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Make fixing mutation and migration a model parameter
Introduce gen_bias as a model parameter (was previously a TCL variable) Migration fix by accumulating as integral amounts between cells Fragmention pump model
1 parent 3a8d1b7 commit 785c6ac

6 files changed

Lines changed: 200 additions & 53 deletions

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‎models/SAR.py‎

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -37,6 +37,10 @@ def av(x):
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#mut_max=float(sys.argv[3]) # mutation rate
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#migration=float(sys.argv[4]) # initial migration rate
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40+
# for this experiment, do not mutate mutation or migration rates
41+
ecolab.fixMutation(True)
42+
ecolab.fixMigration(True)
43+
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print("Replicate, Area, Max mutation, Init. Mig, Init. num sp, Mutation rate, Migration rate, Number of species, Interaction strength^2",flush=True)
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for A in [1, 2, 4, 6, 9, 12, 16]:
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for mut_max in [1e-5, 1e-4, 1e-3]:

‎models/SAR.rvl‎

Lines changed: 70 additions & 37 deletions
Original file line numberDiff line numberDiff line change
@@ -3,64 +3,64 @@
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<minskyVersion>3.22.0</minskyVersion>
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<wires>
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<Wire>
6-
<id>46</id>
6+
<id>49</id>
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<from>21</from>
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<to>19</to>
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</Wire>
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<Wire>
11-
<id>47</id>
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<id>50</id>
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<from>1</from>
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<to>24</to>
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</Wire>
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<Wire>
16-
<id>48</id>
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<from>23</from>
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<to>12</to>
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</Wire>
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<Wire>
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<id>49</id>
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<from>23</from>
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<to>18</to>
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</Wire>
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<Wire>
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<id>50</id>
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<id>51</id>
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<from>17</from>
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<to>27</to>
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</Wire>
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<Wire>
31-
<id>51</id>
21+
<id>52</id>
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<from>35</from>
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<to>33</to>
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</Wire>
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<Wire>
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<id>52</id>
26+
<id>53</id>
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<from>31</from>
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<to>38</to>
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</Wire>
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<Wire>
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<id>53</id>
31+
<id>54</id>
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<from>26</from>
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<to>39</to>
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</Wire>
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<Wire>
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<id>54</id>
36+
<id>55</id>
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<from>37</from>
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<to>42</to>
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</Wire>
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<Wire>
51-
<id>55</id>
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<from>44</from>
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<to>12</to>
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<id>56</id>
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<from>29</from>
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<to>32</to>
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</Wire>
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<Wire>
56-
<id>56</id>
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<id>57</id>
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<from>23</from>
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<to>48</to>
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</Wire>
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<Wire>
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<id>58</id>
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<from>47</from>
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<to>4</to>
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</Wire>
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<Wire>
61-
<id>57</id>
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<from>29</from>
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<to>32</to>
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<id>59</id>
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<from>47</from>
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<to>18</to>
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</Wire>
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<Wire>
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<id>60</id>
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<from>47</from>
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<to>12</to>
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</Wire>
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</wires>
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<items>
@@ -163,8 +163,8 @@
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<first>Mutation&#0032;rate</first>
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<second>
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<description>Mutation&#0032;rate</description>
166-
<x>-30.9017</x>
167-
<y>-95.1057</y>
166+
<x>58.7785</x>
167+
<y>-80.9017</y>
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<collapsed>false</collapsed>
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<displayFilterCaliper>false</displayFilterCaliper>
170170
<reductionOp>sum</reductionOp>
@@ -184,8 +184,8 @@
184184
<first>Replicate</first>
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<second>
186186
<description>Replicate</description>
187-
<x>11.7557</x>
188-
<y>-16.1803</y>
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<x>-6.18034</x>
188+
<y>-19.0211</y>
189189
<collapsed>true</collapsed>
190190
<displayFilterCaliper>false</displayFilterCaliper>
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<reductionOp>max</reductionOp>
@@ -209,16 +209,16 @@
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<y>58.7785</y>
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<collapsed>false</collapsed>
211211
<displayFilterCaliper>true</displayFilterCaliper>
212-
<reductionOp>max</reductionOp>
212+
<reductionOp>sum</reductionOp>
213213
<order>forward</order>
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<format></format>
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<customOrderIsInverted>false</customOrderIsInverted>
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<customOrder>
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</customOrder>
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<customOrderComplement>
219219
</customOrderComplement>
220-
<minLabel>0.006685</minLabel>
221-
<maxLabel>0.019880</maxLabel>
220+
<minLabel>0.000001</minLabel>
221+
<maxLabel>0.032921</maxLabel>
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<sliceLabel></sliceLabel>
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</second>
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</pair>
@@ -513,8 +513,8 @@
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<symbolEvery>1</symbolEvery>
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<id>16</id>
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<type>Operation:gather</type>
516-
<x>535.793</x>
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<y>417.47</y>
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<x>589.793</x>
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<y>389.47</y>
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<itemTabX>NaN</itemTabX>
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<itemTabY>NaN</itemTabY>
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<scaleFactor>1</scaleFactor>
@@ -541,8 +541,8 @@
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<symbolEvery>1</symbolEvery>
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<id>20</id>
543543
<type>VarConstant</type>
544-
<x>494.419</x>
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<y>436.588</y>
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<x>547.419</x>
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<y>398.588</y>
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<itemTabX>NaN</itemTabX>
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<itemTabY>NaN</itemTabY>
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<scaleFactor>1</scaleFactor>
@@ -573,8 +573,8 @@
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<symbolEvery>1</symbolEvery>
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<id>22</id>
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<type>Operation:mean</type>
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<x>412.906</x>
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<y>399.136</y>
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<x>350.906</x>
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<y>268.136</y>
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<itemTabX>NaN</itemTabX>
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<itemTabY>NaN</itemTabY>
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<scaleFactor>1</scaleFactor>
@@ -809,6 +809,39 @@
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</slider>
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<miniPlot>false</miniPlot>
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</Item>
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<Item>
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<name>:&lt;N_{sp}&gt;</name>
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<xmin>NaN</xmin>
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<xmax>NaN</xmax>
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<ymin>NaN</ymin>
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<ymax>NaN</ymax>
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<y1min>NaN</y1min>
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<y1max>NaN</y1max>
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<symbolEvery>1</symbolEvery>
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<id>46</id>
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<type>Variable:flow</type>
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<x>417</x>
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<y>270</y>
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<itemTabX>NaN</itemTabX>
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<itemTabY>NaN</itemTabY>
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<scaleFactor>1</scaleFactor>
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<rotation>0</rotation>
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<width>20</width>
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<height>20</height>
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<ports>
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<int>47</int>
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<int>48</int>
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</ports>
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<bookmark>false</bookmark>
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<slider>
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<stepRel>false</stepRel>
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<visible>true</visible>
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<min>-1</min>
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<max>1</max>
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<step>0.1</step>
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</slider>
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<miniPlot>false</miniPlot>
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</Item>
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</items>
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<groups>
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</groups>

