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

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

place_text()

Place annotations to a specified position

plot_thresh() plot_response() plot_predict() plot_deriv() plot_all_mod()

Helper functions for plot_model

test_tac()

Compute (partial) autocorrelation functions and test for significance

thresh_gam()

Fits a GAM with a threshold-formulation