{\rtf1\adeflang1025\ansi\ansicpg1252\uc1\adeff31507\deff0\stshfdbch31505\stshfloch31506\stshfhich31506\stshfbi31507\deflang2057\deflangfe2057\themelang2057\themelangfe0\themelangcs0{\fonttbl{\f0\fbidi \froman\fcharset0\fprq2{\*\panose 02020603050405020304}Times New Roman;}{\f3\fbidi \froman\fcharset2\fprq2{\*\panose 05050102010706020507}Symbol;}
{\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;}{\f423\fbidi \froman\fcharset238\fprq2 Times New Roman CE;}{\f424\fbidi \froman\fcharset204\fprq2 Times New Roman Cyr;}
{\f426\fbidi \froman\fcharset161\fprq2 Times New Roman Greek;}{\f427\fbidi \froman\fcharset162\fprq2 Times New Roman Tur;}{\f428\fbidi \froman\fcharset177\fprq2 Times New Roman (Hebrew);}{\f429\fbidi \froman\fcharset178\fprq2 Times New Roman (Arabic);}
{\f430\fbidi \froman\fcharset186\fprq2 Times New Roman Baltic;}{\f431\fbidi \froman\fcharset163\fprq2 Times New Roman (Vietnamese);}{\f763\fbidi \froman\fcharset238\fprq2 Cambria Math CE;}{\f764\fbidi \froman\fcharset204\fprq2 Cambria Math Cyr;}
{\f766\fbidi \froman\fcharset161\fprq2 Cambria Math Greek;}{\f767\fbidi \froman\fcharset162\fprq2 Cambria Math Tur;}{\f770\fbidi \froman\fcharset186\fprq2 Cambria Math Baltic;}{\f771\fbidi \froman\fcharset163\fprq2 Cambria Math (Vietnamese);}
{\f793\fbidi \fswiss\fcharset238\fprq2 Calibri CE;}{\f794\fbidi \fswiss\fcharset204\fprq2 Calibri Cyr;}{\f796\fbidi \fswiss\fcharset161\fprq2 Calibri Greek;}{\f797\fbidi \fswiss\fcharset162\fprq2 Calibri Tur;}
{\f798\fbidi \fswiss\fcharset177\fprq2 Calibri (Hebrew);}{\f799\fbidi \fswiss\fcharset178\fprq2 Calibri (Arabic);}{\f800\fbidi \fswiss\fcharset186\fprq2 Calibri Baltic;}{\f801\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);}}
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{\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 \af31507\afs22\alang1025 \ltrch\fcs0 
\fs22\lang2057\langfe2057\loch\af31506\hich\af31506\dbch\af31505\cgrid\langnp2057\langfenp2057 {\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid8682133 \hich\af37\dbch\af31505\loch\f37 MATLAB/Octave package}{\rtlch\fcs1 \af37 
\ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid8682133 
\par \hich\af37\dbch\af31505\loch\f37 Below are definitions of all output/input/defined-in-file objects, and files for different model variants. 
