makeLifeTable: Generate a life table from a matrix population model

Description Usage Arguments Value Author(s) References Examples

Description

This function uses age-from-stage decomposition methods to generate a life table from a matrix population model. A detailed description of these methods can be found in section 5.3 of Caswell (2001).

Usage

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makeLifeTable(matU, matF = NULL, matC = NULL, startLife = 1,
  nSteps = 1000)

Arguments

matU

The survival component of a matrix population model (i.e. a square projection matrix reflecting survival-related transitions; e.g. progression, stasis, and retrogression)

matF

(Optional) The sexual component of a matrix population model (i.e. a square projection matrix reflecting transitions due to sexual reproduction)

matC

(Optional) The clonal component of a matrix population model (i.e. a square projection matrix reflecting transitions due to clonal reproduction).

startLife

The index of the first stage at which the author considers the beginning of life. Defaults to 1.

nSteps

Number of time steps for which the life table will be calculated. Time steps are in the same units as the matrix population model (see MatrixPeriodicity column in metadata of COM(P)ADRE). Defaults to 1000.

Value

A data.frame containing 7-13 columns and nSteps rows. Columns include:

x

age

lx

survivorship to start of age class x

dx

proportion of original cohort dying in interval [x, x+1)

qx

force of mortality at age x

Lx

survivorship to middle of age class x

Tx

proportion of original cohort alive at age x and beyond

ex

remaining life expectancy at age x

If matF is provided, also includes:

mx

per-capita rate of sexual reproduction at age x

lxmx

expected number of sexual offspring per original cohort member produced at age x

If matC is provided, also includes:

cx

per-capita rate of clonal reproduction at age x

lxcx

expected number of clonal offspring per original cohort member produced at age x

If both matF and matC are provided, also includes:

mxcx

per-capita rate of total reproduction (sexual + clonal) at age x

lxmxcx

expected number of total offspring (sexual + clonal) per original cohort member produced at age x

Author(s)

Roberto Salguero-Gómez <[email protected]>

Hal Caswell <[email protected]>

Owen R. Jones <[email protected]>

References

Caswell, H. (2001) Matrix Population Models: Construction, Analysis, and Interpretation. Sinauer Associates; 2nd edition. ISBN: 978-0878930968

Caswell, H. (2006) Applications of Markov chains in demography. pp. 319-334 in A.N. Langville and W.J. Stewart (editors) MAM2006: Markov Anniversary Meeting. Boson Books, Raleigh, North Caroline, USA

Jones, O.R. et al. (2014) Diversity of ageing across the tree of life. Nature, 505(7482), 169–173

Examples

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matU <- rbind(c(0.1,   0,   0,   0),
              c(0.5, 0.2, 0.1,   0),
              c(  0, 0.3, 0.3, 0.1),
              c(  0,   0, 0.5, 0.6))

matF <- rbind(c(  0,   0, 1.1, 1.6),
              c(  0,   0, 0.8, 0.4),
              c(  0,   0,   0,   0),
              c(  0,   0,   0,   0))
              
matC <- rbind(c(  0,   0, 0.4, 0.5),
              c(  0,   0, 0.3, 0.1),
              c(  0,   0,   0,   0),
              c(  0,   0,   0,   0))

makeLifeTable(matU, startLife = 1, nSteps = 100)
makeLifeTable(matU, matF, startLife = 1, nSteps = 100)
makeLifeTable(matU, matF, matC, startLife = 1, nSteps = 100)

jonesor/Rage documentation built on May 22, 2019, 1:42 p.m.