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[simuPOP-devel] SF.net SVN: simupop:[4993] trunk/doc
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From: <bpe...@us...> - 2015-10-30 04:42:04
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Revision: 4993
http://sourceforge.net/p/simupop/code/4993
Author: bpeng2000
Date: 2015-10-30 04:42:01 +0000 (Fri, 30 Oct 2015)
Log Message:
-----------
Add an example of dynamically determined offspring population size
Modified Paths:
--------------
trunk/doc/userGuide.lyx
trunk/doc/userGuide.py
Modified: trunk/doc/userGuide.lyx
===================================================================
--- trunk/doc/userGuide.lyx 2015-09-21 15:46:32 UTC (rev 4992)
+++ trunk/doc/userGuide.lyx 2015-10-30 04:42:01 UTC (rev 4993)
@@ -1,5 +1,5 @@
-#LyX 2.0 created this file. For more info see http://www.lyx.org/
-\lyxformat 413
+#LyX 2.1 created this file. For more info see http://www.lyx.org/
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\begin_document
\begin_header
\textclass manual
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\font_roman default
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\end_layout
\begin_layout Subsection
+Dynamic population size determined by number of offspring *
+\end_layout
+
+\begin_layout Standard
+What we have described so far requires you to determine the size of offspring
+ population in advance.
+ Each mating event produces a number of offspring that is determined by
+ parameter
+\family typewriter
+NumOffspring
+\family default
+.
+ The mating process stops when the offspring population is filled.
+ This works for most scenarios but there are cases where the offspring populatio
+n size is determined dynamically from a fixed number of mating events with
+ random number of offspring.
+ For example, you might design a mating scheme where all males in a population
+ mate only once and produce random number of offspring.
+\end_layout
+
+\begin_layout Standard
+These kind of mating schemes can be simulated using a demographic model
+ that calculates offspring population size from pre-simulated number of
+ offspring for each family.
+ More specifically, we
+\end_layout
+
+\begin_layout Itemize
+Define a demogrphic function (model) that will be called before mating happens.
+\end_layout
+
+\begin_layout Itemize
+This function determines and save the number of offspring for each mating
+ event, and return the total number of offspring as offspring population
+ size.
+\end_layout
+
+\begin_layout Itemize
+Pass a function or generator to parameter numOffspring to pass pre-determined
+ number of offspring.
+ This function will be called each time when number of offspring is needed.
+\end_layout
+
+\begin_layout Standard
+The number of offspring could be saved and retrieved as global variable
+ but a more clever method is to store the numbers of offspring in a demographic
+ model (class).
+ Example
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "dynamicNumOff"
+
+\end_inset
+
+ demonstrates this method by implementing a demographic model that simulate,
+ save, and return the number of offspring.
+ Note that although we determine the number of mating events from number
+ of males in the parental population, a random mating scheme will choose
+ parents with replacement so it is likely that some parents will be chosen
+ multiple times while some others are not chosen at all.
+ Please refer to section
+\begin_inset Quotes eld
+\end_inset
+
+Non-random and customized mating schemes
+\begin_inset Quotes erd
+\end_inset
+
+ to learn how to define a mating scheme that picks parents without replacement.
+
+\begin_inset CommandInset include
+LatexCommand lstinputlisting
+filename "log/dynamicNumOff.log"
+lstparams "caption={Dynamic population size determined by number of offspring},label={dynamicNumOff}"
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Subsection
Determine sex of offspring
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LatexCommand label
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Modified: trunk/doc/userGuide.py
===================================================================
--- trunk/doc/userGuide.py 2015-09-21 15:46:32 UTC (rev 4992)
+++ trunk/doc/userGuide.py 2015-10-30 04:42:01 UTC (rev 4993)
@@ -1389,6 +1389,60 @@
#end_file
+
+#begin_file log/dynamicNumOff.py
+#begin_ignore
+import simuOpt
+simuOpt.setOptions(quiet=True)
+#end_ignore
+import simuPOP as sim
+#begin_ignore
+sim.setRNG(seed=12345)
+#end_ignore
+
+import random
+
+class RandomNumOff:
+ # a demographic model
+ def __init__(self):
+ self.numOff = []
+
+ def getNumOff(self):
+ # return the pre-simulated number of offspring as a generator function
+ for item in self.numOff:
+ yield item
+
+ def __call__(self, pop):
+ # define __call__ so that a RandomNumOff object is callable.
+ #
+ # Each male produce from 1 to 3 offspring. For large population, get the
+ # number of males instead of checking the sex of each individual
+ self.numOff = [random.randint(1, 3) for ind in pop.individuals() if ind.sex() == sim.MALE]
+ # return the total population size
+ print('{} mating events with number of offspring {}'.format(len(self.numOff), self.numOff))
+ return sum(self.numOff)
+
+
+pop = sim.Population(10)
+
+# create a demogranic model
+numOffModel = RandomNumOff()
+
+pop.evolve(
+ preOps=sim.InitSex(),
+ matingScheme=sim.RandomMating(
+ # the model will be called before mating to deteremine
+ # family and population size
+ subPopSize=numOffModel,
+ # the getNumOff function (generator) returns number of offspring
+ # for each mating event
+ numOffspring=numOffModel.getNumOff
+ ),
+ gen=3
+)
+
+#end_file
+
#begin_file log/sexMode.py
#begin_ignore
import simuOpt
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