\par }{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid8682133 \hich\af37\dbch\af31505\loch\f37 A. Prep files
\par \hich\af37\dbch\af31505\loch\f37 Prep pop density input from fluscape data:}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid8682133 
\par }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\cf19\lang9\langfe2057\langnp9\insrsid8682133 \hich\af37\dbch\af31505\loch\f37 [Df,xf,yf]=lscanplot(lscan,fluscapeLocations);}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid8682133 
\par \hich\af37\dbch\af31505\loch\f37 If using pixelated transect:
\par }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\cf19\lang9\langfe2057\langnp9\insrsid8682133 \hich\af37\dbch\af31505\loch\f37 [Ds,Is]=selectSubgrid(Df,xf,yf)}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid8682133 
\par \hich\af37\dbch\af31505\loch\f37 Else just need a grid of pop densities (lscan)
\par }{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid8682133 \hich\af37\dbch\af31505\loch\f37 Prep objects for simulation:}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid8682133 
\par }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\cf19\lang9\langfe2057\langnp9\insrsid8682133 \hich\af37\dbch\af31505\loch\f37 [gamma,NN,n,nbar,na,NNbar,NNrep,minNind,maxNind,maxN,Kbar,K1,Cbar,betaS,betaI,betaD,ages0]=prepFluSub(lscan,R0,stoch,ce
\hich\af37\dbch\af31505\loch\f37 llSet); }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid8682133 \hich\af37\dbch\af31505\loch\f37 (using pixealted fluscape transect)
\par \hich\af37\dbch\af31505\loch\f37 OR }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\cf19\lang9\langfe2057\langnp9\insrsid8682133 \hich\af37\dbch\af31505\loch\f37 =prepFlu(lscan,R0,stoch); }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid8682133 
\hich\af37\dbch\af31505\loch\f37 (using grid: Df or lscan)
\par \hich\af37\dbch\af31505\loch\f37 Generates all objects needed to simulate:
\par {\pntext\pard\plain\ltrpar \rtlch\fcs1 \af37\afs22 \ltrch\fcs0 \f3\fs22\lang9\langfe2057\langnp9 \loch\af3\dbch\af31505\hich\f3 \'b7\tab}}\pard \ltrpar\ql \fi-360\li720\ri0\sa200\sl276\slmult1\nowidctlpar\wrapdefault{\*\pn \pnlvlblt\ilvl0\ls1\pnrnot0
\pnf3 {\pntxtb \'b7}}\faauto\ls1\rin0\lin720\itap0\pararsid10187631 {\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid8682133 \hich\af37\dbch\af31505\loch\f37     gamma (recovery rate): defined in the code, and outputted to workspace

\par {\pntext\pard\plain\ltrpar \rtlch\fcs1 \af37\afs22 \ltrch\fcs0 \f3\fs22\lang9\langfe2057\langnp9 \loch\af3\dbch\af31505\hich\f3 \'b7\tab}\hich\af37\dbch\af31505\loch\f37     NN: vector of pixel populations\hich\af37\dbch\af31505\loch\f37 
 (counting down columns)
\par {\pntext\pard\plain\ltrpar \rtlch\fcs1 \af37\afs22 \ltrch\fcs0 \f3\fs22\lang9\langfe2057\langnp9 \loch\af3\dbch\af31505\hich\f3 \'b7\tab}\hich\af37\dbch\af31505\loch\f37     n: number of cells
\par {\pntext\pard\plain\ltrpar \rtlch\fcs1 \af37\afs22 \ltrch\fcs0 \f3\fs22\lang9\langfe2057\langnp9 \loch\af3\dbch\af31505\hich\f3 \'b7\tab}\hich\af37\dbch\af31505\loch\f37 
    NNbar: vector of populations by age (length 4n, first n entries are age-group 1 population of each pixel etc.)
