprq2 Times New Roman (Arabic);} +{\fbimajor\f31545\fbidi \froman\fcharset186\fprq2 Times New Roman Baltic;}{\fbimajor\f31546\fbidi \froman\fcharset163\fprq2 Times New Roman (Vietnamese);}{\flominor\f31548\fbidi \froman\fcharset238\fprq2 Times New Roman CE;} +{\flominor\f31549\fbidi \froman\fcharset204\fprq2 Times New Roman Cyr;}{\flominor\f31551\fbidi \froman\fcharset161\fprq2 Times New Roman Greek;}{\flominor\f31552\fbidi \froman\fcharset162\fprq2 Times New Roman Tur;} +{\flominor\f31553\fbidi \froman\fcharset177\fprq2 Times New Roman (Hebrew);}{\flominor\f31554\fbidi \froman\fcharset178\fprq2 Times New Roman (Arabic);}{\flominor\f31555\fbidi \froman\fcharset186\fprq2 Times New Roman Baltic;} +{\flominor\f31556\fbidi \froman\fcharset163\fprq2 Times New Roman (Vietnamese);}{\fdbminor\f31558\fbidi \froman\fcharset238\fprq2 Times New Roman CE;}{\fdbminor\f31559\fbidi \froman\fcharset204\fprq2 Times New Roman Cyr;} +{\fdbminor\f31561\fbidi \froman\fcharset161\fprq2 Times New Roman Greek;}{\fdbminor\f31562\fbidi \froman\fcharset162\fprq2 Times New Roman Tur;}{\fdbminor\f31563\fbidi \froman\fcharset177\fprq2 Times New Roman (Hebrew);} +{\fdbminor\f31564\fbidi \froman\fcharset178\fprq2 Times New Roman (Arabic);}{\fdbminor\f31565\fbidi \froman\fcharset186\fprq2 Times New Roman Baltic;}{\fdbminor\f31566\fbidi \froman\fcharset163\fprq2 Times New Roman (Vietnamese);} +{\fhiminor\f31568\fbidi \fswiss\fcharset238\fprq2 Calibri CE;}{\fhiminor\f31569\fbidi \fswiss\fcharset204\fprq2 Calibri Cyr;}{\fhiminor\f31571\fbidi \fswiss\fcharset161\fprq2 Calibri Greek;}{\fhiminor\f31572\fbidi \fswiss\fcharset162\fprq2 Calibri Tur;} +{\fhiminor\f31573\fbidi \fswiss\fcharset177\fprq2 Calibri (Hebrew);}{\fhiminor\f31574\fbidi \fswiss\fcharset178\fprq2 Calibri (Arabic);}{\fhiminor\f31575\fbidi \fswiss\fcharset186\fprq2 Calibri Baltic;} +{\fhiminor\f31576\fbidi \fswiss\fcharset163\fprq2 Calibri (Vietnamese);}{\fbiminor\f31578\fbidi \froman\fcharset238\fprq2 Times New Roman CE;}{\fbiminor\f31579\fbidi \froman\fcharset204\fprq2 Times New Roman Cyr;} +{\fbiminor\f31581\fbidi \froman\fcharset161\fprq2 Times New Roman Greek;}{\fbiminor\f31582\fbidi \froman\fcharset162\fprq2 Times New Roman Tur;}{\fbiminor\f31583\fbidi \froman\fcharset177\fprq2 Times New Roman (Hebrew);} +{\fbiminor\f31584\fbidi \froman\fcharset178\fprq2 Times New Roman (Arabic);}{\fbiminor\f31585\fbidi \froman\fcharset186\fprq2 Times New Roman Baltic;}{\fbiminor\f31586\fbidi \froman\fcharset163\fprq2 Times New Roman (Vietnamese);}} +{\colortbl;\red0\green0\blue0;\red0\green0\blue255;\red0\green255\blue255;\red0\green255\blue0;\red255\green0\blue255;\red255\green0\blue0;\red255\green255\blue0;\red255\green255\blue255;\red0\green0\blue128;\red0\green128\blue128;\red0\green128\blue0; 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+\widctlpar\wrapdefault\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0 \rtlch\fcs1 \af0\afs22\alang1025 \ltrch\fcs0 \fs22\lang2057\langfe2057\loch\f31506\hich\af31506\dbch\af31505\cgrid\langnp2057\langfenp2057 \snext11 \ssemihidden \sunhideused +Normal Table;}}{\*\rsidtbl \rsid743481\rsid789940\rsid1264154\rsid2714238\rsid3230796\rsid5788037\rsid5901157\rsid6760277\rsid7810240\rsid8593726\rsid8988318\rsid11082991\rsid11168090\rsid11427587\rsid11477496\rsid12536294\rsid13377225\rsid14574665 +\rsid14629458\rsid15492084\rsid15862538\rsid15998602\rsid16131051}{\mmathPr\mmathFont34\mbrkBin0\mbrkBinSub0\msmallFrac0\mdispDef1\mlMargin0\mrMargin0\mdefJc1\mwrapIndent1440\mintLim0\mnaryLim1}{\info{\operator David Haw} +{\creatim\yr2019\mo7\dy3\hr9\min47}{\revtim\yr2020\mo2\dy28\hr15\min48}{\version17}{\edmins8539}{\nofpages2}{\nofwords594}{\nofchars3012}{\nofcharsws3589}{\vern121}}{\*\xmlnstbl {\xmlns1 http://schemas.microsoft.com/office/word/2003/wordml}} +\paperw12240\paperh15840\margl1440\margr1440\margt1440\margb1440\gutter0\ltrsect +\widowctrl\ftnbj\aenddoc\trackmoves0\trackformatting1\donotembedsysfont0\relyonvml0\donotembedlingdata1\grfdocevents0\validatexml0\showplaceholdtext0\ignoremixedcontent0\saveinvalidxml0\showxmlerrors0\horzdoc\dghspace120\dgvspace120\dghorigin1701 +\dgvorigin1984\dghshow0\dgvshow3\jcompress\viewkind1\viewscale100\rsidroot15862538 \nouicompat \fet0{\*\wgrffmtfilter 2450}\nofeaturethrottle1\ilfomacatclnup0\ltrpar \sectd \ltrsect\linex0\sectdefaultcl\sectrsid15862538\sftnbj {\*\pnseclvl1 +\pnucrm\pnstart1\pnindent720\pnhang {\pntxta .