Function reference • hetoolkit

Import functions

Functions for importing biology, flow, RHS and water quality data

import_inv(): Importing macroinvertebrate sampling data from the EA Ecology and Fish Data Explorer

import_inv_taxa(): Importing macroinvertebrate abundance data from the EA Ecology and Fish Data Explorer

import_env(): Importing environmental base data from the EA Ecology and Fish Data Explorer

import_flow(): Import flow data from NRFA, HDE and local files

import_hde(): Importing flow data from the Environment Agency (EA) Hydrology Data Explorer (HDE)

import_nrfa(): Importing flow data from the National River Flow Archive (NRFA)

import_flowfiles(): Importing flow data from local files

import_rhs(): Importing River Habitat Survey (RHS) data from the EA's Open Data portal

import_wq(): Importing water quality data from the EA Water Quality Explorer

Processing functions

Functions for processing and joining biology, flow and other environmental data

predict_indices(): Calculating expected scores for macroinvertebrate indices using the RICT2 model

predict_indices_old(): Predict expected scores for macroinvertebrate indices

impute_flow(): Infilling missing records in daily flow time series for one or more sites

calc_flowstats(): Calculating summary statistics describing historical flow conditions.

calc_flowstats_old(): Calculate a suite of long-term and seasonal flow statistics for one or more sites.

calc_rfrstats(): Calculating summary statistics describing historical flow conditions

join_he(): Linking biology samples with time-varying flow statistics for paired biology and flow sites.

join_he_old(): Link biology data to six-monthly flow statistics for paired biology and flow sites.

Plotting functions

Functions for data exploration and visualisation

plot_heatmap(): Visualising and summarising gaps in time series data

plot_sitepca(): Summarising environmental characteristics of biological sampling sites

plot_rngflows(): Visualising the range of flow conditions experienced historically at a site

plot_hev(): Producing time series plots of biology and flow data

shiny_hev(): Producing interactive time series plots of biology and flow data

Modelling functions

Functions for analysis and interpretation of HE models

diag_lmer(): Generating a variety of diagnostic plots for a mixed-effects regression (lmer) model

model_cv(): Performing cross-validation on linear mixed-effects models and hierarchical generalized additive models

model_logocv(): Performing cross-validation on linear mixed-effects models and hierarchical generalized additive models

plot_predictions(): Visualising the time series predictions from a hydro-ecological model