An R implementation and extention of full-annual cycle (FAC) model of Runge & Marra 2004

eq01buildW0vect | Equation 1: Set up current population vector (W0) |

eq02bulidMat | Equation 2: Build winter survival matrix |

eq03 | Equation 3: Make northward migration survival matrix (S.m) |

eq04_Bfc | Equation 4: Allocate breeding females to Source habitat... |

eq05_Bfk | Equation 5: Allocate breeding females to sink habitat (B.fk) |

eq06_Bmc | Equation 6: Allocate breeding males to source habitat. |

eq07_Bmk | Equation 7: Allocate breeding males to sink habitat |

eq08_Bmd | Equation 8: Assigning breeding males to "drain" (aka... |

eq09_Pcgg | Equation 9: Pair formation in source habitat between birds... |

eq10_Pcgp | Equation 10: |

eq11_Pcpg | Equation 11: Proportion of males from poor winter habitat... |

eq12_Pcpp | Equation 12 |

eq13_Pkgg | Equation 13: pairing in sink (.k) habitat |

eq14_Pkgp | Equation 14: proportion in sink habitat, good-poor pairs |

eq15_Pkpg | Equation 15: Proportion in sink poor-poor |

eq16_Pkpp | Equation 16: |

eq17buildVect | Equation 17: Build vector of Breeding ground abundances after... |

eq18buildPmat | Equation 18: Build 2 x 8 matrix of the proporations in each... |

eq18buildRmat | Equation 18: R vector - build vector of reproduction/fecunity... |

eq19buildFmat | Equation xx Fx.make.F.matrix() |

eq19buildMinMat | Equation 19: Build 2 x 2 Diagonal matrix based in minimumbs... |

eq20_build_Sb_mat | Equation 20: BREEDING season mortality |

eq21_build_Sf_mat | Equation 21 - MIGRATION Mortality of ADULTS "Mort during mig... |

eq22_build_Sy_mat | Equation 22: Mortality during migration of OFFSPRING |

eq23_stack_Ai | Equation 23: Build the A matrix (not implemented) |

eq24_competition | Implement equation 24: competition |

eq24_comp_loop | Competition loop |

eq24_make_gamma_vec | Equation 24 - Competition parameters (gamma) |

eq25_comp_constrain | Equation 25: Competition A.i constraint |

eq26_alloc_winter_P | equation 26 Allocate to poor habitat |

eq27_post_comp_pooling | Equation 27 Use of assign() here is probably inefficient/awk;... |

error_check_B0 | Check for errors in B0 (vector of abundances after breeding... |

error_check_Pxxx | Check for errors in pairing equations |

error_check_Y1_sex_ratio | Check offspring sex ratio |

FACavian-package | FACavian: An R implementation and extention of full-annual... |

make_FAC_df | Create FAC output dataframe |

make_multiFAC_df | Make empty dataframe for holding output of runMultiFAC().... |

param_grid | Make combinations of parameters for parameter matrix |

param_ranges | Make paramater ranges |

param_seqs | Create sequence of parameter values between minimum and... |

param_set | Make paramater ranges |

plot_Fig28_3 | Process the output of runMultiFAC() to re-create the 3D Fig... |

plot_Fig28_4 | Replicate plot 28.4 |

plot_Fig28_5 | Figure 28.5: Vary male dominance parameter This varies... |

plot_Fig28_6 | Make plot 28.6 - varying carry over effect c |

plot_runFAC | Plot time series of a single run of a FAC model |

QAQC_param_set | Quality control on parameters entering runFAC() |

runFAC | Run FAC model to equilibirum |

runFAC_check_equilibrium | check model equilibrium |

runFAC_finalize_output | finalize output |

runFAC_multi | Run multiple FAC models to equilibirum accross a range of... |

save_FAC_state | Save current population state |

test_P | Function to test equations 9 through 16 |

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