}}{\*\pnseclvl2\pnucltr\pnstart1\pnindent720\pnhang {\pntxta .}}{\*\pnseclvl3\pndec\pnstart1\pnindent720\pnhang {\pntxta .}}{\*\pnseclvl4\pnlcltr\pnstart1\pnindent720\pnhang {\pntxta )}}{\*\pnseclvl5 +\pndec\pnstart1\pnindent720\pnhang {\pntxtb (}{\pntxta )}}{\*\pnseclvl6\pnlcltr\pnstart1\pnindent720\pnhang {\pntxtb (}{\pntxta )}}{\*\pnseclvl7\pnlcrm\pnstart1\pnindent720\pnhang {\pntxtb (}{\pntxta )}}{\*\pnseclvl8\pnlcltr\pnstart1\pnindent720\pnhang +{\pntxtb (}{\pntxta )}}{\*\pnseclvl9\pnlcrm\pnstart1\pnindent720\pnhang {\pntxtb (}{\pntxta )}}\pard\plain \ltrpar\ql \li0\ri0\sa200\sl276\slmult1\nowidctlpar\wrapdefault\faauto\rin0\lin0\itap0 \rtlch\fcs1 \af0\afs22\alang1025 \ltrch\fcs0 +\fs22\lang2057\langfe2057\loch\af31506\hich\af31506\dbch\af31505\cgrid\langnp2057\langfenp2057 {\rtlch\fcs1 \ab\af37\afs28 \ltrch\fcs0 \b\f37\fs28\ul\lang9\langfe2057\langnp9\insrsid11082991\charrsid13377225 \hich\af37\dbch\af31505\loch\f37 R code: +\par }{\rtlch\fcs1 \ab\af37\afs28 \ltrch\fcs0 \b\f37\fs28\ul\lang9\langfe2057\langnp9\insrsid15862538\charrsid789940 \hich\af37\dbch\af31505\loch\f37 Script: postProcessing.R +\par }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid15862538 \hich\af37\dbch\af31505\loch\f37 Source to produce .csv of summary stats for a set of simulations in working directory}{\rtlch\fcs1 \af37 \ltrch\fcs0 +\f37\lang9\langfe2057\langnp9\insrsid2714238 \hich\af37\dbch\af31505\loch\f37 . }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid15862538 +\par }{\rtlch\fcs1 \ab\af37\afs28 \ltrch\fcs0 \b\f37\fs28\ul\lang9\langfe2057\langnp9\insrsid15862538\charrsid789940 \hich\af37\dbch\af31505\loch\f37 Script: networkProcessing}{\rtlch\fcs1 \ab\af37\afs28 \ltrch\fcs0 +\b\f37\fs28\ul\lang9\langfe2057\langnp9\insrsid15998602 \hich\af37\dbch\af31505\loch\f37 .R}{\rtlch\fcs1 \ab\af37\afs28 \ltrch\fcs0 \b\f37\fs28\ul\lang9\langfe2057\langnp9\insrsid15862538\charrsid789940 +\par }\pard \ltrpar\ql \li0\ri0\sa200\sl276\slmult1\nowidctlpar\wrapdefault\faauto\rin0\lin0\itap0\pararsid15862538 {\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid15862538\charrsid15862538 \hich\af37\dbch\af31505\loch\f37 +RPdistributions\hich\af37\dbch\af31505\loch\f37 (Node_connection_within_household, Node_connection_between_household,}{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid15492084 \hich\af37\dbch\af31505\loch\f37 }{\rtlch\fcs1 +\ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid15862538\charrsid15862538 \hich\af37\dbch\af31505\loch\f37 fname)}{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid15862538 +\par }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid15862538\charrsid15862538 \hich\af37\dbch\af31505\loch\f37 Produces .csv of commuting distributions}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid15862538 +\par }{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid15862538\charrsid15862538 \hich\af37\dbch\af31505\loch\f37 RPHHnet(Node_connection_within_household,}{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 +\b\f37\lang9\langfe2057\langnp9\insrsid15492084 \hich\af37\dbch\af31505\loch\f37 }{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid15862538\charrsid15862538 \hich\af37\dbch\af31505\loch\f37 Node_connection_between_household,}{ +\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid15492084 \hich\af37\dbch\af31505\loch\f37 }{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid15862538\charrsid15862538 \hich\af37\dbch\af31505\loch\f37 fname) + +\par }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid15862538 \hich\af37\dbch\af31505\loch\f37 Produces .csv edge lists for HH-only}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid3230796 +\hich\af37\dbch\af31505\loch\f37 }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid15862538 \hich\af37\dbch\af31505\loch\f37 networks from Rda\hich\af37\dbch\af31505\loch\f37 ta files}{\rtlch\fcs1 \af37 \ltrch\fcs0 +\f37\lang9\langfe2057\langnp9\insrsid2714238 \hich\af37\dbch\af31505\loch\f37 . }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid15862538 +\par }{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid15862538\charrsid15862538 \hich\af37\dbch\af31505\loch\f37 RPcombine(Node_connection_within_household, Node_connection_between_household) +\par }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid15862538\charrsid15862538 \hich\af37\dbch\af31505\loch\f37 Produces single adjacency matrix for whole network as dgCMatrix}{\rtlch\fcs1 \af37 \ltrch\fcs0 +\f37\lang9\langfe2057\langnp9\insrsid3230796 .}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid2714238 \hich\af37\dbch\af31505\loch\f37 }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid15862538 +\par }{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid3230796\charrsid13377225 \hich\af37\dbch\af31505\loch\f37 RPmcluster(G,}{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid16131051 +\hich\af37\dbch\af31505\loch\f37 }{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid3230796\charrsid13377225 \hich\af37\dbch\af31505\loch\f37 N) +\par }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid3230796 \hich\af37\dbch\af31505\loch\f37 Produces clustering\hich\af37\dbch\af31505\loch\f37 coefficients up to order N for every node in }{\rtlch\fcs1 \af37 \ltrch\fcs0 +\f37\lang9\langfe2057\langnp9\insrsid13377225 \hich\af37\dbch\af31505\loch\f37 network represented by dgCMatrix G.}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid2714238 \hich\af37\dbch\af31505\loch\f37 }{\rtlch\fcs1 \af37 +\ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid3230796 +\par }{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid13377225\charrsid13377225 \hich\af37\dbch\af31505\loch\f37 R}{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid789940 \hich\af37\dbch\af31505\loch\f37 P}{ +\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid13377225\charrsid13377225 \hich\af37\dbch\af31505\loch\f37 mclusterSample}{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid16131051 +\hich\af37\dbch\af31505\loch\f37 (G, mmax, sampleNumber)}{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid13377225\charrsid13377225 +\par }\pard \ltrpar\ql \li0\ri0\sa200\sl276\slmult1\nowidctlpar\wrapdefault\faauto\rin0\lin0\itap0 {\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid13377225 \hich\af37\dbch\af31505\loch\f37 +Produces clustering coefficients up to order mmax for sampleNumber nodes in network represented by adjacency dgCMatrix G. Note: this }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid15492084 \hich\af37\dbch\af31505\loch\f37 algorithm}{ +\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid13377225 \hich\af37\dbch\af31505\loch\f37 corresponds to DHCMsampleSpeed in MATLAB/octave code.}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid16131051 +\hich\af37\dbch\af31505\loch\f37 Can be modified to produce summary statistics. }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid11082991 +\par }{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid789940\charrsid789940 \hich\af37\dbch\af31505\loch\f37 mNbr(G, vx1, mMore, vi) +\par }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid789940\charrsid789940 \hich\af37\dbch\af31505\loch\f37 Required for R}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid11168090 \hich\af37\dbch\af31505\loch\f37 P}{ +\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid789940\charrsid789940 \hich\af37\dbch\af31505\loch\f37 mclusterSample. +\par }{\rtlch\fcs1 \ab\af37\afs28 \ltrch\fcs0 \b\f37\fs28\ul\lang9\langfe2057\langnp9\insrsid11082991\charrsid13377225 \hich\af37\dbch\af31505\loch\f37 MATLAB/Octave code:}{\rtlch\fcs1 \ab\af37\afs28 \ltrch\fcs0 +\b\f37\fs28\ul\lang9\langfe2057\langnp9\insrsid11082991 +\par }{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid13377225\charrsid13377225 \hich\af37\dbch\af31505\loch\f37 R}{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid15492084 \hich\af37\dbch\af31505\loch\f37 P}{ +\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid13377225\charrsid13377225 \hich\af37\dbch\af31505\loch\f37 combine}{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid15492084 \hich\af37\dbch\af31505\loch\f37 +(G)}{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid13377225 +\par }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid15492084\charrsid15492084 \hich\af37\dbch\af31505\loch\f37 Input edge list (columns I,J). Prod\hich\af37\dbch\af31505\loch\f37 uces sparse adjacency matrix for a simple graph (binary, }{ +\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid12536294\charrsid15492084 \hich\af37\dbch\af31505\loch\f37 symmetric}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid15492084\charrsid15492084 +\hich\af37\dbch\af31505\loch\f37 , no self-loops)}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid16131051 .}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid15492084\charrsid15492084 +\par }{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid13377225 \hich\af37\dbch\af31505\loch\f37 DHCMall}{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid15492084 \hich\af37\dbch\af31505\loch\f37 (G,m)}{ +\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid13377225 +\par }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid1264154\charrsid1264154 \hich\af37\dbch\af31505\loch\f37 Calculates clustering coefficients up to order }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid1264154 +\hich\af37\dbch\af31505\loch\f37 m}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid1264154\charrsid1264154 \hich\af37\dbch\af31505\loch\f37 + for every node in network represented by G. Produces summary statistics as required by plotting functions. +\par }{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid13377225 \hich\af37\dbch\af31505\loch\f37 DH\hich\af37\dbch\af31505\loch\f37 CMsampling}{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid15492084 +\hich\af37\dbch\af31505\loch\f37 (G,m,sampleNumber)}{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid13377225 +\par }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid1264154\charrsid1264154 \hich\af37\dbch\af31505\loch\f37 Calculates clustering coefficients up to order }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid1264154 +\hich\af37\dbch\af31505\loch\f37 m}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid1264154\charrsid1264154 \hich\af37\dbch\af31505\loch\f37 for }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid1264154 +\hich\af37\dbch\af31505\loch\f37 sampleNumber nodes}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid1264154\charrsid1264154 \hich\af37\dbch\af31505\loch\f37 + in network represented by G. Produces summary statistics as required by plotting functions. }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid11427587 \hich\af37\dbch\af31505\loch\f37 \hich\f37 +If using Octave, statistics package is required (\'93}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid11427587\charrsid11427587 \hich\af37\dbch\af31505\loch\f37 pkg load stat\hich\af37\dbch\af31505\loch\f37 istics}{\rtlch\fcs1 \af37 +\ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid11427587 \loch\af37\dbch\af31505\hich\f37 \'94\loch\f37 ). }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid1264154\charrsid1264154 +\par }{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid13377225 \hich\af37\dbch\af31505\loch\f37 DHCMsamplingSpeed}{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid15492084 \hich\af37\dbch\af31505\loch\f37 +(G,m,sampleNumber)}{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid13377225 +\par }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid1264154\charrsid1264154 \hich\af37\dbch\af31505\loch\f37 Calculates clustering coefficients up to order }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid1264154 +\hich\af37\dbch\af31505\loch\f37 m}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid1264154\charrsid1264154 \hich\af37\dbch\af31505\loch\f37 for }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid1264154 +\hich\af37\dbch\af31505\loch\f37 sampleNumber nodes}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid1264154\charrsid1264154 \hich\af37\dbch\af31505\loch\f37 + in network represented by G. Produces summary statistics as required by plotting functions.