all_environmental_fit {island} | R Documentation |
Environmental fit for a single dataset
Description
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.
Usage
all_environmental_fit(dataset, vector, env, c, e, aic, verbose = FALSE)
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 = FALSE)
Arguments
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. |
Details
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.
Value
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.
Note
AIC is recommended to be higher than the AIC of the most simple model (i.e. not including environmental variables).
See Also
Examples
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)
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]))