Man pages for brouwern/FACavian
An R implementation and extension of full-annual cycle (FAC) model of Runge & Marra *2005)
| eq01buildW0vect | Equation 1: Set up current population vector (W0) |
| eq02buildW1Mat | Equation 2: Build winter survival matrix (S.w) |
| eq03buildW2Mat | 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 (B.mc) |
| eq07_Bmk | Equation 7: Allocate breeding males to sink habitat (B.mk) |
| 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: proportion males from good winter habitat paired... |
| eq11_Pcpg | Equation 11: Proportion of males in source (c) from poor... |
| eq12_Pcpp | Equation 12: Proportion of pairs between a male and female... |
| eq13_Pkgg | Equation 13: Pairing in sink (k) habitat of good-good pairs... |
| eq14_Pkgp | Equation 14: Proportion of pairs in sink habitat (k)... |
| eq15_Pkpg | Equation 15: Proportion in of pairsin sink habitat which are... |
| eq16_Pkpp | Equation 16: Proportion of pairs in sink (k) composed of... |
| eq17buildB0Vect | Equation 17: Build vector of Breeding ground abundances after... |
| eq18AbuildRvec | Equation 18: Build vector of reproduction/fecundity values... |
| eq18BbuildPmat | Equation 18: P matrix - Build 2 x 8 matrix of the... |
| eq19AbuildFmat | Equation 19: Matrix of sex ratios at birth (f.mat) |
| eq19BbuildMinMat | Equation 19: Build 2 x 2 Diagonal matrix based on minimnums... |
| eq20buildSbmat | Equation 20: Breeding-season mortality matrix (S.b) |
| eq21buildSfmat | Equation 21: Migration mortality matrix for adults (S.f) |
| eq22buildSymat | Equation 22: Mortality during migration of young/offspring... |
| eq23_stack_Ai | Equation 23: Build the A matrix (A.i) (not implemented)-????? |
| eq24_competition | Equation 24: competition for winter habitats |
| eq24_comp_loop | Equation 24: Competition loop |
| eq24_make_gamma_vec | Equation 24: Make relative competitivness parameters for... |
| eq25_comp_constrain | Equation 25: Competition A.i constraint |
| eq26_alloc_winter_P | Equation 26: Allocate birds to poor winter habitat (A.i.P) |
| eq27_post_comp_pooling | Equation 27: |
| error_check_B0 | QA/QC: Check for errors in B0 (vector of abundances after... |
| error_check_build_Ptest_df | QA/QC: Build sequences of parameters for testing mate pairing... |
| error_check_param_set | QA/QC: Check that input into runFAC() is correct size |
| error_check_P_test | Test mate pairing equation against test dataframe |
| error_check_Pxxx | QA/QC: Check for errors in pairing equations |
| error_check_summer | QA/QC: Check output of breeding season processes for errors |
| error_check_Y1_sex_ratio | QA/QC: Check offspring sex ratio |
| make_FAC_df | Create FAC output dataframe |
| make_multiFAC_df | Make empty dataframe for holding output of runMultiFAC() |
| param_grid | Make all combinations of parameters for parameter matrix |
| param_ranges | Set minimum and maximum values for all parameters. |
| param_seqs | Create sequence of parameter values between minimum and... |
| param_seqs2 | Create sequence of parameter values between minimum and... |
| param_set | Set individual parameter values. |
| plot_Fig28_3 | Replicate 3D Figure 28.3 varying summar and winter carrying... |
| plot_Fig28_4 | Replicate line graph Plot 28.4 showing changes in age... |
| plot_Fig28_4_IBM | Replicate plot 28.4 |
| plot_Fig28_5 | Replicate line graph Figure 28.5 varying male dominance... |
| plot_Fig28_6 | Replicate Figure 28.6 varying carryover effect c |
| plot_runFAC | Plot time series of a single run of a FAC model |
| RandVitalRateResponseSurface | Random Vital Rate Response surface |
| redstart-package | redstart: An R implementation and extension of full-annual... |
| runFAC | Run a single FAC model to equilibirum |
| runFAC_check_equilibrium | Check a model being run for equilibrium |
| runFAC_finalize_output | Finalize output of a single run of FAC |
| runFAC_multi | Run multiple FAC models to equilibirum accross a range of... |
| runFAC_multi_finalize_output | Finalize output from runFAC_multi() |
| runFAC_store_pop_state_i | Save current population state of model being run |
| r_vitals | Generate random life histories/vital rates |
| step0_set_up | FAC Step 0: Set up survival matrices & other preliminaries |
| step1_winter_survival | FAC step 1: Execute 1st step of Runge & Marra FAC model:... |
| step3_substepA1_hab_acquire_IB | FAC-IBM Step 3, Substep A1: Breeding habitat acquisition... |
| step3_substepA1_hab_acquire_RM | FAC Step 3, Substep A1: Breeding habitat acquisition substep... |
| step3_substepA2_mate_acquire_IB | FAC-IBM Step 3, Substep A2: Mate acquition |
| step3_substepA2_mate_acquire_RM | Step 3 Substep A2 |
| step5_winter_habitat_acquisition | FAC Step 5: winter habitat acquisition |
| test_dat_P | Test data object test.dat.P for DOTO what for |
| test_P | QA/AC: Function to test equations 9 through 16 |
| test_P_df_maker | QA/QC: Make dataframe for testing functions (internal... |
