param_set: Set individual parameter values.

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

Set individual parameter values.

Description

Sets individual parameter values for a single run of the model with runFAC().

Usage

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
)

Arguments

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

Details

See param_ranges() for setting the min and max of parameters that vary when using runFAC_multi

Value

param.set 30 x 1 dataframe of theparameter values that will be used.

References

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.

Examples

# Default values
## Print out default values (only 1st 10 show.  Remove "[1:10]" to see all)
param_set()[1:10]

## 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])

# 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]

brouwern/FACavian documentation built on June 1, 2024, 10:32 p.m.