}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid1264154 \hich\af37\dbch\af31505\loch\f37 This algorithm is \hich\af37\dbch\af31505\loch\f37 +slower on small networks but much faster on larger ones.}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid11427587 \hich\af37\dbch\af31505\loch\f37 \hich\f37 If using Octave, statistics package is required (\'93}{\rtlch\fcs1 \af37 +\ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid11427587\charrsid11427587 \hich\af37\dbch\af31505\loch\f37 pkg load statistics}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid11427587 \loch\af37\dbch\af31505\hich\f37 \'94\loch\f37 ). +}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid1264154\charrsid1264154 +\par }{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid15492084 \hich\af37\dbch\af31505\loch\f37 RpdiffAlphaProcessNets}{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid13377225 +\par }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid8988318\charrsid8988318 \hich\af37\dbch\af31505\loch\f37 Set to produce one network per alpha}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid11477496 +\hich\af37\dbch\af31505\loch\f37 }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid8988318\charrsid8988318 \hich\af37\dbch\af31505\loch\f37 value from C code output}{\rtlch\fcs1 \af37 \ltrch\fcs0 +\f37\lang9\langfe2057\langnp9\insrsid11477496 \hich\af37\dbch\af31505\loch\f37 (one simulation per alpha).}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid8988318\charrsid8988318 \hich\af37\dbch\af31505\loch\f37 Can be modif +\hich\af37\dbch\af31505\loch\f37 ied to input/loop through different parameter sets. }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid15492084\charrsid8988318 +\par }{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid15492084 \hich\af37\dbch\af31505\loch\f37 R}{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid8988318 \hich\af37\dbch\af31505\loch\f37 p}{\rtlch\fcs1 +\ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid15492084 \hich\af37\dbch\af31505\loch\f37 diffAlphaProcessEpis +\par }\pard \ltrpar\ql \li0\ri0\sa200\sl276\slmult1\nowidctlpar\wrapdefault\faauto\rin0\lin0\itap0\pararsid8988318 {\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid11477496 \hich\af37\dbch\af31505\loch\f37 +Set to produce f=peak size, g=final size, h=cell array of epidemic curves, one row per alpha and one column per run, }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid8988318\charrsid8988318 \hich\af37\dbch\af31505\loch\f37 +from C code output \hich\af37\dbch\af31505\loch\f37 for a given R* (Rs) and R0 range. X is a matrix}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid8988318 \hich\af37\dbch\af31505\loch\f37 (one row per alpha, one column per run)}{ +\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid8988318\charrsid8988318 \hich\af37\dbch\af31505\loch\f37 of R0 values}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid8988318 \hich\af37\dbch\af31505\loch\f37 + obtained}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid8988318\charrsid8988318 \hich\af37\dbch\af31505\loch\f37 \hich\f37 from R code \'93\loch\f37 \hich\f37 postProcessing.R\'94\loch\f37 +. Can be modified to input/loop through different parameter sets. }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid8988318 +\par }{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid5901157\charrsid5901157 \hich\af37\dbch\af31505\loch\f37 RpmclusPlotsError(cellMean) +\par }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid5901157 \hich\af37\dbch\af31505\loch\f37 +Plots CCm against alpha where cellMean is a 1 by a cell (a=number of alpha values). Each cell entry is a set of Cm summary statistics. If plotting for more }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid5788037 +\hich\af37\dbch\af31505\loch\f37 