R/StartingParams.R

In downscale: Downscaling Species Occupancy

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# 
# StartingParams.R
# Version 1.3
# 16/05/2023
#
# Updates:
#   16/05/2023: Simple reformatting
#   18/08/2016: names of starting parameters harmonised with paper
#   30/01/2015: Thomas model added
#
# Data frames containing the starting parameters for the optimisation procedure
# fitting model parameters to observed coarse-scale occupancy data:
#   Nachman   Nachman model
#   PL        Power Law model
#   Logis     Logistic model
#   Poisson   Poisson model
#   NB        Negative binomial model
#   GNB       Generalised negative binomial model
#   INB       Improved negative binomial model
#   FNB       Finite negative binomial model
#   Thomas    Thomas model
#
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### Nachman model
ParamsNachman <- data.frame(C = 0.01,
                            z = 0.01)

### Power Law model
ParamsPL <- data.frame(C = 0.01,
                       z = 0.01)

### Logistic model
ParamsLogis <- data.frame(C = 0.01,
                          z = 0.01)

### Poisson model
ParamsPoisson <- data.frame(gamma = 1e-8)

### Negative binomial model
ParamsNB <- data.frame(gamma = 0.01,
                       k     = 0.01)

### Generalised negative binomial model
ParamsGNB <- data.frame(C = 0.00001,
                        z = 1,
                        k = 0.01)

### Improved negative binomial model
ParamsINB <- data.frame(C     = 1,
                        gamma = 0.01,
                        b     = 0.1)

### Finite negative binomial model
ParamsFNB <- data.frame(N = 10,
                        k = 10)

### Thomas model
ParamsThomas <- data.frame(rho   = 1e-8,
                           mu    = 10,
                           sigma = 1)