Man pages for brouwern/FACavian
An R implementation and extension of full-annual cycle (FAC) model of Runge & Marra *2005)

eq01buildW0vectEquation 1: Set up current population vector (W0)
eq02buildW1MatEquation 2: Build winter survival matrix (S.w)
eq03buildW2MatEquation 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 (B.mc)
eq07_BmkEquation 7: Allocate breeding males to sink habitat (B.mk)
eq08_BmdEquation 8: Assigning breeding males to "drain" (aka...
eq09_PcggEquation 9: Pair formation in source habitat between birds...
eq10_PcgpEquation 10: proportion males from good winter habitat paired...
eq11_PcpgEquation 11: Proportion of males in source (c) from poor...
eq12_PcppEquation 12: Proportion of pairs between a male and female...
eq13_PkggEquation 13: Pairing in sink (k) habitat of good-good pairs...
eq14_PkgpEquation 14: Proportion of pairs in sink habitat (k)...
eq15_PkpgEquation 15: Proportion in of pairsin sink habitat which are...
eq16_PkppEquation 16: Proportion of pairs in sink (k) composed of...
eq17buildB0VectEquation 17: Build vector of Breeding ground abundances after...
eq18AbuildRvecEquation 18: Build vector of reproduction/fecundity values...
eq18BbuildPmatEquation 18: P matrix - Build 2 x 8 matrix of the...
eq19AbuildFmatEquation 19: Matrix of sex ratios at birth (f.mat)
eq19BbuildMinMatEquation 19: Build 2 x 2 Diagonal matrix based on minimnums...
eq20buildSbmatEquation 20: Breeding-season mortality matrix (S.b)
eq21buildSfmatEquation 21: Migration mortality matrix for adults (S.f)
eq22buildSymatEquation 22: Mortality during migration of young/offspring...
eq23_stack_AiEquation 23: Build the A matrix (A.i) (not implemented)-?????
eq24_competitionEquation 24: competition for winter habitats
eq24_comp_loopEquation 24: Competition loop
eq24_make_gamma_vecEquation 24: Make relative competitivness parameters for...
eq25_comp_constrainEquation 25: Competition A.i constraint
eq26_alloc_winter_PEquation 26: Allocate birds to poor winter habitat (A.i.P)
eq27_post_comp_poolingEquation 27:
error_check_B0QA/QC: Check for errors in B0 (vector of abundances after...
error_check_build_Ptest_dfQA/QC: Build sequences of parameters for testing mate pairing...
error_check_param_setQA/QC: Check that input into runFAC() is correct size
error_check_P_testTest mate pairing equation against test dataframe
error_check_PxxxQA/QC: Check for errors in pairing equations
error_check_summerQA/QC: Check output of breeding season processes for errors
error_check_Y1_sex_ratioQA/QC: Check offspring sex ratio
make_FAC_dfCreate FAC output dataframe
make_multiFAC_dfMake empty dataframe for holding output of runMultiFAC()
param_gridMake all combinations of parameters for parameter matrix
param_rangesSet minimum and maximum values for all parameters.
param_seqsCreate sequence of parameter values between minimum and...
param_seqs2Create sequence of parameter values between minimum and...
param_setSet individual parameter values.
plot_Fig28_3Replicate 3D Figure 28.3 varying summar and winter carrying...
plot_Fig28_4Replicate line graph Plot 28.4 showing changes in age...
plot_Fig28_4_IBMReplicate plot 28.4
plot_Fig28_5Replicate line graph Figure 28.5 varying male dominance...
plot_Fig28_6Replicate Figure 28.6 varying carryover effect c
plot_runFACPlot time series of a single run of a FAC model
RandVitalRateResponseSurfaceRandom Vital Rate Response surface
redstart-packageredstart: An R implementation and extension of full-annual...
runFACRun a single FAC model to equilibirum
runFAC_check_equilibriumCheck a model being run for equilibrium
runFAC_finalize_outputFinalize output of a single run of FAC
runFAC_multiRun multiple FAC models to equilibirum accross a range of...
runFAC_multi_finalize_outputFinalize output from runFAC_multi()
runFAC_store_pop_state_iSave current population state of model being run
r_vitalsGenerate random life histories/vital rates
step0_set_upFAC Step 0: Set up survival matrices & other preliminaries
step1_winter_survivalFAC step 1: Execute 1st step of Runge & Marra FAC model:...
step3_substepA1_hab_acquire_IBFAC-IBM Step 3, Substep A1: Breeding habitat acquisition...
step3_substepA1_hab_acquire_RMFAC Step 3, Substep A1: Breeding habitat acquisition substep...
step3_substepA2_mate_acquire_IBFAC-IBM Step 3, Substep A2: Mate acquition
step3_substepA2_mate_acquire_RMStep 3 Substep A2
step5_winter_habitat_acquisitionFAC Step 5: winter habitat acquisition
test_dat_PTest data object test.dat.P for DOTO what for
test_PQA/AC: Function to test equations 9 through 16
test_P_df_makerQA/QC: Make dataframe for testing functions (internal...
brouwern/FACavian documentation built on June 1, 2024, 10:32 p.m.