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Code and data for the COMPADRE Plant Matrix Database and COMADRE Animal Matrix Database
License: GNU General Public License v2.0
This project forked from jonesor/compadredb
Code and data for the COMPADRE Plant Matrix Database and COMADRE Animal Matrix Database
License: GNU General Public License v2.0
There are various unresolved queries in this function relating to the way it should work. Summarising these:
More details are in the function documentation:
https://github.com/tdjames1/compadreDB/blob/master/Mage/R/reprodStages.R
Need to deal with degenerate matrices that create NaN values.
Example: matrix with juvenile survival and transition both specified as zero.
!> comadre$version
$Version
[1] "X.X.X"
$DateCreated
[1] "Jun_09_2017"
$NumberAcceptedSpecies
[1] 456
$NumberStudies
[1] 586
$NumberMatrices
[1] 2207
$Agreement
[1] "http://www.compadre-db.org/Page/UserAgreement"
!> comadre$mat[[454]]
$matA
A1 A2
[1,] 0 2.630585000
[2,] 0 0.002427184
$matU
U1 U2
[1,] 0 0.000000000
[2,] 0 0.002427184
$matF
F1 F2
[1,] 0 2.630585
[2,] 0 0.000000
$matC
C1 C2
[1,] 0 0
[2,] 0 0
E.g. use descriptions of parameters matU, matF etc from lifetimeRepEvents() documentation.
The structure of the matrix given in the example is not appropriate for the vital rate extraction procedure.
Create an example for rearrangeMatrix() that demonstrates the function's purpose, i.e. a matrix containing non-reproductive stages.
This function is supposed to handle the whole process of collapsing a matrix to standard form and calculating standardized vital rates. Need to figure out if it does what it's supposed to do.
https://github.com/tdjames1/compadreDB/blob/master/Mage/R/standardizedvitalrates.R
Example from Bernt-Erik Sæther, Øvind Bakke. 2000. Life history variation and contribution of different demographic traits to the population growth rate in birds: a comparative approach. Ecology 81: 642-653.
saetherMatrices$`Diomedea exulans`
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11]
[1,] 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 NA
[2,] 0.92 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
[3,] 0.00 0.92 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
[4,] 0.00 0.00 0.92 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
[5,] 0.00 0.00 0.00 0.92 0.00 0.00 0.00 0.00 0.00 0.00 0.00
[6,] 0.00 0.00 0.00 0.00 0.92 0.00 0.00 0.00 0.00 0.00 0.00
[7,] 0.00 0.00 0.00 0.00 0.00 0.92 0.00 0.00 0.00 0.00 0.00
[8,] 0.00 0.00 0.00 0.00 0.00 0.00 0.92 0.00 0.00 0.00 0.00
[9,] 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.92 0.00 0.00 0.00
[10,] 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.92 0.00 0.00
[11,] 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.92 0.92
Decomposed using values above the diagonal as the fecundity matrix, remaining values as growth/transition.
[1] "Species: Diomedea exulans"
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11]
[1,] 0 0 0 0 0 0 0 0 0 0 NA
[2,] 0 0 0 0 0 0 0 0 0 0 0
[3,] 0 0 0 0 0 0 0 0 0 0 0
[4,] 0 0 0 0 0 0 0 0 0 0 0
[5,] 0 0 0 0 0 0 0 0 0 0 0
[6,] 0 0 0 0 0 0 0 0 0 0 0
[7,] 0 0 0 0 0 0 0 0 0 0 0
[8,] 0 0 0 0 0 0 0 0 0 0 0
[9,] 0 0 0 0 0 0 0 0 0 0 0
[10,] 0 0 0 0 0 0 0 0 0 0 0
[11,] 0 0 0 0 0 0 0 0 0 0 0
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11]
[1,] 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
[2,] 0.92 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
[3,] 0.00 0.92 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
[4,] 0.00 0.00 0.92 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
[5,] 0.00 0.00 0.00 0.92 0.00 0.00 0.00 0.00 0.00 0.00 0.00
[6,] 0.00 0.00 0.00 0.00 0.92 0.00 0.00 0.00 0.00 0.00 0.00
[7,] 0.00 0.00 0.00 0.00 0.00 0.92 0.00 0.00 0.00 0.00 0.00
[8,] 0.00 0.00 0.00 0.00 0.00 0.00 0.92 0.00 0.00 0.00 0.00
[9,] 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.92 0.00 0.00 0.00
[10,] 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.92 0.00 0.00
[11,] 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.92 0.92
Error in Rep[1]:Rep[length(Rep)] : argument of length 0
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