\par {\pntext\pard\plain\ltrpar \rtlch\fcs1 \af37\afs22 \ltrch\fcs0 \f3\fs22\lang9\langfe2057\langnp9 \loch\af3\dbch\af31505\hich\f3 \'b7\tab}\hich\af37\dbch\af31505\loch\f37     NNrep: 4 copies of NN (same length as NNbar, but values are total population)

\par {\pntext\pard\plain\ltrpar \rtlch\fcs1 \af37\afs22 \ltrch\fcs0 \f3\fs22\lang9\langfe2057\langnp9 \loch\af3\dbch\af31505\hich\f3 \'b7\tab}\hich\af37\dbch\af31505\loch\f37    \hich\af37\dbch\af31505\loch\f37 
 minNind, maxNind: indices of min and max popualtion (or first occurence thereof) - excluding zeros? These are unused at present
\par {\pntext\pard\plain\ltrpar \rtlch\fcs1 \af37\afs22 \ltrch\fcs0 \f3\fs22\lang9\langfe2057\langnp9 \loch\af3\dbch\af31505\hich\f3 \'b7\tab}\hich\af37\dbch\af31505\loch\f37     maxN: maximum population of a given pixel - useful for plot axes
\par {\pntext\pard\plain\ltrpar \rtlch\fcs1 \af37\afs22 \ltrch\fcs0 \f3\fs22\lang9\langfe2057\langnp9 \loch\af3\dbch\af31505\hich\f3 \'b7\tab}\hich\af37\dbch\af31505\loch\f37     Kbar, K1, Cbar: expanded matrices for FOI (c.f. fi
\hich\af37\dbch\af31505\loch\f37 rst paper)
\par {\pntext\pard\plain\ltrpar \rtlch\fcs1 \af37\afs22 \ltrch\fcs0 \f3\fs22\lang9\langfe2057\langnp9 \loch\af3\dbch\af31505\hich\f3 \'b7\tab}\hich\af37\dbch\af31505\loch\f37 
    betaS, betaI, betaD: betas generated for given R_0, allowing for dependency on mobility assumption
\par {\pntext\pard\plain\ltrpar \rtlch\fcs1 \af37\afs22 \ltrch\fcs0 \f3\fs22\lang9\langfe2057\langnp9 \loch\af3\dbch\af31505\hich\f3 \'b7\tab}\hich\af37\dbch\af31505\loch\f37     ages0: initial age distribution (used in stochastic model)
\par }\pard \ltrpar\ql \li0\ri0\sa200\sl276\slmult1\nowidctlpar\wrapdefault\faauto\rin0\lin0\itap0 {\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid8682133 \hich\af37\dbch\af31505\loch\f37 Inputs:
\par {\pntext\pard\plain\ltrpar \rtlch\fcs1 \af37\afs22 \ltrch\fcs0 \f3\fs22\lang9\langfe2057\langnp9 \loch\af3\dbch\af31505\hich\f3 \'b7\tab}}\pard \ltrpar\ql \fi-360\li720\ri0\sa200\sl276\slmult1\nowidctlpar\wrapdefault{\*\pn \pnlvlblt\ilvl0\ls1\pnrnot0
\pnf3 {\pntxtb \'b7}}\faauto\ls1\rin0\lin720\itap0\pararsid10187631 {\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid8682133 \hich\af37\dbch\af31505\loch\f37     lscan=Df OR Ds: grid of pop densities
\par {\pntext\pard\plain\ltrpar \rtlch\fcs1 \af37\afs22 \ltrch\fcs0 \f3\fs22\lang9\langfe2057\langnp9 \loch\af3\dbch\af31505\hich\f3 \'b7\tab}\hich\af37\dbch\af31505\loch\f37     R0: R_0
\par {\pntext\pard\plain\ltrpar \rtlch\fcs1 \af37\afs22 \ltrch\fcs0 \f3\fs22\lang9\langfe2057\langnp9 \loch\af3\dbch\af31505\hich\f3 \'b7\tab}\hich\af37\dbch\af31505\loch\f37 
    stoch: =0 for final size or ODE (solvetype=1/2), =1 if running stochastic comp. model (solvetype=3) - aged populations are rounded to integers
