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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,
- to input their measured concentration,
- to compare the predicted and measured concentrations of the APIs by
means of the PEC/MEC ratio,
- to establish whether the predicted equations used tend to
underestimate or overestimate measured values.
- It provides a consistent interactive user interface in a familiar
dashboard layout, enabling users to visualise predicted values and
compare with their measured values without any hassles.
- Users can download data and graphs generated using the tool in .csv
or publication ready images (.pdf, .eps).
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,
Prescribing data and Practice information are from the monthly
files published by the NHS Business Service Authority, used under the
terms of the Open Government Licence.
BNF codes and names are also from the NHS Business Service
Authority’s Information Portal, used under the terms of the Open
Government Licence.
dm+d weekly release data is also from the NHS Business Service
Authority’s Information Portal, used under the terms of the Open
Government Licence.
WWTP Data:
The following dataset are provided from WWTP collaborators,
Catchment map used to define the boundaries and capture the GP
Practices inside the catchments for the prescription data
calculations.
Daily flow data used to calculate the load and population
equivalent.
Population Equivalent number of inhabitants per catchment
zone.
Site information required to predict information such as recovery
percentage.
Water quality parameters to predict population
equivalent.
API properties
- Metabolites and Excretion factors collected from research articles
and data repositories such as Drug bank.
- Recovery percentage collected from research articles, calculated
from measured concentration from previous experiments, predicted using
WWTP site information.
- Physio-chemical properties collected from research articles and data
repositories.
- Site information required to predict information such as recovery
percentage.
- Eco-toxicity data collected from research articles and data
repositories.
Workflow
The workflow in this tutorial consists of the following steps, as in
the Figure 1.
Upload Data: Download template for the dataset and upload in the
corresponding input holders.
Analysis and Visualisation (AV) Panel: Click on the relevant
analysis and visualisation panel. PERK features three AV panels (1)
Predicted, (2) Measured, (3) Predicted vs Measured.
Analysis and Visualisation settings (AVS): Click respective
analysis and visualisation setting (AVS) tab, to select the option to
analyse and visualise datatable/plot
Plot settings: Click on the plot settings such as, color and line
width for the better/suitable visualisation.
Download data: Click on the download buttons to download
generated plot/data in publication friendly .pdf/.eps or .csv
files.
PERK Features
PERK consist of several features, broadly categorized as three
panels
- Upload Data
- Predicted
- Measured
- Predicted vs Measured
Overview of the individual panels and their options can be found
in Figure 2 and will be discussed in the following
sections.
Upload Data
Table 1. Upload Data: Data Input
| 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 |
- In this panel, user can
Download template for the
dataset and upload in the corresponding input holders as in
Figure 3.
- User can click on the
Download template button to
generate the comma separated value (.csv) file.
- Once the template is downloaded, user can add in or convert their
dataset to corresponding template and upload it in the corresponding
input holders to do the analysis and visualisation.
Predicted (PC)
- Predicted (PC) panel, has two sub-panels
- Prescription: to analyse and visualise the prescription trends
and
- Predicted Concentrations: to analyse and visualise the prediction
trends based on user inputs.
Predicted: Prescription
Different parts of the Predicted: Prescription
sub-panel and PERK dashboard is highlighted in the
Figure 4 and listed in the Table
2.
In Prescription sub-panel, user can select the period of their
interest using the Data Range option, and select
prescription type (raw or population normalized) value using
Target type and the site using Select the site
options in the analysis and visualisation settings (AVS) tab, as in
Figure 4
Table 2. Predicted: Prescription Sub-Panel
| 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 |
Prescription trends in the Predicted (PC) panel, can generate
long-term month wise raw prescription trends (kg/month), as in
Figure 5 and population normalized daily loads based on
prescription (PNDP) (mg/day/1000 inhabitants) as in Figure
6 .
User can download the generated plot as publication-friendly
images in .pdf/.eps format, user can also download the images in .png
format and data generated for the plot as .csv file using the download
buttons present below the plot.
User can view the data table by checking the
Show Datatable check box present below the download
buttons.
Predicted: Predicted Concentration
- Different parts of the
Predicted: Predicted Concentrations sub-panel and
PERK dashboard is highlighted in the Figure
7 and listed in the Table 3.
Table 3. Predicted: Predicted Concentrations
Sub-Panel
| 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 |
In the predicted concentrations sub-panel, user can select the
period of their interest using the Data Range option, and
select prediction sample type (wastewater influent INF,
wastewater effluent EFF and river RDOWN) using
Sample type and the site using Select the site
options in the analysis and visualisation settings (AVS) tab, as in
Figure 7
Two types of prediction values can be visualised in this panel
based on the prescription data,
PEC_I: This prediction considers prescription based on
individual month,PEC_II: This prediction is based on the prescription
per year.
