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| Individual () |
| | Default constructor for original individuals.
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| Individual (const std::vector< Loci > &egg, const std::vector< Loci > &sperm, const bool is_male=false) |
| | Constructor for sexual reproduction.
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| Individual (const std::vector< unsigned long > &) |
| | Homozygous initialization by bit values.
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| double | effective_carrying_capacity_quad_unnormalized () const |
| | \(K_e(I)\) with quadratic \(\Xi\) before normalization (v3u) More...
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double | effective_carrying_capacity_exp_unnormalized () const |
| | \(K_e(I)\) with exponential \(\Xi\)
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double | effective_carrying_capacity_old_exp_unnormalized () const |
| | \(K_e(I)\) with old resource distribution and exponential \(\Xi\) before normalization
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double | effective_carrying_capacity_cache () const |
| | Find \(K_e(I)\) in KE_CACHE_ or calculate.
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| double | preference_overlap (const Individual &other) const |
| | Exponent of \(C_y(I, J)\): competition on habitat preference. More...
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| double | morphology_overlap (const Individual &other) const |
| | Exponent of \(C_x(I, J)\): competition on morphology. More...
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double | resource_overlap (const Individual &other) const |
| | \(C(I, J) = C_x(I,J) C_y(I,J)\) for competition
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| double | survival_probability (const double effective_num_competitors) const |
| | Probability of survival \(w(I)\). More...
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| double | mating_probability (const Individual &male) const |
| | \(P(I,I') = \psi(I,I') C_y(I,I')\) More...
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| double | mating_probability_debarre (const Individual &male) const |
| | \(P(I,I') = \psi(I,I') C_y(I,I')\) with Debarre 2012 More...
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| double | mating_probability_TPG2013 (const Individual &male) const |
| | \(P(I,I') = \psi(I,I') C_y(I,I')\) with Thibert-Plante and Gavrilets 2013 More...
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| std::vector< Loci > | gametogenesis (URBG &) const |
| | Gametogenesis with free recombination and mutation. More...
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bool | is_male () const |
| | Get sex_.
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void | change_sex () |
| | Change sex_.
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bool | operator< (const Individual &other) const |
| | Operator required to be std::map key.
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std::string | str_detail () const |
| | detailed str() for testing/debugging
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| double | habitat_preference_exp (const double height, const double diameter) const |
| | Exponent of \(\Xi(I, u, v)\) in anolis_v2. More...
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| double | habitat_preference_quadratic (const double height, const double diameter) const |
| | \(\Xi(I, u, v)\) quadratic approximation in anolis_v3 More...
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| double | calc_DI_analytical () const |
| | \(D_I\) analytical computation by Mathematica (fast but limited) More...
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| double | calc_DI_numerical () const |
| | \(D_I\) numerical computation (slow) More...
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| double | calc_Dxi_analytical () const |
| | Calculate quadratic \(\Xi(I, u, v)\) normalizer with analytical solution. More...
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| double | calc_Dxi_numerical () const |
| | Numerical integration of quadratic \(\xi(I, u, v)\). More...
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| double | fitness (const double height, const double diameter) const |
| | Exponent of \(W(x_0, x_1 \mid u, v)\): measure adaptation to habitat. More...
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| std::vector< double > | calc_phenotype () const |
| | calculates phenotypic values from genotype More...
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std::vector< double > | intermediate_phenotypes () const |
| | aggregation of intermediate phenotype values
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static constexpr size_t | NUM_LOCI_ = 8 |
| | The number of loci per trait.
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static constexpr unsigned long | FULL_BITS = (1u << NUM_LOCI_) - 1u |
| | Genotype that produce trait value = 1.0, i.e., 11111111
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static constexpr unsigned long | HALF_BITS = (1u << (NUM_LOCI_ / 2u)) - 1u |
| | Genotype that produce trait value = 0.5, i.e., 00001111
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static constexpr double | INV_NUM_LOCI_ = 0.5 / NUM_LOCI_ |
| | Compile-time constant value used in init_phenotype()
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static constexpr size_t | NUM_STEPS_ = 32 |
| | Precision of numerical integration.
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static std::map< std::vector< double >, double > | KE_CACHE_ |
| | Store \(K_e(I)\) with ecological traits as keys.
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| static const std::vector< std::string > | INTERMEDIATE_KEYS_ |
| | labels for intermediate phenotypes More...
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static param_type | PARAM_ |
| | Parameters shared among instances.
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std::ostream & | operator<< (std::ostream &ost, const Individual &ind) |
| | put CSV on ostream
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double | pdf_beta (const double height, const double diameter) |
| | Beta distribution function for resource abundance.
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double | pdf_normal (const double height, const double diameter) |
| | Distribution of tree height given diameter.
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double | pdf_exp (const double height, const double diameter) |
| | Distribution of twig diameter given height.
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template<class Func > |
| double | integrate_triangle (Func &&func) |
| | Integral over \(0 \leq u \leq 1\) and \(0 \leq v \leq 1 - u\).
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template<class Func > |
| double | integrate_square (Func &&func) |
| | Integral over \(0 \leq u,v \leq 1\).
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sexual, diploid, additive, unlinked, diallelic
Individuals are sexual and diploid. Each individual has a number of additive quantitative characters:
- two “morphological” characters \( x_0 \) (toepad size) and \( x_1 \) (limb length) that control viability;
- two “habitat preference” characters: the most preferred height \( y_0 \) and the most preferred diameter \( y_1 \)
- three “mating compatibility” characters \( m \), \( f \), and \( c \).
The male display trait \( m \) is expressed in males only, whereas female mating preference \( f \) and tolerance \( c \) are expressed in females only. Other traits are expressed in both sexes. All traits are scaled to be between 0 and 1, and are controlled by different unlinked diallelic loci with equal effects. Mutations occur at equal rates across all loci; the probabilities of forward and backward mutations are equal.
