thresh_gam: Fits a GAM with a threshold-formulation
In INDperform: Evaluation of Indicator Performances for Assessing Ecosystem States

Description Usage Arguments Details Value See Also Examples

thresh_gam fits a Generalized Additive Model (GAM) with a threshold formulation using the by argument in the smoothing function s: gam(IND ~ s(pressure1, by = threshold_variable_low) + s(pressure 1, by = threshold threshold_variable_high)). The threshold value is estimated from the data and chosen by minimizing the GCV score (termed "gcvv" in the threshold-GAM object) over an interval defined by the lower and upper quantiles (see the a and b arguments respectively) of the threshold variable.

1	thresh_gam(model, ind_vec, press_vec, t_var, name_t_var, k, a, b)

`model`	A single GAM object from the model tibble needed to extract the family and the link function.
`ind_vec`	A vector with the IND training observations (including or excluding defined outliers).
`press_vec`	A vector with the training observations (including or excluding defined outliers) of pressure 1 (i.e. the original significant pressure in the GAM(M)).
`t_var`	A vector with the training observations (including or excluding defined outliers) of the threshold variable (i.e. a second pressure variable).
`name_t_var`	The name of the threshold variable (pressure 2). t_var will be named after this string in the model formula.
`k`	Choice of knots (for the smoothing function `s`); the default is 4 to avoid over-parameterization.
`a`	The lower quantile value of the selected threshold variable, which the estimated threshold is not allowed to exceed; the default is 0.2.
`b`	The upper quantile value of the selected threshold variable, which the estimated threshold is not allowed to exceed; the default is 0.8.

thresh_gam creates first a sequence of evenly spaced threshold values within the boundaries set by the lower and upper quantiles (defined by a and b). For each threshold value that leads to a new splitting of the threshold variables a threshold-GAM is applied: one smoothing function is applied to only those observations where the threshold variable has been below the threshold value for the given time step (year). A second smoothing function is applied to observations where the threshold variable is above the prior defined threshold. From the list of computed models the threshold-GAM with the lowest Generalized Cross Validation (GCV) and its threshold value are selected and returned. For more infos on threshold-GAMs see also the details section in test_interaction.

The function returns a gam object with the additional class tgam. All method functions for gam can be applied to this function. The object has four additional elements:

mr: The threshold value of the best threshold-GAM.
mgcv: The GCV of the best threshold-GAM.
gcvv: A vector of the GCV values of all fitted threshold-GAMs.
t_val: A vector of all tested threshold values within the boundaries set by the lower and upper quantiles.
train_na: A logical vector indicating missing values.

test_interaction and loocv_thresh_gam which apply the function

# Using some models of the Baltic Sea demo data in this package
test <- thresh_gam(model = model_gam_ex$model[[1]],
  ind_vec = ind_init_ex$ind_train[[1]],
  press_vec = ind_init_ex$press_train[[1]],
  t_var = ind_init_ex$press_train[[2]],
  name_t_var = "Ssum", k = 4, a = 0.2, b = 0.8)