This panel visualise prediction per month for the selected period
(ng/L) as in the Figure 8, and total
prediction per selected period (ng/L), as in the
Figure 9
In addition, this panel also enables to compare month wise and
total predicted concentration of selected pharmaceuticals over different
environmental matrices, such as, INF, EFF and
RDOWN and compare over different WWTPs in the
study.
User can download the generated plot as publication-friendly
images in .pdf/.eps format, user can also download the images in .png
format and data generated for the plot as .csv file using the download
buttons present below the plot.
User can view the data table by checking the
Show Datatable check box present below the download
buttons.
Measured (MC)
- Different parts of the
Measured tab and
PERK dashboard is highlighted in the Figure
10 and listed in the Table 4.
Table 4. Measured Panel
| 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 |
In Measured panel as in the Figure
10, user can select the period of their interest using the
Data Range option, and select sample matrix type
(INF - wastewater influent, EFF - wastewater
effluent, RDOWN - River Downstream, RUP -
River upstream, SPM - Solids) using
Sample type, based on the user input dataset.
User can select the measurement type (Concentration, DL - Daily
Load, PNDL - Population normalised daily load) using
Measurement Type, and the site by
Select the site options in the analysis and visualisation
settings (AVS) tab, as in Figure 10
User can download the generated plot as publication-friendly
images in .pdf/.eps format, user can also download the images in .png
format and data generated for the plot as .csv file using the download
buttons present below the plot.
User can view the data table by checking the
Show Datatable check box present below the download
buttons.
Three types of measured values can be visualised in this panel
based on the measurement data uploaded by the user,
Concentration (ng/L): This is the raw concentration
values based on individual measurements.
DL (mg/day): This is the Daily Load (DL) values based
on measurments normalised with the daily flow of wastewater for the
INFand EFF, and river for the
RDOWN and RUP.PNDL (mg/day/1000 inhabitants): This is the Population
Normalised Daily Load values calculated based on the population in the
WWTP catchment and the daily flow.
This panel visualise measurement per month for the selected
period (ng/L) as in the Figure 11, and
total measurement per selected period (ng/L), as in the
Figure 12
Predicted vs Measured
- Predicted vs Measured (PC vs MC) panel, has two sub-panels
- Predicted vs Measured: to analyse and visualise the predicted trends
vs measured trends and
- Prediction Accuracy - PA: to analyse and visualise the prediction
accuracy.
Predicted vs Measured: Predicted vs Measured
- Different parts of the
Predicted vs Measured: Predicted vs Measured sub-panel and
PERK dashboard is highlighted in the Figure
13 and listed in the Table 5.
Table 5. Predicted vs Measured: Predicted vs Measured
Sub-Panel
| 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 |
In Predicted vs Measured sub-panel, user can select
the period of their interest using the Select Period
option, and select sample type (wastewater influent INF,
wastewater effluent EFF and river RDOWN) using
Select Sample type and the site using
Select the site options in the analysis and visualisation
settings (AVS) tab, as in Figure 13
Predicted vs Measured trends in the
Predicted vs Measured (PCvsMC) panel, can generate measured
concentration vs PEC_I and PEC_II, predictions
based on monthly prescription as in Figure 14 and
prediction based on the prescription per year Figure 15
respectively.
User can download the generated plot as publication-friendly
images in .pdf/.eps format, user can also download the images in .png
format and data generated for the plot as .csv file using the download
buttons present below the plot.
User can view the data table by checking the
Show Datatable check box present below the download
buttons.
Predicted vs Measured: Prediction Accuracy
- Different parts of the
Predicted vs Measured: Prediction Accuracy sub-panel and
PERK dashboard is highlighted in the Figure
16 and listed in the Table 6.
Table 6. Predicted vs Measured: Prediction Accuracy
Sub-Panel
| 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 |
- In
Prediction Accuracy sub-panel, user can select the
period of their interest using the Select Period option,
and select sample type (wastewater influent INF, wastewater
effluent EFF and river RDOWN) using
Select Sample type and the site using
Select the site options in the analysis and visualisation
settings (AVS) tab, as in Figure 16
- Prediction Accuracy trends in the
Prediction Accuracy
(PA) panel, can generate trends in PA_I and
PA_II, predictions based on monthly prescription as in
Figure 17 and prediction based on the prescription per
year respectively.
User can download the generated plot as publication-friendly
images in .pdf/.eps format, user can also download the images in .png
format and data generated for the plot as .csv file using the download
buttons present below the plot.
User can view the data table by checking the
Show Datatable check box present below the download
buttons.
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.
Health stats visible at Monitor.
