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PERK-Walkthrough

Introduction

The aim of PERK is to predict and visualize concentrations of pharmaceuticals in the aqueous environment.

PERK acronym for Predicting Environmental concentration and RisK, is an R/Shiny application tool, aims to facilitate automated modelling and reporting of predicted environmental concentrations of a comprehensive set of pharmaceuticals derived from a wide range of therapeutic classes with different mode of action.

The tool helps users,

Data sources:

Prescription Data For England:

This tool uses the prescription data from PrAna, an R package to calculate and visualize England NHS prescribing data.

The data used in PrAna are as follows,

WWTP Data:

The following dataset are provided from WWTP collaborators,

API properties

Workflow

The workflow in this tutorial consists of the following steps, as in the Figure 1.

Figure 1: PERK Workflow

Figure 1: PERK Workflow

PERK Features

Figure 2. PERK: Features

Figure 2. PERK: Features

Upload Data

Figure 3. PERK: Upload Data

Figure 3. PERK: Upload Data

Table 1. Upload Data: Data Input
Part Remarks
1 Analysis and Visualisation (AV) Panel
2 Full screen
3 Dark and Light mode
4 Plot settings
5 Data selection Area
6 Upload File Button
7 Download Template for the file
8 User Logout

Predicted (PC)

Predicted: Prescription

Figure 4. Predicted: Prescription - AV Panel.

Figure 4. Predicted: Prescription - AV Panel.

Table 2. Predicted: Prescription Sub-Panel
Part Remarks
1 Analysis and Visualisation (AV) Panel
2 Full screen
3 Dark and Light mode
4 Plot settings
5 Plot generated based on user selection
6 Analysis and Visualisation settings (AVS) panel
7 User log-out
8 Download buttons to download the generated plot as .pdf or .eps and data as .csv format
9 Show Datatable
Figure 6. PC: PNDP.

Figure 6. PC: PNDP.

Predicted: Predicted Concentration

Figure 7. Predicted: Predicted Concentrations - AV Panel.

Figure 7. Predicted: Predicted Concentrations - AV Panel.

Table 3. Predicted: Predicted Concentrations Sub-Panel
Part Remarks
1 Analysis and Visualisation (AV) Panel
2 Full screen
3 Dark and Light mode
4 Plot settings
5 Plot generated based on user selection
6 Analysis and Visualisation settings (AVS) panel
7 User log-out
8 Download buttons to download the generated plot as .pdf or .eps and data as .csv format
9 Show Data table
Figure 8. PC: concentration/month.

Figure 8. PC: concentration/month.

Figure 9. PC: concentration/period.

Figure 9. PC: concentration/period.

Measured (MC)

Figure 10. Measured: Measured Concentrations - AV Panel.

Figure 10. Measured: Measured Concentrations - AV Panel.

Table 4. Measured Panel
Part Remarks
1 Analysis and Visualisation (AV) Panel
2 Full screen
3 Dark and Light mode
4 Plot settings
5 Plot generated based on user selection
6 Analysis and Visualisation settings (AVS) panel
7 User log-out
8 Download buttons to download the generated plot as .pdf or .eps and data as .csv format
9 Show Datatable
Figure 11. MC: concentration/month.

Figure 11. MC: concentration/month.

Figure 12. MC: concentration/period.

Figure 12. MC: concentration/period.

Predicted vs Measured

Predicted vs Measured: Predicted vs Measured

Figure 13. Predicted vs Measured: Predicted vs Measured - AV Panel.

Figure 13. Predicted vs Measured: Predicted vs Measured - AV Panel.

Table 5. Predicted vs Measured: Predicted vs Measured Sub-Panel
Part Remarks
1 Analysis and Visualisation (AV) Panel
2 Full screen
3 Dark and Light mode
4 Plot settings
5 Plot generated based on user selection
6 Analysis and Visualisation settings (AVS) panel
7 User log-out
8 Download buttons to download the generated plot as .pdf or .eps and data as .csv format
9 Show Datatable
Figure 14. PCvsMC: PEC-I.

Figure 14. PCvsMC: PEC-I.

Figure 15. PCvsMC: PEC-II.

Figure 15. PCvsMC: PEC-II.

Predicted vs Measured: Prediction Accuracy

Table 6. Predicted vs Measured: Prediction Accuracy Sub-Panel
Part Remarks
1 Analysis and Visualisation (AV) Panel
2 Full screen
3 Dark and Light mode
4 Plot settings
5 Plot generated based on user selection
6 Analysis and Visualisation settings (AVS) panel
7 User log-out
8 Download buttons to download the generated plot as .pdf or .eps and data as .csv format
9 Show Datatable
Figure 17. PCvsMC: PA-I.

Figure 17. PCvsMC: PA-I.

Acknowledgements

This package was built as a part of the Wastewater Fingerprinting for Public Health Assessment (ENTRUST) and Innovative Pathway Control (IPC) project funded by Wessex Water and EPSRC IAA (grant no. EP/R51164X/1).

Disclaimer

We accept no liability for any errors in the data or its publication here: use this data at your own risk. You should not use this data to make individual prescribing decisions.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.