02.Caswell {popbio}

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

secder

section 9.7. Second derivatives of eigenvalues

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.sens

section 14.4.1. Senstivity and elasticity of stochastic growth rate from numerical simultations

stoch.projection

section 14.5.3. Project stochastic growth from a sequence of matrices in a uniform and nonuniform environment

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