Description Usage Arguments Value Author(s) Source References See Also Examples
This function takes parameters derived from population counts and calculates the probability of extinction with bootstrap confidence intervals for a density-independent model, using a diffusion approximation.
1 | countCDFxt(mu, sig2, nt, Nc, Ne, tq=nt, tmax=50, Nboot=500, plot=TRUE)
|
mu |
estimated value of mean mu |
sig2 |
estimated value of sample variance |
nt |
number of transitions in the data set |
Nc |
current population size |
Ne |
quasi-extinction threshold |
tq |
length of the census (in years), default is number of transitions |
tmax |
latest time to calculate extinction probability, default 50 |
Nboot |
number of bootstrap samples for calculating confidence intervals for extinction probabilities, default 500) |
plot |
draw extinction time CDF plot with log-scale on y-axis |
The function plots the cumulative probabilities of quasi-extinction through time with 95% confidence intervals. It also returns a data frame with the extinction time CDF for the best parameter estimates (Gbest), and the lower and upper bootstrap confidence limits for extinction probabilites (Glo, Gup).
Adapted to R by Patrick Nantel, 4 May 2005, from program 'extprob' of Morris \& Doak (2002: 79-86)
converted Matlab code from Box 3.4 in Morris and Doak (2002)
Dennis et al. 1991, Ecological Monographs 61: 115-143.
Morris, W. F., and D. F. Doak. 2002. Quantitative conservation biology: Theory and practice of population viability analysis. Sinauer, Sunderland, Massachusetts, USA.
1 2 3 4 |
Gbest Glo Gup
1 0.000000e+00 0.000000e+00 0.000000e+00
2 0.000000e+00 0.000000e+00 2.361382e-15
3 2.287164e-17 0.000000e+00 9.602855e-11
4 1.749670e-13 0.000000e+00 2.305749e-08
5 2.573501e-11 1.161762e-18 6.321349e-07
6 7.244728e-10 2.372296e-16 5.831555e-06
7 7.910368e-09 5.733624e-15 2.880315e-05
8 4.771862e-08 6.663260e-14 9.613739e-05
9 1.936400e-07 4.375137e-13 2.468663e-04
10 5.949815e-07 1.930367e-12 5.272621e-04
11 1.492680e-06 6.377968e-12 9.844644e-04
12 3.215557e-06 1.696506e-11 1.661219e-03
13 6.159393e-06 3.819860e-11 2.627116e-03
14 1.075628e-05 7.546435e-11 4.043451e-03
15 1.744208e-05 1.343025e-10 5.883368e-03
16 2.662762e-05 2.196190e-10 8.177492e-03
17 3.867670e-05 3.350295e-10 1.094455e-02
18 5.389156e-05 4.824499e-10 1.419249e-02
19 7.250537e-05 6.619627e-10 1.791997e-02
20 9.468039e-05 8.719225e-10 2.211799e-02
21 1.205103e-04 1.109231e-09 2.677147e-02
22 1.500258e-04 1.369706e-09 3.186069e-02
23 1.832011e-04 1.648478e-09 3.738471e-02
24 2.199622e-04 1.940368e-09 4.346325e-02
25 2.601949e-04 2.240203e-09 4.993725e-02
26 3.037522e-04 2.543077e-09 5.677833e-02
27 3.504619e-04 2.844530e-09 6.395764e-02
28 4.001330e-04 3.140663e-09 7.144637e-02
29 4.525611e-04 3.428203e-09 7.921614e-02
30 5.075339e-04 3.704508e-09 8.723937e-02
31 5.648346e-04 3.967556e-09 9.548943e-02
32 6.242461e-04 4.215892e-09 1.039409e-01
33 6.855533e-04 4.448573e-09 1.125695e-01
34 7.485458e-04 4.665100e-09 1.213524e-01
35 8.130190e-04 4.865349e-09 1.302681e-01
36 8.787761e-04 5.049500e-09 1.392965e-01
37 9.456289e-04 5.217979e-09 1.484185e-01
38 1.013398e-03 5.371395e-09 1.576168e-01
39 1.081915e-03 5.510495e-09 1.668750e-01
40 1.151019e-03 5.636117e-09 1.761781e-01
41 1.220561e-03 5.749154e-09 1.855122e-01
42 1.290401e-03 5.850527e-09 1.948644e-01
43 1.360410e-03 5.941158e-09 2.042229e-01
44 1.430467e-03 6.021955e-09 2.135770e-01
45 1.500460e-03 6.093792e-09 2.229166e-01
46 1.570287e-03 6.157508e-09 2.322329e-01
47 1.639854e-03 6.213891e-09 2.415175e-01
48 1.709074e-03 6.263679e-09 2.507630e-01
49 1.777870e-03 6.307557e-09 2.599625e-01
50 1.846170e-03 6.346155e-09 2.691098e-01
Warning message:
In xy.coords(x, y, xlabel, ylabel, log) :
2 y values <= 0 omitted from logarithmic plot
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