Ecological Archives E095-205-A1

Paméla Lagrange, Roger Pradel, Marc Bélisle, Olivier Gimenez. 2014. Estimating dispersal among numerous sites using capture–recapture data. Ecology 95:2316–2323. http://dx.doi.org/10.1890/13-1564.1

Appendix A. Implementation of the new dispersal model in E-SURGE.

Here, we provide details and instructions to implement the new multievent capture-recapture model to estimate dispersal in program E-SURGE 1.8.5, which can be freely downloaded at http://www.cefe.cnrs.fr/en/biostatistics-and-biology-of-populations/software.

The first step is to define the number of states, events and other elements that are not used in our study (covariate, age classes etc…). Here, we have:

The states:

The events:

We will be using the following parameters:

Second, one needs to provide the structure of the transition matrices using the GEPAT interface. The symbol '*' indicates the complement of the sum of a row while the symbol '-' indicates inactive cells associated to a probability of 0. Note that the same letter in two cells does not imply equality in parameter values. Lastly, it is important to remember that in the vector of initial state probabilities, the state 'dead' does not appear in GEPAT by default. We have:

Vector of Initial State:

vector

Matrices of Transition between states:

Step 1: Survival                                   Step 2: Fidelity                                   Step 3: Recapture

matrix

Matrix of Event (detection): states in lines, events in columns.

matrix of event

Third, the GEMACO interface allows to specify effects of interest for each parameter. Shortcuts can be used to indicate if the relation is time-dependent, state-specific or any other effect.

For example, in the fidelity matrix, one can estimate a fidelity probability (the complementary probability of the probability to disperse), by specifying f(1:6) where 'f' is the shortcut for 'from' (distinguishing each parameter by rows in the matrix) and ':' for equality, meaning that all F parameters are equal in the matrix. Alternatively, one can add a memory effect by using the syntax f(1:3,4:6) to estimate one fidelity probability for individuals previously faithful (1:3) and for individuals previously dispersing (4:6), where ',' is used to separate the 2 probabilities.

Fourth, one needs to go through the IVFV interface to define initial values or set parameters to some specific values. Here, we use the initial values provided by E-SURGE by default.

We refer to the E-SURGE manual: Choquet and Nogué 2011 and Choquet et al. 2009 for more details.

Literature cited

Choquet, R., and E. Nogué. 2011. E-SURGE 1-8 user's manual. cefe, UMR 5175, Montpellier, France. http://www.cefe.cnrs.fr/images/stories/DPTEEvolution/biostatistiques/LOGICIELS/E-SURGE-MANUAL.pdf

Choquet, R., L. Rouan, and R. Pradel. 2009. Program E-SURGE: a software application for fitting multievent models. Pages 845–865 Modeling demographic processes in marked populations. Springer.


[Back to E095-205]