Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/phenology_MHmcmc.R

Run the Metropolis-Hastings algorithm for data.

The number of iterations is n.iter+n.adapt+1 because the initial likelihood is also displayed.

I recommend thin=1 because the method to estimate SE uses resampling.

As initial point is maximum likelihood, n.adapt = 0 is a good solution.

The parameters intermediate and filename are used to save intermediate results every 'intermediate' iterations (for example 1000). Results are saved in a file of name filename.

The parameter previous is used to indicate the list that has been save using the parameters intermediate and filename. It permits to continue a mcmc search.

These options are used to prevent the consequences of computer crash or if the run is very very long and computer processes at time limited.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | ```
phenology_MHmcmc(
result = stop("An output from fit_phenology() must be provided"),
n.iter = 10000,
parametersMCMC = stop("A model generated with phenology_MHmcmc_p() must be provided"),
n.chains = 1,
n.adapt = 0,
thin = 1,
trace = FALSE,
traceML = FALSE,
adaptive = FALSE,
adaptive.lag = 500,
adaptive.fun = function(x) { ifelse(x > 0.234, 1.3, 0.7) },
intermediate = NULL,
filename = "intermediate.Rdata",
previous = NULL
)
``` |

`result` |
An object obtained after a SearchR fit |

`n.iter` |
Number of iterations for each step |

`parametersMCMC` |
A set of parameters used as initial point for searching with information on priors |

`n.chains` |
Number of replicates |

`n.adapt` |
Number of iterations before to store outputs |

`thin` |
Number of iterations between each stored output |

`trace` |
TRUE or FALSE or period, shows progress |

`traceML` |
TRUE or FALSE to show ML |

`adaptive` |
Should an adaptive process for SDProp be used |

`adaptive.lag` |
Lag to analyze the SDProp value in an adaptive content |

`adaptive.fun` |
Function used to change the SDProp |

`intermediate` |
Period for saving intermediate result, NULL for no save |

`filename` |
If intermediate is not NULL, save intermediate result in this file |

`previous` |
Previous result to be continued. Can be the filename in which intermediate results are saved. |

phenology_MHmcmc runs the Metropolis-Hastings algorithm for data (Bayesian MCMC)

A list with resultMCMC being mcmc.list object, resultLnL being likelihoods and parametersMCMC being the parameters used

Marc Girondot

Other Phenology model:
`AutoFitPhenology()`

,
`BE_to_LBLE()`

,
`Gratiot`

,
`LBLE_to_BE()`

,
`LBLE_to_L()`

,
`L_to_LBLE()`

,
`MarineTurtles_2002`

,
`MinBMinE_to_Min()`

,
`adapt_parameters()`

,
`add_SE()`

,
`add_phenology()`

,
`extract_result()`

,
`fit_phenology()`

,
`likelihood_phenology()`

,
`logLik.phenology()`

,
`map_Gratiot`

,
`map_phenology()`

,
`par_init()`

,
`phenology2fitRMU()`

,
`phenology_MHmcmc_p()`

,
`phenology()`

,
`plot.phenologymap()`

,
`plot.phenology()`

,
`plot_delta()`

,
`plot_phi()`

,
`print.phenologymap()`

,
`print.phenologyout()`

,
`print.phenology()`

,
`remove_site()`

,
`result_Gratiot1`

,
`result_Gratiot2`

,
`result_Gratiot_Flat`

,
`result_Gratiot_mcmc`

,
`result_Gratiot`

,
`summary.phenologymap()`

,
`summary.phenologyout()`

,
`summary.phenology()`

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 | ```
## Not run:
library(phenology)
data(Gratiot)
# Generate a formatted list named data_Gratiot
data_Gratiot <- add_phenology(Gratiot, name="Complete",
reference=as.Date("2001-01-01"), format="%d/%m/%Y")
# Generate initial points for the optimisation
parg <- par_init(data_Gratiot, fixed.parameters=NULL)
# Run the optimisation
result_Gratiot <- fit_phenology(data=data_Gratiot,
fitted.parameters=parg, fixed.parameters=NULL)
# Generate set of priors for Bayesian analysis
pmcmc <- phenology_MHmcmc_p(result_Gratiot, accept = TRUE)
result_Gratiot_mcmc <- phenology_MHmcmc(result = result_Gratiot, n.iter = 10000,
parametersMCMC = pmcmc, n.chains = 1, n.adapt = 0, thin = 1, trace = FALSE)
# Get standard error of parameters
summary(result_Gratiot_mcmc)
# Make diagnostics of the mcmc results using coda package
mcmc <- as.mcmc(result_Gratiot_mcmc)
require(coda)
heidel.diag(mcmc)
raftery.diag(mcmc)
autocorr.diag(mcmc)
acf(mcmc[[1]][,"LengthB"], lag.max=200, bty="n", las=1)
acf(mcmc[[1]][,"Max_Gratiot"], lag.max=50, bty="n", las=1)
batchSE(mcmc, batchSize=100)
# The batch standard error procedure is usually thought to
# be not as accurate as the time series methods used in summary
summary(mcmc)$statistics[,"Time-series SE"]
plot(result_Gratiot_mcmc, parameters=3, las=1, xlim=c(-10, 300))
## End(Not run)
``` |

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