DFRF: Distribution and Response Functions

In akeyel/spatialdemography: A Spatially Explicit Metacommunity Model

Description

Distribution functions govern the creation (e.g., of species, of dispersal distances, or environmental layer values), while response functions define how species respond to environmental conditions. This is accomplished through creation of a modifier (constrained to be between 0 and 1)

Details

Distribution functions are given in the following table:

Function Code	Function	Description
1	log-normal	Draw values from a log-normal distribution; par1 specifies the mean and par2 specifies the SD (mean & SD in log-space, but see note below)
2	normal	Draw values from a normal distribution; par1 specifies the mean and par2 specifies the SD
3	constant	Only enter a constant value. Only par1 is used.
4	uniform	Draw values from a uniform distribution. The lower bound is given by par1 and the upper by par2
5	uniform, rounded to nearest integer	Draw values from a uniform distribution, but round to the nearest integer. The lower bound is given by par1 and the upper by par2. Both bounds must be integers.
'cover'	cover	Values are assigned relative to proporition of cover, with par1 specifying cover proportions. Only can be used for environmental layer setup.

Response functions are given here:

Function Code	Function	Description
101	matching	if the value of an environmental layer in a given cell matches the species' target value, then the appropriate vital rate is multiplied by param1. If the value does not match, then the appropriate vital rate is multiplied by param2.
102	quadratic, decreasing	-par1 * (env.val - target.val)^2 + 1 Where env.val is the value of the environmental layer in a given cell, and target.val is the species' target value.
103	environmental	Take modifier value directly from cell's environmental layer Note that these modifiers are not constrained to be between 0 and 1, and choosing biologically plausible/realistic/possible values is left to the investigator
104	seed fertility	Get seed number based on the approach in the Stochastic Plants paper (in prep) opt.val = value specified as base vr for clone production (allows calculation of the modifier) par1 = Three entries separated by colons: biomass.adult:biomass.seed:biomass.clone par2 = Two entries separated by a colon: relative.allocation.reproduction: ratio.sex.allocation. relative.allocation.reproduction is (a) and ratio.sex.allocation is (g) q = biomass.adult * a * fertility #fertility is given by the environmental layer and is in grams num.seeds = q * (1 - g) / biomass.seeds (For funct == 105, num.clones = q * g / biomass.clones) modifier = num.seeds / opt.val #This will later be multiplied by opt.val, allowing that part to cancel out leaving the new seed number.
105	clone fertility	Get clone number based on the approach in the Stochastic Plants paper. See details in function 104.
106	threshold	Apply lower and upper thresholds. Format is "NA;106;LT;UT" If environmental value is lower than the lower threshold (LT) or higher than the upper threshold (UT), the vital rate is set to 0. Otherwise it is unaffected. No optimal value is needed.

akeyel/spatialdemography documentation built on May 12, 2019, 4:43 a.m.