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,
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.
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.
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 consist of several features, broadly categorized as three panels
Overview of the individual panels and their options can be found in Figure 2 and will be discussed in the following sections.
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 |
Download template
for the
dataset and upload in the corresponding input holders as in
Figure 3.Download template
button to
generate the comma separated value (.csv) file.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
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 |
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.