Simulation of Ecological and Environmental Models

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Documentation for package ‘seem’ version 1.0

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C D E F G H I K L M N O P Q R S T V Z

seem-package Simulation of Ecological and Environmental Models

-- C --

cerio.F Wrapper for simulation programs in Fortran and C

-- D --

D.H.est Functions to define tree responses
D.plot Stability analysis and plots (didactic purpose)
dD.dt.analysis Functions to define tree responses
dD.dt.calibra Functions to define tree responses
dD.rate Functions to define tree responses
DH.allom Functions to define tree responses
diversity Functions to define community dynamics models for simulation, to determine equilibrium points, and calculate diversity from simulation output.
Dl.allom Functions to define tree responses
DO.PP.pond Functions to determine primary productivity

-- E --

env.factors.analysis Functions to define tree responses
eq.2sp Functions to define community dynamics models for simulation, to determine equilibrium points, and calculate diversity from simulation output.
euler Numerical integration methods: Euler, Runge-Kutta 4th order, Monte Carlo, RK4 with discontinuities, and Ramos method.
expon Functions to define exponential models for simulation
expon.alf Functions to define tree responses
expon.forced Functions to define exponential models for simulation
expon.g Functions to define exponential models for simulation
expon.rand Functions to define exponential models for simulation
expon.var Functions to define exponential models for simulation
expon.z Functions to define exponential models for simulation

-- F --

forsucc.C Wrapper for simulation programs in Fortran and C

-- G --

gauss.smf Functions to define tree responses
ge.growth Functions to define tree responses
green.ampt.maila Soil water dynamics
green.ampt.ramos Soil water dynamics

-- H --

holling.tanner Functions to define community dynamics models for simulation, to determine equilibrium points, and calculate diversity from simulation output.

-- I --

infilt.rate Soil water dynamics

-- K --

kT.rate Functions to define temperature response.

-- L --

logistic Functions to define logistic and M3 (Michaelis-Menten-Monod) models for simulation
logistic.forced Functions to define logistic and M3 (Michaelis-Menten-Monod) models for simulation
logistic.g Functions to define logistic and M3 (Michaelis-Menten-Monod) models for simulation
logistic.var Functions to define logistic and M3 (Michaelis-Menten-Monod) models for simulation
logistic.z Functions to define logistic and M3 (Michaelis-Menten-Monod) models for simulation
LVint.2sp Functions to define community dynamics models for simulation, to determine equilibrium points, and calculate diversity from simulation output.
LVint.3sp Functions to define community dynamics models for simulation, to determine equilibrium points, and calculate diversity from simulation output.

-- M --

M3 Functions to define logistic and M3 (Michaelis-Menten-Monod) models for simulation
markov.rain Weather simulation
markov.rain.seq Weather simulation
model.eval Model evaluation and sensitivity analysis
monod.batch Functions to define logistic and M3 (Michaelis-Menten-Monod) models for simulation
mruns.out Simulator output functions
msens Model evaluation and sensitivity analysis
mway.fact Model evaluation and sensitivity analysis
mway.samp Model evaluation and sensitivity analysis

-- N --

nut.cycle Functions to define ecosystem models for simulation.
nut.cycle.g Functions to define ecosystem models for simulation.
nut.cycle.z Functions to define ecosystem models for simulation.
nut.river Functions to define ecosystem models for simulation.

-- O --

onerun.out Simulator output functions

-- P --

parab Functions to define temperature response.
parab1 Functions to define tree responses
pet Weather simulation
phase.plot Stability analysis and plots (didactic purpose)
PP.Eilers Functions to determine primary productivity
PP.Smith Functions to determine primary productivity
PP.Steele Functions to determine primary productivity
PP.Thornley Functions to determine primary productivity
PPrates.depth Functions to determine primary productivity
PPT.Smith Functions to determine primary productivity
PPT.Steele Functions to determine primary productivity

-- Q --

Q10 Functions to define temperature response.
Q10.mruns Functions to define temperature response.

-- R --

rain.day Weather simulation
ramos Numerical integration methods: Euler, Runge-Kutta 4th order, Monte Carlo, RK4 with discontinuities, and Ramos method.
ran.exp Custom random number generators for didactic purposes
ran.norm Custom random number generators for didactic purposes
ran.unif Custom random number generators for didactic purposes
read.plot.cerio.out Read and plot output from Fortran and C simulation programs
read.plot.forsucc.out Read and plot output from Fortran and C simulation programs
read.plot.river.out Read and plot output from Fortran and C simulation programs
read.plot.semi.out Read and plot output from Fortran and C simulation programs
read.plot.zelig.out Read and plot output from Fortran and C simulation programs
ReIm.plot Stability analysis and plots (didactic purpose)
river.C Wrapper for simulation programs in Fortran and C
RK4 Numerical integration methods: Euler, Runge-Kutta 4th order, Monte Carlo, RK4 with discontinuities, and Ramos method.
RK4D Numerical integration methods: Euler, Runge-Kutta 4th order, Monte Carlo, RK4 with discontinuities, and Ramos method.
rnum Numerical integration methods: Euler, Runge-Kutta 4th order, Monte Carlo, RK4 with discontinuities, and Ramos method.
rnum.out Simulator output functions
root.locus.quad Stability analysis and plots (didactic purpose)
root.plot Stability analysis and plots (didactic purpose)

-- S --

seem Simulation of Ecological and Environmental Models
semi.F Wrapper for simulation programs in Fortran and C
sens Model evaluation and sensitivity analysis
sim Simulation functions
sim.comp Simulation functions
sim.ga Soil water dynamics
sim.mruns Simulation functions
sim.proj Matrix projection
sim.rnum Simulation functions
simd Simulation functions
simr Simulation functions
simt Simulation functions
soil.water Soil water dynamics
soilwat.1 Soil water dynamics
soilwat.n Soil water dynamics
sta.plot Stability analysis and plots (didactic purpose)
succession Functions to define community dynamics models for simulation, to determine equilibrium points, and calculate diversity from simulation output.
succession.g Functions to define community dynamics models for simulation, to determine equilibrium points, and calculate diversity from simulation output.
succession.z Functions to define community dynamics models for simulation, to determine equilibrium points, and calculate diversity from simulation output.
sun.atmos Solar radiation functions
sun.dec Solar radiation functions
sun.elev.hr Solar radiation functions
sun.elev.max Solar radiation functions
sun.path Solar radiation functions
sun.rad.hr Solar radiation functions
sun.rad.hr.mult Solar radiation functions
sun.rad.yr Solar radiation functions

-- T --

toxi.multi.bioacc Functions to define ecotoxicology models for simulation
toxi1.bioacc Functions to define ecotoxicology models for simulation
toxi2.bioacc Functions to define ecotoxicology models for simulation
two.stage.cont Functions to define structured population models for simulation
two.stage.cont.delay Functions to define structured population models for simulation
two.stage.x0 Functions to define structured population models for simulation

-- V --

vars.out Simulator output functions

-- Z --

zelig.F Wrapper for simulation programs in Fortran and C