R help - Feb 2012 - How would you program an Adverse Events statistical table using R code?

A graph != A table.
I'm talking about a page full of summary statistics and advanced
statistics, with lots of cross categories on the top and left margin
of the table, as opposed to a visual display with x-axis and y-axis,
which is totally different.

(An example of how this is done in another language is available  at
http://fivetimesfaster.blogspot.com )

For an AE table, you have an N and % column for every treatment group,
and for all patients combined. On the right side, a categorical
p-value (chi-sq or Fisher's) for every preferred term (every row!
forget multiple testing issues, this is what the boss is asking
for(it's ad-hoc safety analysis))
There's a row for grand total N for each group.
A row for N and % of patients with any event (regardless of body
system and preferred term)
For each body system, there's a section of rows that include:
  A row for N and % of patients with any event (this body system)
  A row for N and % of patients who do NOT have an event( this body system)
  And , of course, within body system, a row for each preferred term
(again N and % for each group , and also the p-value)

Body system and preferred term are, of course broad medical category
and specific medical category.


In the Pharma industry, they use the SAS programming language. Each
table often needs several hundred lines of code. Essentially it's a
combination of analysis and (visual)-reporting mixed together, with
some prerequisite data transformation. (And yes, with this new
language, it can be done in under 20 lines of code).

I have not seen people discuss attempts to do such things with the R
programming language, and how successful such attempts have been. How
hard is it, how much code is it?

In general, we are talking about a variety of complex,
somewhat-nonhomogeneous statistical tables with a variety of different
row sections and row categories, and different column sections and
column categories, and a mixture of summary statistics and advanced
statistics (p-value , least square mean, etc), and sometimes
statistics from different statistical procedures on the same page.

Robert Wilkins

Robert,

Plase look at the ae.dotplot function in the HH package.

AE (Adverse Events) dotplot of incidence and relative risk

## install.packages("HH") ## if necessary
library(HH)
?ae.dotplot

In addition to command line access to the function, we have direct access
using
RExcel from an Excel workbook.

install.packages("RthroughExcelWorkbooksInstaller")

Rich


On Fri, Feb 24, 2012 at 7:13 PM, Robert Wilkins
<irishhacker@gmail.com>wrote:
> A graph != A table.
> I'm talking about a page full of summary statistics and advanced
> statistics, with lots of cross categories on the top and left margin
> of the table, as opposed to a visual display with x-axis and y-axis,
> which is totally different.
>
> (An example of how this is done in another language is available  at
> http://fivetimesfaster.blogspot.com )
>
> For an AE table, you have an N and % column for every treatment group,
> and for all patients combined. On the right side, a categorical
> p-value (chi-sq or Fisher's) for every preferred term (every row!
> forget multiple testing issues, this is what the boss is asking
> for(it's ad-hoc safety analysis))
> There's a row for grand total N for each group.
> A row for N and % of patients with any event (regardless of body
> system and preferred term)
> For each body system, there's a section of rows that include:
>  A row for N and % of patients with any event (this body system)
>  A row for N and % of patients who do NOT have an event( this body system)
>  And , of course, within body system, a row for each preferred term
> (again N and % for each group , and also the p-value)
>
> Body system and preferred term are, of course broad medical category
> and specific medical category.
>
>
> In the Pharma industry, they use the SAS programming language. Each
> table often needs several hundred lines of code. Essentially it's a
> combination of analysis and (visual)-reporting mixed together, with
> some prerequisite data transformation. (And yes, with this new
> language, it can be done in under 20 lines of code).
>
> I have not seen people discuss attempts to do such things with the R
> programming language, and how successful such attempts have been. How
> hard is it, how much code is it?
>
> In general, we are talking about a variety of complex,
> somewhat-nonhomogeneous statistical tables with a variety of different
> row sections and row categories, and different column sections and
> column categories, and a mixture of summary statistics and advanced
> statistics (p-value , least square mean, etc), and sometimes
> statistics from different statistical procedures on the same page.
>
> Robert Wilkins
>
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
>
http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html>
> and provide commented, minimal, self-contained, reproducible code.
>
	[[alternative HTML version deleted]]

Hi Robert,

I think you might find it helpful to start with 
http://biostat.mc.vanderbilt.edu/wiki/pub/Main/StatReport/summary.pdf

Best,
Ista

On Friday, February 24, 2012 07:13:10 PM Robert Wilkins
wrote:
> A graph != A table.
> I'm talking about a page full of summary statistics and advanced
> statistics, with lots of cross categories on the top and left margin
> of the table, as opposed to a visual display with x-axis and y-axis,
> which is totally different.
> 
> (An example of how this is done in another language is available  at
> http://fivetimesfaster.blogspot.com )
> 
> For an AE table, you have an N and % column for every treatment group,
> and for all patients combined. On the right side, a categorical
> p-value (chi-sq or Fisher's) for every preferred term (every row!
> forget multiple testing issues, this is what the boss is asking
> for(it's ad-hoc safety analysis))
> There's a row for grand total N for each group.
> A row for N and % of patients with any event (regardless of body
> system and preferred term)
> For each body system, there's a section of rows that include:
>   A row for N and % of patients with any event (this body system)
>   A row for N and % of patients who do NOT have an event( this body system)
>   And , of course, within body system, a row for each preferred term
> (again N and % for each group , and also the p-value)
> 
> Body system and preferred term are, of course broad medical category
> and specific medical category.
> 
> 
> In the Pharma industry, they use the SAS programming language. Each
> table often needs several hundred lines of code. Essentially it's a
> combination of analysis and (visual)-reporting mixed together, with
> some prerequisite data transformation. (And yes, with this new
> language, it can be done in under 20 lines of code).
> 
> I have not seen people discuss attempts to do such things with the R
> programming language, and how successful such attempts have been. How
> hard is it, how much code is it?
> 
> In general, we are talking about a variety of complex,
> somewhat-nonhomogeneous statistical tables with a variety of different
> row sections and row categories, and different column sections and
> column categories, and a mixture of summary statistics and advanced
> statistics (p-value , least square mean, etc), and sometimes
> statistics from different statistical procedures on the same page.
> 
> Robert Wilkins
> 
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.