02.Caswell {popbio}R Documentation

Converted Matlab functions from Caswell (2001)

Description

Chapter 2. Age-classified matrix models

pop.projection
section 2.2. Projection of population growth rates.

Chapter 4. Stage-classified matrix models

lambda
section 4.4. Returns the dominant eigenvalue
stable.stage
section 4.5. Returns the stable stage distribution (right eigenvector)
reproductive.value
section 4.6. Returns the reproductive value (left eigenvector)
damping.ratio
section 4.7. Returns the damping ratio
eigen.analysis
section 4.8. Computes eigenvalues and vectors, including the dominant eigenvalue , stable stage distribution, reproductive value, damping ratio, sensitivities, and elasticities. Since version 2.0, these are now included as separate functions as well

Chapter 5. Events in the Life Cycle

fundamental.matrix
section 5.3.1. Calculate age-specific survival from a stage classified matrix using the fundamental matrix N
net.reproductive.rate
section 5.3.4. Calculate the net reproductive rate of a stage classified matrix using the dominant eigenvalue of the matrix R.
generation.time
section 5.3.5. Calculate the generation time of a stage-classified matrix

Age-specific survivorship and fertility curves in Fig 5.1 and 5.2 are now included in demo(Caswell).

Chapter 6. Parameter estimation

projection.matrix
section 6.1.1. Estimate vital rates and construct a projection matrix using transtion frequency tables
QPmat
section 6.2.2. Construct a projection matrix from a time series of individuals per stage using Wood's quadratic programming method. Requires quadprog library.

Chapter 9. Sensitivity analysis

sensitivity
section 9.1. Calculate sensitivities.
elasticity
section 9.2. Calculate elasticities.

See the secder function in the demogR package for second derivatives of eigenvalues described in section 9.7

Chapter 10. Life Table Response Experiments

LTRE
section 10.1 and 10.2. Fixed designs in LTREs. See demo(Caswell) for variance decomposition in random design (Fig 10.10).

Chapter 12. Statistical inference

boot.transitions
section 12.1.4. Resample observed census transitions in a stage-fate data frame
resample
section 12.1.5.2. Resample transitions in a projction matrix from a multinomial distribution (and fertilites from a log normal)

Chapter 14. Environmental stochasticity

stoch.growth.rate
section 14.3. Calculate the log stochastic growth rate by simulation and Tuljapukar's approximation
stoch.projection
section 14.5.3. Project stochastic growth from a sequence of matrices in a uniform and nonuniform environment

See the stoch.sens function in the demogR package for senstivity and elasticity of log stochastic growth rate described in section 14.4.

Chapter 15. Demographic stochasticity

multiresultm
section 15.1.3. Incorporate demographic stochasticity into population projections. The example uses the whale dataset to create a plot like figure 15.3.

Author(s)

Chris Stubben


[Package popbio version 2.0 Index]