\par }\pard \ltrpar\ql \li0\ri0\sa200\sl276\slmult1\nowidctlpar\wrapdefault\faauto\rin0\lin0\itap0 {\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid8682133 \hich\af37\dbch\af31505\loch\f37 Defined in script:
\par {\pntext\pard\plain\ltrpar \rtlch\fcs1 \af37\afs22 \ltrch\fcs0 \f3\fs22\lang9\langfe2057\langnp9 \loch\af3\dbch\af31505\hich\f3 \'b7\tab}}\pard \ltrpar\ql \fi-360\li720\ri0\sa200\sl276\slmult1\nowidctlpar\wrapdefault{\*\pn \pnlvlblt\ilvl0\ls1\pnrnot0
\pnf3 {\pntxtb \'b7}}\faauto\ls1\rin0\lin720\itap0\pararsid10187631 {\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid8682133 \hich\af37\dbch\af31505\loch\f37 aa/alpha/p (a, alpha and p in offsety gravity kernel)
\par {\pntext\pard\plain\ltrpar \rtlch\fcs1 \af37\afs22 \ltrch\fcs0 \f3\fs22\lang9\langfe2057\langnp9 \loch\af3\dbch\af31505\hich\f3 \'b7\tab}\hich\af37\dbch\af31505\loch\f37 gamma
\par {\pntext\pard\plain\ltrpar \rtlch\fcs1 \af37\afs22 \ltrch\fcs0 \f3\fs22\lang9\langfe2057\langnp9 \loch\af3\dbch\af31505\hich\f3 \'b7\tab}\hich\af37\dbch\af31505\loch\f37 celldist: distance betw\hich\af37\dbch\af31505\loch\f37 een cells (km)
\par {\pntext\pard\plain\ltrpar \rtlch\fcs1 \af37\afs22 \ltrch\fcs0 \f3\fs22\lang9\langfe2057\langnp9 \loch\af3\dbch\af31505\hich\f3 \'b7\tab}\hich\af37\dbch\af31505\loch\f37 a1immobile: =1 to turn off mobility in children (naive option)
\par {\pntext\pard\plain\ltrpar \rtlch\fcs1 \af37\afs22 \ltrch\fcs0 \f3\fs22\lang9\langfe2057\langnp9 \loch\af3\dbch\af31505\hich\f3 \'b7\tab}\hich\af37\dbch\af31505\loch\f37 normaliseKernel: =1 for row=normalised K, =0 otherwise
\par {\pntext\pard\plain\ltrpar \rtlch\fcs1 \af37\afs22 \ltrch\fcs0 \f3\fs22\lang9\langfe2057\langnp9 \loch\af3\dbch\af31505\hich\f3 \'b7\tab}\hich\af37\dbch\af31505\loch\f37 
Cnum/Cdur: define age-mixing matrices (number and duration of contacts). Set C=Cnum/Cnum*Cdur/ones(4) for number/numb\hich\af37\dbch\af31505\loch\f37 
er x duration/age-off. Note: using more or fewer that 4 age-groups requires additional modifications to the code
\par }\pard \ltrpar\ql \li0\ri0\sa200\sl276\slmult1\nowidctlpar\wrapdefault\faauto\rin0\lin0\itap0 {\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid8682133 \hich\af37\dbch\af31505\loch\f37 Other options:
\par {\pntext\pard\plain\ltrpar \rtlch\fcs1 \af37\afs22 \ltrch\fcs0 \f3\fs22\lang9\langfe2057\langnp9 \loch\af3\dbch\af31505\hich\f3 \'b7\tab}}\pard \ltrpar\ql \fi-360\li720\ri0\sa200\sl276\slmult1\nowidctlpar\wrapdefault{\*\pn \pnlvlblt\ilvl0\ls1\pnrnot0
\pnf3 {\pntxtb \'b7}}\faauto\ls1\rin0\lin720\itap0\pararsid10187631 {\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid8682133 \hich\af37\dbch\af31505\loch\f37     prepFluAge - for non-uniform distribution of age
