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RandVitalRateResponseSurface()
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Random Vital Rate Response surface |
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eq01buildW0vect()
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Equation 1: Set up current population vector (W0) |
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eq02buildW1Mat()
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Equation 2: Build winter survival matrix (S.w) |
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eq03buildW2Mat()
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Equation 3: Make northward migration survival matrix (S.m) |
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eq04_Bfc()
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Equation 4: Allocate breeding females to Source habitat (B.fc) |
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eq05_Bfk()
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Equation 5: Allocate breeding females to sink habitat (B.fk) |
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eq06_Bmc()
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Equation 6: Allocate breeding males to source habitat (B.mc) |
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eq07_Bmk()
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Equation 7: Allocate breeding males to sink habitat (B.mk) |
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eq08_Bmd()
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Equation 8: Assigning breeding males to "drain" (aka "floater") status |
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eq09_Pcgg()
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Equation 9: Pair formation in source habitat between birds which both originated from good winter habitat (P.cgg) |
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eq10_Pcgp()
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Equation 10: proportion males from good winter habitat paired with females from poor winter habitat (P.cgp) |
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eq11_Pcpg()
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Equation 11: Proportion of males in source (c) from poor winter habitat (p) mated with females from good (g) winter habitat (P.cpg) |
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eq12_Pcpp()
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Equation 12: Proportion of pairs between a male and female both from poor habitat (P.cpp) |
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eq13_Pkgg()
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Equation 13: Pairing in sink (k) habitat of good-good pairs (P.kgg) |
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eq14_Pkgp()
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Equation 14: Proportion of pairs in sink habitat (k) good-poor pairs (P.kgp) |
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eq15_Pkpg()
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Equation 15: Proportion in of pairsin sink habitat which are between poor males and good females (P.kpg) |
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eq16_Pkpp()
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Equation 16: Proportion of pairs in sink (k) composed of poor-poor pairings (P.kpp) |
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eq17buildB0Vect()
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Equation 17: Build vector of Breeding ground abundances after pairing (B0) |
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eq18AbuildRvec()
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Equation 18: Build vector of reproduction/fecundity values (R.all) |
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eq18BbuildPmat()
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Equation 18: P matrix - Build 2 x 8 matrix of the proporations in each habitat combo (P.all) |
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eq19AbuildFmat()
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Equation 19: Matrix of sex ratios at birth (f.mat) |
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eq19BbuildMinMat()
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Equation 19: Build 2 x 2 Diagonal matrix based on minimnums of B.mc vs B.fc and B.mk vs. B.fk (min.mat) |
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eq20buildSbmat()
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Equation 20: Breeding-season mortality matrix (S.b) |
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eq21buildSfmat()
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Equation 21: Migration mortality matrix for adults (S.f) |
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eq22buildSymat()
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Equation 22: Mortality during migration of young/offspring (S.y) |
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eq23_stack_Ai()
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Equation 23: Build the A matrix (A.i) (not implemented)-????? |
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eq24_comp_loop()
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Equation 24: Competition loop |
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eq24_competition()
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Equation 24: competition for winter habitats |
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eq24_make_gamma_vec()
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Equation 24: Make relative competitivness parameters for winter habitat acquition |
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eq25_comp_constrain()
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Equation 25: Competition A.i constraint |
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eq26_alloc_winter_P()
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Equation 26: Allocate birds to poor winter habitat (A.i.P) |
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eq27_post_comp_pooling()
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Equation 27: |
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error_check_B0()
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QA/QC: Check for errors in B0 (vector of abundances after breeding habiatat acquisition) |
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error_check_P_test()
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Test mate pairing equation against test dataframe |
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error_check_Pxxx()
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QA/QC: Check for errors in pairing equations |
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error_check_Y1_sex_ratio()
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QA/QC: Check offspring sex ratio |
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error_check_build_Ptest_df()
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QA/QC: Build sequences of parameters for testing mate pairing equations |
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error_check_param_set()
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QA/QC: Check that input into runFAC() is correct size |
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error_check_summer()
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QA/QC: Check output of breeding season processes for errors |
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make_FAC_df()
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Create FAC output dataframe |
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make_multiFAC_df()
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Make empty dataframe for holding output of runMultiFAC() |
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param_grid()
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Make all combinations of parameters for parameter matrix |
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param_ranges()
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Set minimum and maximum values for all parameters. |
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param_seqs()
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Create sequence of parameter values between minimum and maximum. |
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param_seqs2()
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Create sequence of parameter values between minimum and maximum. |
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param_set()
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Set individual parameter values. |
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plot_Fig28_3()
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Replicate 3D Figure 28.3 varying summar and winter carrying capacities (K) |
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plot_Fig28_4()
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Replicate line graph Plot 28.4 showing changes in age structure as carrying capacity changes. |
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plot_Fig28_4_IBM()
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Replicate plot 28.4 |
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plot_Fig28_5()
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Replicate line graph Figure 28.5 varying male dominance parameter gamma |
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plot_Fig28_6()
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Replicate Figure 28.6 varying carryover effect c |
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plot_runFAC()
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Plot time series of a single run of a FAC model |
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r_vitals()
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Generate random life histories/vital rates |
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runFAC()
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Run a single FAC model to equilibirum |
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runFAC_check_equilibrium()
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Check a model being run for equilibrium |
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runFAC_finalize_output()
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Finalize output of a single run of FAC |
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runFAC_multi()
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Run multiple FAC models to equilibirum accross a range of parameters |
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runFAC_multi_finalize_output()
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Finalize output from runFAC_multi() |
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runFAC_store_pop_state_i()
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Save current population state of model being run |
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step0_set_up()
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FAC Step 0: Set up survival matrices & other preliminaries |
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step1_winter_survival()
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FAC step 1: Execute 1st step of Runge & Marra FAC model: overwinter survival 1.RM and W1.IB, the pop stucture after overwinter survival |
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step3_substepA1_hab_acquire_IB()
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FAC-IBM Step 3, Substep A1: Breeding habitat acquisition substep of pre-breeding step of breeding season using individual-based (IB) approach |
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step3_substepA1_hab_acquire_RM()
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FAC Step 3, Substep A1: Breeding habitat acquisition substep of pre-breeding step of breeding season using original Runge & Marra allocation functions |
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step3_substepA2_mate_acquire_IB()
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FAC-IBM Step 3, Substep A2: Mate acquition |
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step3_substepA2_mate_acquire_RM()
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Step 3 Substep A2 |
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step5_winter_habitat_acquisition()
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FAC Step 5: winter habitat acquisition |
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test_P()
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QA/AC: Function to test equations 9 through 16 |
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test_P_df_maker()
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QA/QC: Make dataframe for testing functions (internal function) |
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test_dat_P
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Test data object test.dat.P for DOTO what for |