countCDFxt              package:popbio              R Documentation

_C_a_l_c_u_l_a_t_e _c_o_u_n_t-_b_a_s_e_d _e_x_t_i_n_c_t_i_o_n _p_r_o_b_a_b_i_l_i_t_i_e_s _a_n_d _b_o_o_t_s_t_r_a_p
_c_o_n_f_i_d_e_n_c_e _i_n_t_e_r_v_a_l_s

_D_e_s_c_r_i_p_t_i_o_n:

     This function takes parameters derived from abundance time-series
     and calculates the probability of extinction with bootstrap
     confidence intervals for a density-independent model, using a
     diffusion approximation.

_U_s_a_g_e:

     countCDFxt(mu, sig2, nt, tq, Nc, Ne, tmax=50, Nboot=500)

_A_r_g_u_m_e_n_t_s:

     mu : estimated value of mean mu

    sig2: estimated value of sample variance 

      nt: number of transitions in the data set

      tq: length of the census (in years)

      Nc: current population size

     Ne : quasi-extinction threshold

    tmax: latest time to calculate extinction probability, default 50

   Nboot: number of bootstrap samples for calculating confidence
          intervals for extinction probabilities, default 500)

_V_a_l_u_e:

     The function plots the cumulative probabilities of
     quasi-extinction through time, with 95% confidence interval. It
     also creates 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).

_A_u_t_h_o_r(_s):

     Adapted to R by Patrick Nantel, 4 May 2005, from program 'extprob'
     of Morris & Doak (2002: 79-86)

_S_o_u_r_c_e:

     converted Matlab code from  Box 3.4 in Morris and Doak (2002)

_R_e_f_e_r_e_n_c_e_s:

     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.

_E_x_a_m_p_l_e_s:

     ## Return a graph like Figure 3.8 in Morris and Doak (2002: 84).
     ## based on census counts of adult female grizzly bears, 1958-1998
     countCDFxt(mu=0.02134, sig2=0.01305, nt=38, tq=38, Nc=99, Ne=20)

