Function reference • INDperform

Indicator and pressure data Example data from the Baltic Sea
`ind_ex`	Food web indicators of the Central Baltic Sea (Bornholm Basin).
`press_ex`	Environmental variables representing pressures for pelagic food webs in the Central Baltic Sea (Bornholm Basin).
`press_type_ex`	Pressure variables and their associated pressure types from our example data
Templates Scoring template which can be modified for scoring() function
`crit_scores_tmpl`	Template of (sub-)criteria and corresponding scoring information
Example output tibbles Output tibbles from the different modelling function
`model_trend_ex`	Model output tibble from the `model_trend` function
`ind_init_ex`	Output tibble from the `ind_init` function
`model_gam_ex`	Model output tibble from the `model_gam` function
`model_gamm_ex`	Model output tibble from the `model_gamm` function
`merge_models_ex`	Output tibble from the `merge_models` function
`all_results_ex`	Output tibble after applying all IND~pressure modeling functions
Modelling functions Modelling indicator trends or pressure relationships
`model_trend()`	Modeling of indicator trends
`ind_init()`	Initialization of indicator-pressure models
`model_gam()`	Modeling of indicator responses to single pressures with GAMs
`model_gamm()`	Modeling of indicator responses to single pressures with GAMMs
`select_model()`	Select the best correlation structure in the GAMM
`merge_models()`	Merging two model output tibbles.
`calc_deriv()`	Calculate the derivatives of the IND response functions and the proportion of pressure range in which the response is significant
`select_interaction()`	Create tibble of all potential pressure combinations to test for interactions.
`test_interaction()`	Test for interactions between 2 pressure variables
`calc_nrmse()`	Calculates the Normalized Root Mean Square Error (NRMSE) for a list of models
Scoring function Assessing the indicator performance based on model results
`scoring()`	Scoring of indicator performance
`expect_resp()`	Score adjustments for sub-criterion 10.1
`summary_sc()`	Summary of indicator performance scores
`dist_sc()`	Score-based distance matrix
`dist_sc_group()`	Distance matrix averaged across group scores
`clust_sc()`	Score-based cluster analysis
Status assessment Calculate Euclidean state space and convex hull
`statespace_ed()`	Euclidean distance in state space
`statespace_ch()`	Convex hull in 2-dimensional space
Plotting functions
`plot_diagnostics()`	Diagnostic plots for a fitted GAM, GAMM or threshold-GAM(M)
`plot_trend()`	Create indicator trend plot
`plot_model()`	Visualization of all IND~pressure-model results relevant for the scoring
`plot_spiechart()`	Create score-based spie chart
`plot_clust_sc()`	Dendrogram of the cluster analysis.
`plot_statespace_ed()`	Time series plot of Euclidean distance
`plot_statespace_ch()`	Convex hull plot
Internal functions and helpers
`approx_deriv()`	Alternative method for confidence interval approximations of derivatives
`calc_pred()`	Calculate predicted values and their confidence intervals for GAM(M)s
`check_ind_press()`	Check class and variable names and types of ind and press data
`check_input_tbl()`	Check class, existing variables and data types of input objects
`check_input_vec()`	Check class and data type of input vector
`compare_thresholds()`	Compare changes in t_var based on different threshold levels.
`cond_boot()`	Conditional bootstraps
`cooks_dist_gamm()`	Calculates the Cook`s distance for Generalized Additive Mixed Models (GAMM)
`find_id()`	Extracts the IND~pressure IDs in the tibble.
`get_signif_code()`	Create a code indicating the significance of values given by p_val.
`get_sum_output()`	Extract specific outputs from the GAM(M) summary
`is_value()`	Returns a logical vector whether input
`loocv_thresh_gam()`	Leave-One-Out Cross-Validation (LOOCV) procedure for (threshold-)GAMs
`nrmse()`	Normalized Root Mean Square Error
`place_text()`	Place annotations to a specified position
`plot_thresh()` `plot_response()` `plot_predict()` `plot_deriv()` `plot_all_mod()`	Helper functions for plot_model
`sort_output_tbl()`	Rearrange columns in output tibble from IND~pressure modeling functions
`test_tac()`	Compute (partial) autocorrelation functions and test for significance
`thresh_gam()`	Fits a GAM with a threshold-formulation

Reference

Indicator and pressure data

Templates

Example output tibbles

Modelling functions

Scoring function

Status assessment

Plotting functions

Internal functions and helpers