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]