Description Usage Arguments Details Value Note See Also Examples

View source: R/EnvironmentalFit.R

`all_environmental_fit`

estimates the best expressions for colonization
and extinction rates given their dependency on environmental variables.

`greedy_environmental_fit`

estimates expressions for colonization and
extinction rates given their dependency on environmental variables using a
greedy algorithm.

`custom_environmental_fit`

estimates the m.l.e. of
the parameters describing the relationship between colonization and
extinction rates and environmental variables.

`NLL_env`

returns the
Negative Log-Likelihood of a pair of colonization and extinction rates for a
given dataset with an specific relationship with environmental variables.

1 2 3 4 5 6 7 | ```
all_environmental_fit(dataset, vector, env, c, e, aic, verbose = F)
custom_environmental_fit(dataset, vector, params, c_expression, e_expression)
NLL_env(dataset, vector, params, c_expression, e_expression)
greedy_environmental_fit(dataset, vector, env, c, e, aic, verbose = F)
``` |

`dataset` |
A single dataset. |

`vector` |
A vector indicating the columns with presence-absence data. |

`env` |
The names of the environmental variables to be considered. |

`c` |
Tentative colonization rate. |

`e` |
Tentative extinction rate. |

`aic` |
Tentative AIC to be improved by the optimizer. |

`verbose` |
Logical. Do you want to get the intermediate steps looking for the best model? |

`params` |
A vector with priors of the parameters in c_expression and e_expression. |

`c_expression` |
Expression for colonization. |

`e_expression` |
Expression for extinction. |

`all_environmental_fit`

calculates all the combinations of
parameters, that increase exponentially with the number of parameters. We
advise to keep low the number of parameters.

`greedy_environmental_fit`

adds sequentially environmental variables
to the expressions of colonization and extinction rates and fix one at a
time until termination, when only adding one variable does not improve the
AIC of the last accepted model.

A list with three components: a expression for colonization, a
expression for extinction and the output of the optimization function, or
the output of the optimization function in the custom environmental fit.

In the case of `NLL_env`

, returns the NLL of an specific set or
parameters describing the relationship of environmental covariates with
colonizaiton and extinction.

AIC is recommended to be higher than the AIC of the most simple model (i.e. not including environmental variables).

1 2 3 4 5 6 7 8 9 10 11 12 13 | ```
## Not run:
all_environmental_fit(idaho[[1]],3:23,c("idaho[[2]]$TOTAL.ppt",
"idaho[[2]]$ANNUAL.temp"),0.13,0.19,100000)
greedy_environmental_fit(idaho[[1]],3:23,c("idaho[[2]]$TOTAL.ppt",
"idaho[[2]]$ANNUAL.temp"),0.13,0.19,100000)
## End(Not run)
custom_environmental_fit(idaho[[1]], 3:23, c(-0.00497925, -0.01729602,
0.19006501, 0.93486956), expression(params[1] * idaho[[2]]$TOTAL.ppt[i] +
params[3]), expression(params[2] * idaho[[2]]$ANNUAL.temp[i] + params[4]))
NLL_env(idaho[[1]], 3:23, c(-0.00497925, -0.01729602,
0.19006501, 0.93486956), expression(params[1] * idaho[[2]]$TOTAL.ppt[i] +
params[3]), expression(params[2] * idaho[[2]]$ANNUAL.temp[i] + params[4]))
``` |

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