https://github.com/bayer-group/bic-breasy

https://github.com/bayer-group/bic-breasy

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README.Rmd

---
output: github_document
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# BReasy 





The BReasy R Shiny app provides a handy platform for structured benefit-risk assessment using clinical study or pooled data.
With the provided forest plot estimates for all relevant efficacy and safety outcomes can be shown in one graph. In the graphical display the presented outcomes can be separated into efficacy and safety. To enable a structured and transparent approach to assessing the benefit-risk profile, the outcomes shown in the forest plot are based on the same analysis sets and data scopes. 
Furthermore, a presentation by study (in case of pooled data), stratum and subgroups is possible to assess the benefit-risk profile in subpopulations of interest.

The following estimates for comparison can be presented with the BReasy Shiny app:

* Hazard Ratios;
* Excess number of subjects, for example based on Kaplan-Meier differences or risk differences;
* Odds Ratios; 
* Risk Differences;
* Relative risks.

An optional display of the following data is possible to be added to the forest plot:

* The actual estimates displayed in the forest plot;
* Event and patient counts; 
* Number needed to treat (NNT) / Number needed to harm (NNH).



Additionally, the BReasy app includes the possibility of creating a value tree showing the relevant benefit and risk criteria. Benefit criteria will be colour-coded as green, and the risk criteria will be colour-coded as red. The interactively created value tree can be saved in html format, please see below for an example.



## Installation

You can install and load the development version from [GitHub](https://github.com/) with:

``` r
# install.packages("devtools")
devtools::install_github("Bayer-Group/BIC-BReasy")
library(breasy)
```

and start the app with:

```{r example}
#run_app()
```

## Data Manual

BReasy is designed to upload a CSV file containing effect estimates for outcomes of interest.


### File Structure

When uploading a CSV file the following formats are allowed and can be chosen in the app:

* Separator between variables
  + Comma, Semicolon or Tab 
* Quote highlighting variables
  + None, Double Quote (",'"',") or Single Quote (')
* Decimal character
  + None, Point (.) or Comma (,)
  
In case an incorrect setting is chosen the app might run into an error. 

### File Format

In order to use the BReasy, the CSV file has to include the following variables: 




          
 Variable: 
 Description: 
 
 Type: 


 Required Variables 
 ESTIMATE 
 Type of estimate as basis for comparison, e.g. crude incidence or Kaplan-Meier cumulative incidence 
 Character 


ANALYSIS_SET
Analyis set
Character


 OUTCOME 
 Outcome of interest 
 Character 


 EFFECT_xx 
 Variable containing the value of the estimate used for comparison
xx indicates the estimate chosen:
ARD = Risk difference
EXCESS = Excess number of subjects
HR = Hazard Ratio
OR = Odds Ratio
RR = Relative risk 
 Numeric 


 LOWERxx 
 Corresponding lower Confidence interval bound with xx indicating 1-alpha  
 Numeric 


 UPPERxx 
 Corresponding upper Confidence interval bound with xx indicating 1-alpha 
 Numeric  



 Optional variables 
 NUMBER_EVENTS_VERUM 
 Number of events in verum group for the combination of required variables estimate,
outcome and analysis set and optional variables study, data scope, stratum, subgroup category 
 Integer 



NUMBER_PATIENTS_VERUM 
Number of patients in the verum group for the combination of required variables analysis set and optional variables study, stratum and subgroup category 
Integer 



NUMBER_EVENTS_COMP 
Number of events in comparator group for the combination of required variables estimate, outcome and analysis set and optional variables study, data scope, stratum, subgroup category 
 Integer



NUMBER_PATIENTS_COMP 
 Number of patients in the comparator group for the combination of required variables analysis set and optional variables study, stratum and subgroup category
 Integer



STUDY/TRIALNO 
 Study identifier 
Character 



 DATA_SCOPE/AVISIT
 Data scope, e.g. treatment-emergent
 Character



SUBGROUP 
Subgroup of Interest - Values of 'Any', 'All' or 'Overall' or 'None' can be used for overall estimates 
Character 



SUBLEVEL 
 Subgroup category corresponding to SUBGROUP
Character 



STRATUM 
 Stratum
 Character



 NNT
 Number needed to treat (NNT) / Number needed to harm (NNH)
 Integer



If the data is stored in more than one file of the same format, it is possible to upload several CSV files into BReasy.

The maximal file size is 40 MB.

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