\par {\pntext\pard\plain\ltrpar \rtlch\fcs1 \af37\afs22 \ltrch\fcs0 \f3\fs22\lang9\langfe2057\langnp9 \loch\af3\dbch\af31505\hich\f3 \'b7\tab}\hich\af37\dbch\af31505\loch\f37     prepFluDE - delta and epsilon (c.f. first paper)
\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\insrsid8682133 \hich\af37\dbch\af31505\loch\f37 B. Simulation fil
\hich\af37\dbch\af31505\loch\f37 es}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid8682133 
\par }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\cf19\lang9\langfe2057\langnp9\insrsid8682133 \hich\af37\dbch\af31505\loch\f37 [f,g]=finalSizeMulti2sub(gamma,n,nbar,na,NN,NNbar,NNrep,minNind,maxNind,maxN,Kbar,K1,Cbar,betaS,betaI,betaD,isdual);}{\rtlch\fcs1 \af37 
\ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid8682133 
\par \hich\af37\dbch\af31505\loch\f37 OR }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\cf19\lang9\langfe2057\langnp9\insrsid8682133 \hich\af37\dbch\af31505\loch\f37 =finalSizeMulti();}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid8682133 
\par \hich\af37\dbch\af31505\loch\f37 Generates attack rates (f=season-specific, g=total immunity)
\par \hich\af37\dbch\af31505\loch\f37 Additional inputs (other than outputs of prep files):
\par {\pntext\pard\plain\ltrpar \rtlch\fcs1 \af37\afs22 \ltrch\fcs0 \f3\fs22\lang9\langfe2057\langnp9 \loch\af3\dbch\af31505\hich\f3 \'b7\tab}}\pard \ltrpar\ql \fi-360\li720\ri0\sa200\sl276\slmult1\nowidctlpar\wrapdefault{\*\pn \pnlvlblt\ilvl0\ls1\pnrnot0
\pnf3 {\pntxtb \'b7}}\faauto\ls1\rin0\lin720\itap0\pararsid10187631 {\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid8682133 \hich\af37\dbch\af31505\loch\f37     solvetype: =1/2/3 for FSC/ODE/SCM (finalSizeMulti only)
\par {\pntext\pard\plain\ltrpar \rtlch\fcs1 \af37\afs22 \ltrch\fcs0 \f3\fs22\lang9\langfe2057\langnp9 \loch\af3\dbch\af31505\hich\f3 \'b7\tab}\hich\af37\dbch\af31505\loch\f37     numseed (see below - currently an input in finalSizeMulti)
\par {\pntext\pard\plain\ltrpar \rtlch\fcs1 \af37\afs22 \ltrch\fcs0 \f3\fs22\lang9\langfe2057\langnp9 \loch\af3\dbch\af31505\hich\f3 \'b7\tab}\hich\af37\dbch\af31505\loch\f37     isdual: =0/1/2 for S/dual/I-mobility
\par }\pard \ltrpar\ql \li0\ri0\sa200\sl276\slmult1\nowidctlpar\wrapdefault\faauto\rin0\lin0\itap0 {\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid8682133 \hich\af37\dbch\af31505\loch\f37 Defined in script:
\par {\pntext\pard\plain\ltrpar \rtlch\fcs1 \af37\afs22 \ltrch\fcs0 \f3\fs22\lang9\langfe2057\langnp9 \loch\af3\dbch\af31505\hich\f3 \'b7\tab}}\pard \ltrpar\ql \fi-360\li720\ri0\sa200\sl276\slmult1\nowidctlpar\wrapdefault{\*\pn \pnlvlblt\ilvl0\ls1\pnrnot0
\pnf3 {\pntxtb \'b7}}\faauto\ls1\rin0\lin720\itap0\pararsid10187631 {\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid8682133 \hich\af37\dbch\af31505\loch\f37     eps: parameter for Prow2 (see below)