‎models/ecolab_model.cc‎

Lines changed: 10 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -387,17 +387,15 @@ double ModelData::connectivity() const
387387

388388

389389
/* do the offdiagonal mutations */
390-
void do_row_or_col(array<double>& tmp, double range, double minval, double gdist)
390+
void do_row_or_col(array<double>& tmp, Float range, Float minval, Float gdist, Float gen_bias)
391391
{
392392
double r;
393393
unsigned ntrue;
394394
int j, pos;
395-
//tclvar gen_bias("generalization_bias"); /* gen \in [-1,1] */
396-
double gen= /*exists(gen_bias)? (double)gen_bias:*/0.0;
397395

398396
/* create or delete some connections */
399-
r = (2.0*rand())/RAND_MAX - 1+gen;
400-
r = (r>0)? r/(1+gen): r/(1-gen);
397+
r = (2.0*rand())/RAND_MAX - 1+gen_bias;
398+
r = (r>0)? r/(1+gen_bias): r/(1-gen_bias);
401399
if (r!=0) ntrue=(int)(1/fabs(r))-1;
402400
else ntrue = tmp.size();
403401

@@ -448,12 +446,14 @@ void ModelData::mutate(const array<int>& new_sp)
448446
repro_rate <<= new_repro_rate;
449447

450448
array<double> new_mutation(mutation[new_sp]);
451-
//lgspread( new_mutation, gdist );
449+
if (!fixMutation)
450+
lgspread( new_mutation, gdist );
452451
/* limit mutation rate to mut_max */
453452
mutation <<= merge( new_mutation < mut_max, new_mutation, mut_max);
454453

455454
array<double> new_migration(migration[new_sp]);
456-
//lgspread( new_migration, gdist );
455+
if (!fixMigration)
456+
lgspread( new_migration, gdist );
457457
/* limit mutation rate to mut_max */
458458
migration <<= new_migration;
459459

@@ -483,7 +483,7 @@ void ModelData::mutate(const array<int>& new_sp)
483483
pack(interaction.val,mask,ntrue);
484484
tmp1[ new_sp[i] ] = interaction.diag[new_sp[i]];
485485

486-
do_row_or_col(tmp1,range,odiag_min,gdist[i]);
486+
do_row_or_col(tmp1,range,odiag_min,gdist[i],gen_bias);
487487

488488
/* project out connections for col[new_sp[i]] */
489489
mask = interaction.col==unsigned(new_sp[i]);
@@ -492,7 +492,7 @@ void ModelData::mutate(const array<int>& new_sp)
492492
pack( interaction.val, mask, ntrue);
493493
tmp2[ new_sp[i] ] = interaction.diag[new_sp[i]];
494494

495-
do_row_or_col(tmp2,range,odiag_min,gdist[i]);
495+
do_row_or_col(tmp2,range,odiag_min,gdist[i],gen_bias);
496496

497497
/* adjust offdiag vals so that n.\beta n<0 for all positive n */
498498
/* construct list of offdiag vals that sum positively */
@@ -670,7 +670,7 @@ unsigned SpatialModel::migrate()
670670
{
671671
auto& nbr=*n->as<EcolabCell>();
672672
Float salt=&c<&nbr? c.salt: nbr.salt;
673-
array<Float> m=capped_migration * (nbr.density-c.density);
673+
array<int> m=capped_migration * (nbr.density-c.density);
674674
delta[c.idx()]+=m;//*(1 + salt * (abs(m)<cap*array_ns::min(nbr.density,c.density)));
675675
assert(all(c.density>=-delta[c.idx()]));
676676
}

‎models/ecolab_model.h‎

Lines changed: 4 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -46,8 +46,10 @@ struct ModelData
4646
sparse_mat_graph foodweb;
4747
unsigned long long tstep=0, last_mut_tstep=0, last_mig_tstep=0;
4848
//mutation parameters
49-
float sp_sep=0.1, mut_max=0, repro_min=0, repro_max=1, odiag_min=0, odiag_max=1;
50-
49+
Float sp_sep=0.1, mut_max=0, repro_min=0, repro_max=1, odiag_min=0, odiag_max=1, gen_bias=0;
50+
/// flags to disable mutation of mutation and migration rates
51+
bool fixMutation=false, fixMigration=false;
52+
5153
void makeConsistent(size_t nsp);
5254
void random_interaction(unsigned conn, double sigma);
5355
void condense(const array<bool>& mask, size_t mask_true);

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