Man pages for brouwern/FACavian
An R implementation and extention of full-annual cycle (FAC) model of Runge & Marra 2004

eq01buildW0vectEquation 1: Set up current population vector (W0)
eq02bulidMatEquation 2: Build winter survival matrix
eq03Equation 3: Make northward migration survival matrix (S.m)
eq04_BfcEquation 4: Allocate breeding females to Source habitat...
eq05_BfkEquation 5: Allocate breeding females to sink habitat (B.fk)
eq06_BmcEquation 6: Allocate breeding males to source habitat.
eq07_BmkEquation 7: Allocate breeding males to sink habitat
eq08_BmdEquation 8: Assigning breeding males to "drain" (aka...
eq09_PcggEquation 9: Pair formation in source habitat between birds...
eq10_PcgpEquation 10:
eq11_PcpgEquation 11: Proportion of males from poor winter habitat...
eq12_PcppEquation 12
eq13_PkggEquation 13: pairing in sink (.k) habitat
eq14_PkgpEquation 14: proportion in sink habitat, good-poor pairs
eq15_PkpgEquation 15: Proportion in sink poor-poor
eq16_PkppEquation 16:
eq17buildVectEquation 17: Build vector of Breeding ground abundances after...
eq18buildPmatEquation 18: Build 2 x 8 matrix of the proporations in each...
eq18buildRmatEquation 18: R vector - build vector of reproduction/fecunity...
eq19buildFmatEquation xx Fx.make.F.matrix()
eq19buildMinMatEquation 19: Build 2 x 2 Diagonal matrix based in minimumbs...
eq20_build_Sb_matEquation 20: BREEDING season mortality
eq21_build_Sf_matEquation 21 - MIGRATION Mortality of ADULTS "Mort during mig...
eq22_build_Sy_matEquation 22: Mortality during migration of OFFSPRING
eq23_stack_AiEquation 23: Build the A matrix (not implemented)
eq24_competitionImplement equation 24: competition
eq24_comp_loopCompetition loop
eq24_make_gamma_vecEquation 24 - Competition parameters (gamma)
eq25_comp_constrainEquation 25: Competition A.i constraint
eq26_alloc_winter_Pequation 26 Allocate to poor habitat
eq27_post_comp_poolingEquation 27 Use of assign() here is probably inefficient/awk;...
error_check_B0Check for errors in B0 (vector of abundances after breeding...
error_check_PxxxCheck for errors in pairing equations
error_check_Y1_sex_ratioCheck offspring sex ratio
FACavian-packageFACavian: An R implementation and extention of full-annual...
make_FAC_dfCreate FAC output dataframe
make_multiFAC_dfMake empty dataframe for holding output of runMultiFAC()....
param_gridMake combinations of parameters for parameter matrix
param_rangesMake paramater ranges
param_seqsCreate sequence of parameter values between minimum and...
param_setMake paramater ranges
plot_Fig28_3Process the output of runMultiFAC() to re-create the 3D Fig...
plot_Fig28_4Replicate plot 28.4
plot_Fig28_5Figure 28.5: Vary male dominance parameter This varies...
plot_Fig28_6Make plot 28.6 - varying carry over effect c
plot_runFACPlot time series of a single run of a FAC model
QAQC_param_setQuality control on parameters entering runFAC()
runFACRun FAC model to equilibirum
runFAC_check_equilibriumcheck model equilibrium
runFAC_finalize_outputfinalize output
runFAC_multiRun multiple FAC models to equilibirum accross a range of...
save_FAC_stateSave current population state
test_PFunction to test equations 9 through 16
brouwern/FACavian documentation built on Aug. 15, 2018, 4:12 p.m.