\par {\pntext\pard\plain\ltrpar \rtlch\fcs1 \af37\afs22 \ltrch\fcs0 \f3\fs22\lang9\langfe2057\langnp9 \loch\af3\dbch\af31505\hich\f3 \'b7\tab}\hich\af37\dbch\af31505\loch\f37     cross: cross im\hich\af37\dbch\af31505\loch\f37 munity
\par {\pntext\pard\plain\ltrpar \rtlch\fcs1 \af37\afs22 \ltrch\fcs0 \f3\fs22\lang9\langfe2057\langnp9 \loch\af3\dbch\af31505\hich\f3 \'b7\tab}\hich\af37\dbch\af31505\loch\f37     demog: =1 for aging on, =0 for aging off
\par {\pntext\pard\plain\ltrpar \rtlch\fcs1 \af37\afs22 \ltrch\fcs0 \f3\fs22\lang9\langfe2057\langnp9 \loch\af3\dbch\af31505\hich\f3 \'b7\tab}\hich\af37\dbch\af31505\loch\f37     amax: maximum age (cyclic aging)
\par {\pntext\pard\plain\ltrpar \rtlch\fcs1 \af37\afs22 \ltrch\fcs0 \f3\fs22\lang9\langfe2057\langnp9 \loch\af3\dbch\af31505\hich\f3 \'b7\tab}\hich\af37\dbch\af31505\loch\f37     tauend: number of consecutive seasons to simulate
\par {\pntext\pard\plain\ltrpar \rtlch\fcs1 \af37\afs22 \ltrch\fcs0 \f3\fs22\lang9\langfe2057\langnp9 \loch\af3\dbch\af31505\hich\f3 \'b7\tab}\hich\af37\dbch\af31505\loch\f37 
    plotTau: option to plot epi curve for a given year (=0 for no plot - useful for debugging)
\par {\pntext\pard\plain\ltrpar \rtlch\fcs1 \af37\afs22 \ltrch\fcs0 \f3\fs22\lang9\langfe2057\langnp9 \loch\af3\dbch\af31505\hich\f3 \'b7\tab}\hich\af37\dbch\af31505\loch\f37     tend\hich\af37\dbch\af31505\loch\f37 : time (days) to simulate for each epidemic

\par {\pntext\pard\plain\ltrpar \rtlch\fcs1 \af37\afs22 \ltrch\fcs0 \f3\fs22\lang9\langfe2057\langnp9 \loch\af3\dbch\af31505\hich\f3 \'b7\tab}\hich\af37\dbch\af31505\loch\f37     mu: death rate (in addition to demography - unused)
\par {\pntext\pard\plain\ltrpar \rtlch\fcs1 \af37\afs22 \ltrch\fcs0 \f3\fs22\lang9\langfe2057\langnp9 \loch\af3\dbch\af31505\hich\f3 \'b7\tab}\hich\af37\dbch\af31505\loch\f37 
    phi1, phi2: seasonality (phi=phi1-phi2 cos(pi t/180) - currently turned off in "integr8all")
\par {\pntext\pard\plain\ltrpar \rtlch\fcs1 \af37\afs22 \ltrch\fcs0 \f3\fs22\lang9\langfe2057\langnp9 \loch\af3\dbch\af31505\hich\f3 \'b7\tab}\hich\af37\dbch\af31505\loch\f37     numseed: seed proportion
\par {\pntext\pard\plain\ltrpar \rtlch\fcs1 \af37\afs22 \ltrch\fcs0 \f3\fs22\lang9\langfe2057\langnp9 \loch\af3\dbch\af31505\hich\f3 \'b7\tab}\hich\af37\dbch\af31505\loch\f37 
    Prow1, Prow2: Theta_1 and Theta_2 (modification required inside of loop for these objects to depend on year)
\par }\pard \ltrpar\ql \li0\ri0\sa200\sl276\slmult1\nowidctlpar\wrapdefault\faauto\rin0\lin0\itap0 {\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid8682133 \hich\af37\dbch\af31505\loch\f37 Other options:
\par {\pntext\pard\plain\ltrpar \rtlch\fcs1 \af37\afs22 \ltrch\fcs0 \f3\fs22\lang9\langfe2057\langnp9 \loch\af3\dbch\af31505\hich\f3 \'b7\tab}}\pard \ltrpar\ql \fi-360\li720\ri0\sa200\sl276\slmult1\nowidctlpar\wrapdefault{\*\pn \pnlvlblt\ilvl0\ls1\pnrnot0
