param_set.RdSets individual parameter values for a single run of the model with runFAC().
param_set( scenario = NA, figure = NA, gamma. = 5, c. = 1, K.bc. = 1000, K.bk. = 10000, K.wg. = 900, S.w.mg. = 0.8, S.w.mp. = 0.8, S.w.fg. = 0.8, S.w.fp. = 0.8, S.m.mg. = 0.9, S.m.mp. = 0.9, S.m.fg. = 0.9, S.m.fp. = 0.9, R.base.rate. = 1.8, R.hab.effect. = 0.5, co. = 1, f. = 0.5, S.b.mc. = 0.95, S.b.mk. = 0.85, S.b.md. = 0.8, S.b.fc. = 0.95, S.b.fk. = 0.85, S.f.mc. = 0.8, S.f.mk. = 0.75, S.f.md. = 0.8, S.f.fc. = 0.8, S.f.fk. = 0.75, S.y.mc. = 0.8, S.y.mk. = 0.75, S.y.fc. = 0.8, S.y.fk. = 0.75 )
| scenario | Different habitat scenarios defined by Runge & Marra 2004. In particular sets carrying capacity for breeding source habitat (K.bc) and winter good habitat (K.wg) If set overides other varibles that may have been set using other arguements. |
|---|---|
| figure | deprecated. See param_ranges() |
| gamma. | Strength of male dominance. |
| c. | Strength of winter to breeding season carry over. |
| K.bc. | Carrying capacity (K) of source (high quality) breeding habitat. |
| K.bk. | Carrying capacity (K) of sink (low quality) breeding habitat. |
| K.wg. | Carrying capacity (K) of winter good (high quality) habitat. |
| S.w.mg. | Survival (S) during winter (.w.) of males (.m) in good habitat (g). Note that there is no age structure in winter. |
| S.w.mp. | Survival (S) during winter (.w.) of males (.m) in poor habitat (p). |
| S.w.fg. | Survival (S) during winter (.w.) of females (.f) in good habitat (g). |
| S.w.fp. | Survival (S) during winter (.w.) of females (.f) in good habitat (p). |
| S.m.mg. | Survival (S) during spring migration (.m.) of males (.m) originating from good (g) winter habitat. |
| S.m.mp. | Survival (S) during spring migration (.m.) of males (.m) originating from poor (p) winter habitat. |
| S.m.fg. | Survival (S) during spring migration (.m.) of females (.f) originating from good (g) winter habitat. |
| S.m.fp. | Survival (S) during spring migration (.m.) of females (.m) originating from poor (p) winter habitat. |
| R.base.rate. | Fecundity base rate (?) |
| R.hab.effect. | Effect on fecundity of a pair breeding in poor habitat |
| co. | Magnitude of carry over effect; c = 1 is no carry over |
| f. | Sex ratio |
| S.b.mc. | Survival (S) during breeding (.b.) of males (.m) in source (c) habitat (source = good habitat) |
| S.b.mk. | Survival (S) during breeding (.b.) of males (.m) in sink (k) habitat (sink = poor habitat) |
| S.b.md. | Survival (S) during breeding (.b.) of males (.m) with drain (d) status (drain = floater or unpaired) |
| S.b.fc. | Survival (S) during breeding (.b.) of females (.f) in source (c) habitat (source = good habitat) |
| S.b.fk. | Survival (S) during breeding (.b.) of females (.f) in sink (k) habitat (sink = poor habitat) |
| S.f.mc. | Survival (S) during fall (.f.) migration of males (.m) originating from source (c) habitat |
| S.f.mk. | Survival (S) during fall (.f.) migration of males (.m) originating from sink (k) habitat |
| S.f.md. | Survival (S) during fall (.f.) migration of males (.m) with drain (d) status (aka floater, unpaired) |
| S.f.fc. | Survival (S) during fall (.f.) migration of females (.f) originating from source (c) habitat |
| S.f.fk. | Survival (S) during fall (.f.) migration of females (.f) originating from sink (k) habitat |
| S.y.mc. | Survival (S) during fall migration of young (.y.) males (.m) originating from source (c) habitat |
| S.y.mk. | Survival (S) during fall migration of young (.y.) males (.m) originating from sink (k) habitat |
| S.y.fc. | Survival (S) during fall migration of young (.y.) females (.f) originating from source (c) habitat |
| S.y.fk. | Survival (S) during fall migration of young (.y.) females (.f) originating from sink (k) habitat |
param.set 30 x 1 dataframe of theparameter values that will be used.
See param_ranges() for setting the min and max of parameters that vary when using runFAC_multi
Runge, MC and PP Marra. 2004. Modeling seasonal interactions in the population dynamics of migratory birds. In Greenberg, R and PP Marra, eds. Birds of two worlds: The ecology & evolution of migration. Johns Hopkins University Press, Baltimore.
# Default values ## Print out default values (only 1st 10 show. Remove "[1:10]" to see all) param_set()[1:10] #> gamma co K.bc K.bk K.wg S.w.mg S.w.mp S.w.fg S.w.fp S.m.mg #> 1 5 1 1000 10000 900 0.8 0.8 0.8 0.8 0.9 ## Print defaults in a column by taking the transpose using t() ## (only 1st 10 show. Remove "[1:10]" to see all) t(param_set()[1:10]) #> [,1] #> gamma 5e+00 #> co 1e+00 #> K.bc 1e+03 #> K.bk 1e+04 #> K.wg 9e+02 #> S.w.mg 8e-01 #> S.w.mp 8e-01 #> S.w.fg 8e-01 #> S.w.fp 8e-01 #> S.m.mg 9e-01 # Set parameters for the different scenarios plotted in figure Figure 28.5 in Runge & Marra (2004) ## (note that to actually replicate Fig 28.5 param_rangs() and param_seqs() need to be used) ## to set up full parameter grid with the male dominanc parameter gamma varying. ## winter limited winter <- param_set(scenario = "winter.limited") ## intermediate scenario intermediate <- param_set(scenario = "intermediate") ## summer limited scenario summer <- param_set(scenario = "summer.limited") ## compare the scenarios ### K.bc varies ### k.bk fixed ### K.wg varies rbind(winter = winter, intermed = intermediate, summer = summer)[, 1:10] #> gamma co K.bc K.bk K.wg S.w.mg S.w.mp S.w.fg S.w.fp S.m.mg #> winter 5 1 800 10000 485 0.8 0.8 0.8 0.8 0.9 #> intermed 5 1 224 10000 580 0.8 0.8 0.8 0.8 0.9 #> summer 5 1 205 10000 900 0.8 0.8 0.8 0.8 0.9