TARE.MLA.Annotated.nb

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InitMatrix gives a  recombination table (transmission matrrix) for 36 \
possible mating combinations of 6 male and female genotypes. This model has \
TARE only, so only one locus with three possible alleles - wildtype (w1), \
TARE(T), and TARE-resistant non-functional allele (S). The elements within \
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genotype 1, ... ,Proportion of offspring with genotype 6}. The genotype \
numbers correspond to the following order - w1/w1, w1/S, w1/T, T/T, T/S, S/S. \

This matrix is incorporated later as \[OpenCurlyQuote]OgMatrix\
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Each row gives {Number of TARE carriers, Number of wildtype phenotype} in \
each discrete generation. Data shown here is only until TARE was present in \
all individuals (TARE homozygotes + heterozygotes).\
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TareGerm, when called, executes germline TARE action (TARE disruption) on the \
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TareEmbryo, when called, executes Embryonic TARE action (TARE disruption) on \
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The genMatrix function modifies the transmission matrix (OgMatrix) for mating \
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Generate 6 mate choice fitness parameters for 6 male genotypes (based on the \
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Generate 36 fecundity parameters for 36 mating pairs. The 36 parameters are 6 \
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StartGenoFreq is a vector of 12 genotypic frequencies in the starting \
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The StepHelp function uses values from \[OpenCurlyQuote]StartGenoFreq\
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The Step function could allow one to change the dominance pattern of \
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pattern, instead simply making all fitness costs multiplicative (codominant). \
The pattern can be altered by changing the selection functions inside Step.\
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This function converts the twelve predicted genotype frequencies into two \
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This function converts two observed genotypic frequencies to 12 (estimated) \
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generations except the starting generation (where we know the parental \
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Rho function produces \[OpenCurlyQuote]R\[CloseCurlyQuote], the LogLikelihood \
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LogLGen creates an optimizable function with a single output of the \
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Note: vS describes the reduced fitness of individuals that carry a single \
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Cell["\<\
Relationship between parameters m and fT (inability of MLE to distinguish \
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Cell["\<\
The plot below shows the the inability of the MLE model to reliably \
distinguish between the parameters m and fT (note diagonal shape of the 95% \
confidence interval )\
\>", "Text",
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Cell["\<\
Setting Ne at the MLE value and plotting ML across values of m and fT\
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