\pnf3 {\pntxtb \'b7}}\faauto\ls1\rin0\lin720\itap0\pararsid10187631 {\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid8682133 \hich\af37\dbch\af31505\loch\f37 
    finalSizeMultiAge - for non-uniform distribution of age (requires prepFluAge)
\par {\pntext\pard\plain\ltrpar \rtlch\fcs1 \af31506\afs22 \ltrch\fcs0 \f3\fs22\lang9\langfe2057\langnp9\charrsid10187631 \loch\af3\dbch\af31505\hich\f3 \'b7\tab}}{\rtlch\fcs1 \af31506 \ltrch\fcs0 \lang9\langfe2057\langnp9\insrsid8682133\charrsid10187631 
\hich\af31506\dbch\af31505\loch\f31506     }{\rtlch\fcs1 \af31506 \ltrch\fcs0 \cf19\lang9\langfe2057\langnp9\insrsid8682133\charrsid10187631 \hich\af31506\dbch\af31505\loch\f31506 [f,g]=MA1D2sub(eps,cross): }{\rtlch\fcs1 \af31506 \ltrch\fcs0 
\lang9\langfe2057\langnp9\insrsid8682133\charrsid10187631 \hich\af31506\dbch\af31505\loch\f31506 1D 2-subtype model (with population 1)
\par }\pard \ltrpar\ql \li0\ri0\sa200\sl276\slmult1\nowidctlpar\wrapdefault\faauto\rin0\lin0\itap0 {\rtlch\fcs1 \ab\af31506 \ltrch\fcs0 \b\lang9\langfe2057\langnp9\insrsid8682133\charrsid10187631 \hich\af31506\dbch\af31505\loch\f31506 C. Plotting files}{
\rtlch\fcs1 \af31506 \ltrch\fcs0 \lang9\langfe2057\langnp9\insrsid8682133\charrsid10187631 
\par \hich\af31506\dbch\af31505\loch\f31506 FYI - these are the files that are most often messed with for specific occasions.
\par }\pard \ltrpar\ql \li0\ri0\widctlpar\wrapdefault\faauto\rin0\lin0\itap0\pararsid14176871 {\rtlch\fcs1 \af31506 \ltrch\fcs0 \cf20\insrsid14176871\charrsid13458640 \hich\af31506\dbch\af31505\loch\f31506 t}{\rtlch\fcs1 \af31506 \ltrch\fcs0 
\cf20\insrsid10187631\charrsid13458640 \hich\af31506\dbch\af31505\loch\f31506 ransectplo}{\rtlch\fcs1 \af31506 \ltrch\fcs0 \cf1\insrsid10187631\charrsid10187631 \hich\af31506\dbch\af31505\loch\f31506 t}{\rtlch\fcs1 \af31506 \ltrch\fcs0 
\cf1\insrsid14176871 \hich\af31506\dbch\af31505\loch\f31506 : plot the pixelated transect and fluscape locations, with remainer of rectangle shade\hich\af31506\dbch\af31505\loch\f31506 d blue.
\par }{\rtlch\fcs1 \af31506 \ltrch\fcs0 \insrsid14176871\charrsid14176871 
\par }\pard \ltrpar\ql \li0\ri0\sa200\sl276\slmult1\nowidctlpar\wrapdefault\faauto\rin0\lin0\itap0 {\rtlch\fcs1 \af31506 \ltrch\fcs0 \cf19\lang9\langfe2057\langnp9\insrsid8682133\charrsid10187631 \hich\af31506\dbch\af31505\loch\f31506 trimbyk}{\rtlch\fcs1 
\af31506 \ltrch\fcs0 \lang9\langfe2057\langnp9\insrsid8682133\charrsid10187631 \hich\af31506\dbch\af31505\loch\f31506 : for square grid only, takes vector of attack rates and dimensions of original grid and removes k-thick bound
\hich\af31506\dbch\af31505\loch\f31506 ary (k defined in code), returning new population and attack rate vectors. Called in plotAR, but must be commented out for non-rectangular inputs.