than}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid5901157 \hich\af37\dbch\af31505\loch\f37 one network, is }{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 +\b\f37\lang9\langfe2057\langnp9\insrsid5901157\charrsid5901157 \hich\af37\dbch\af31505\loch\f37 RPcellMean.m}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid5901157 \hich\af37\dbch\af31505\loch\f37 + to calculate mean values. Max clustering order is calculated from \hich\af37\dbch\af31505\loch\f37 cellMean\{1\}. All cell entries must be same size (i.e. to same order). }{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 +\b\f37\lang9\langfe2057\langnp9\insrsid2714238\charrsid2714238 \hich\af37\dbch\af31505\loch\f37 This was used to produce figure 4A.}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid2714238 \hich\af37\dbch\af31505\loch\f37 }{ +\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid5901157 +\par }{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid5901157\charrsid5901157 \hich\af37\dbch\af31505\loch\f37 RpcellMean.m +\par }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid5901157 \hich\af37\dbch\af31505\loch\f37 Calculates pointwise mean of corresponding entries in 3 cell arrays. Can be modified to calculate for arbitrary number of cells. +\par \hich\af37\dbch\af31505\loch\f37 RpincG\hich\af37\dbch\af31505\loch\f37 en2}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid5788037 \hich\af37\dbch\af31505\loch\f37 (yCell,cCell)}{\rtlch\fcs1 \af37 \ltrch\fcs0 +\f37\lang9\langfe2057\langnp9\insrsid5901157 +\par }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid2714238 \hich\af37\dbch\af31505\loch\f37 Plots peak size/final size against clustering of each order, with linear fit and 95% confidence intervals. }{\rtlch\fcs1 \af37 \ltrch\fcs0 +\f37\lang9\langfe2057\langnp9\insrsid5788037 \hich\af37\dbch\af31505\loch\f37 Inputs are n by 1 (or 1 by n) cell arrays with one entry per network. yCell\{i\}=[p,z] where p is a column vector of mean peak sizes a\hich\af37\dbch\af31505\loch\f37 +nd z a column vector of mean final sizes. cCell\{i\} is a 1 by a cell (a=number of alpha values), and each cell entry is a set of Cm summary statistics. }{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid7810240\charrsid2714238 +\hich\af37\dbch\af31505\loch\f37 This was used to produce figure}{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid7810240 \hich\af37\dbch\af31505\loch\f37 s}{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 +\b\f37\lang9\langfe2057\langnp9\insrsid7810240\charrsid2714238 \hich\af37\dbch\af31505\loch\f37 4}{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid7810240 \hich\af37\dbch\af31505\loch\f37 B and 4C}{\rtlch\fcs1 \ab\af37 +\ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid7810240\charrsid2714238 .}{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid2714238 +\par }{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid743481 +\par }\pard \ltrpar\ql \li0\ri0\sa200\sl276\slmult1\nowidctlpar\wrapdefault\faauto\rin0\lin0\itap0 {\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid743481 \hich\af37\dbch\af31505\loch\f37 +Note: plotting figures 1 and 2 is a straightforward task fro\hich\af37\dbch\af31505\loch\f37 m the outputs of postProcessing.\hich\af37\dbch\af31505\loch\f37 R}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid8988318\charrsid14629458 + +\par }{\*\themedata 504b030414000600080000002100e9de0fbfff0000001c020000130000005b436f6e74656e745f54797065735d2e786d6cac91cb4ec3301045f748fc83e52d4a +9cb2400825e982c78ec7a27cc0c8992416c9d8b2a755fbf74cd25442a820166c2cd933f79e3be372bd1f07b5c3989ca74aaff2422b24eb1b475da5df374fd9ad +5689811a183c61a50f98f4babebc2837878049899a52a57be670674cb23d8e90721f90a4d2fa3802cb35762680fd800ecd7551dc18eb899138e3c943d7e503b6 +b01d583deee5f99824e290b4ba3f364eac4a430883b3c092d4eca8f946c916422ecab927f52ea42b89a1cd59c254f919b0e85e6535d135a8de20f20b8c12c3b0 +0c895fcf6720192de6bf3b9e89ecdbd6596cbcdd8eb28e7c365ecc4ec1ff1460f53fe813d3cc7f5b7f020000ffff0300504b030414000600080000002100a5d6 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