\par }{\rtlch\fcs1 \af31506 \ltrch\fcs0 \cf19\lang9\langfe2057\langnp9\insrsid8682133\charrsid10187631 \hich\af31506\dbch\af31505\loch\f31506 plotAR}{\rtlch\fcs1 \af31506 \ltrch\fcs0 \lang9\langfe2057\langnp9\insrsid8682133\charrsid10187631 
\hich\af31506\dbch\af31505\loch\f31506 : Plot for single column of }{\rtlch\fcs1 \af31506 \ltrch\fcs0 \cf19\lang9\langfe2057\langnp9\insrsid8682133\charrsid10187631 \hich\af31506\dbch\af31505\loch\f31506 finalSizeMulti}{\rtlch\fcs1 \af31506 \ltrch\fcs0 
\lang9\langfe2057\langnp9\insrsid8682133\charrsid10187631 \hich\af31506\dbch\af31505\loch\f31506  output (f or g - same for pandemic case). Plots singe vector\hich\af31506\dbch\af31505\loch\f31506  of attack rates against log population.
\par }{\rtlch\fcs1 \af31506 \ltrch\fcs0 \cf19\lang9\langfe2057\langnp9\insrsid8682133\charrsid10187631 \hich\af31506\dbch\af31505\loch\f31506 plotMA}{\rtlch\fcs1 \af31506 \ltrch\fcs0 \lang9\langfe2057\langnp9\insrsid8682133\charrsid10187631 
\hich\af31506\dbch\af31505\loch\f31506 : Plot for}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid8682133 \hich\af37\dbch\af31505\loch\f37  multiple columns of }{\rtlch\fcs1 \af37 \ltrch\fcs0 
\f37\cf19\lang9\langfe2057\langnp9\insrsid8682133 \hich\af37\dbch\af31505\loch\f37 finalSizeMulti}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid8682133 \hich\af37\dbch\af31505\loch\f37 
 outputs (A=f, Acum=g). Plots single-subtype model output as time series, option to plot only a sample of cells. Colormap shows log population density.
\par }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\cf19\lang9\langfe2057\langnp9\insrsid8682133 \hich\af37\dbch\af31505\loch\f37 plotMAnospac\hich\af37\dbch\af31505\loch\f37 e}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid8682133 
\hich\af37\dbch\af31505\loch\f37 : plot for output of }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\cf19\lang9\langfe2057\langnp9\insrsid8682133 \hich\af37\dbch\af31505\loch\f37 MA1D2sub}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid8682133 
\hich\af37\dbch\af31505\loch\f37  (Asus=f, Arec=g). Set ar=1 for season-specific attack, ar=0 for susceptibility profiles.
\par }{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\cf19\lang9\langfe2057\langnp9\insrsid8682133 \hich\af37\dbch\af31505\loch\f37 plotMAspace}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid8682133 \hich\af37\dbch\af31505\loch\f37 
: plot for finalSizeMulti2sub (Asus=f, Arec=g). Only plots season-specific attack.
\par \hich\af37\dbch\af31505\loch\f37 There are more files entitled "plotSomethi\hich\af37\dbch\af31505\loch\f37 ng.m" - see filenames/descriptions in the comments for details.
\par }{\rtlch\fcs1 \ab\af37 \ltrch\fcs0 \b\f37\lang9\langfe2057\langnp9\insrsid8682133 \hich\af37\dbch\af31505\loch\f37 X. Other applications}{\rtlch\fcs1 \af37 \ltrch\fcs0 \f37\lang9\langfe2057\langnp9\insrsid8682133 
\par \hich\af37\dbch\af31505\loch\f37 All files starting with "RP" use a modification of the above model that gives mean-field approximations of the behaviour of epidemics on spatially embedded networks. }{\rtlch\fcs1 \af37 \ltrch\fcs0 
\f37\lang9\langfe2057\langnp9\insrsid8682133 
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