R help - Mar 2008 - Table of basic descriptive statistics like SPSS

Dear list readers,
I want to:

1. Get a table of basic descriptive statistics for my variables
with the variable names one below the other
like SPSS descriptive statistics:

Varname N Min Max Mean SD
xxxx    x  x  x    x   x
xxx     x  x  x    x   x
....

2. Delete some variables from a data frame or exclude variables
from beeing analyzed.

3. Create a text file / redirect the terminal output to a
file (it is supposed to be easy, but I could not find a solution)?

4. Create a latex/dvi file

5. Create a PDF file (can that be done within R?)

This code took me some ours (I am new to R). What do you think about
my solution? Are there easier ones? Comments welcome! Sorry if
my questions look very basic and I hope they are understandable.


#here is my code
setwd("c:\\temp") #set working directory

library(psych)
library(xtable)
library(tools)

#Create example data frame with many variables
df <- as.data.frame(matrix( rnorm(1000), ncol=100))

df <- describe(df) #describe from lib psych

#How Can I create a text file with the output of "describe"?
#The "save as" function from the GUI saves
#only last part of the output to a text file (the first part is cut)


#delete some variables. Or can I exclude variables from
#beeing analyzed by "describe" to reduce the numer of cols?
df$kurtosis <- df$skew <- df$se <- NULL

x.df <- xtable(df) #Create an xtable object
print(x.df, tabular.environment = "longtable", , floating = FALSE,
      file="c:\\temp\\descript.tex") #create latex file

# produce dvi file in working directory (from tools)
texi2dvi("c:\\temp\\descript.tex")  #the lines below have to be added

#Problem: these lines have to be added "manually" to the latex
#before calling "texi2dvi":

#\documentclass{article}
#\usepackage{longtable}
# Latex code
#\end{document


#Can I prodcuce a PDF file within R?


Thanks a lot in advance!
Udo

Hi Udo,
See the Hmisc and Design libraries by Frank Harrell, and some  
associated PDF docs by Alzola and Harrell describing data management  
and display.
Hank
On Mar 17, 2008, at 2:05 PM, ukoenig at med.uni-marburg.de wrote:
> Dear list readers,
> I want to:
>
> 1. Get a table of basic descriptive statistics for my variables
> with the variable names one below the other
> like SPSS descriptive statistics:
>
> Varname N Min Max Mean SD
> xxxx    x  x  x    x   x
> xxx     x  x  x    x   x
> ....
>
> 2. Delete some variables from a data frame or exclude variables
> from beeing analyzed.
>
> 3. Create a text file / redirect the terminal output to a
> file (it is supposed to be easy, but I could not find a solution)?
>
> 4. Create a latex/dvi file
>
> 5. Create a PDF file (can that be done within R?)
>
> This code took me some ours (I am new to R). What do you think about
> my solution? Are there easier ones? Comments welcome! Sorry if
> my questions look very basic and I hope they are understandable.
>
>
> #here is my code
> setwd("c:\\temp") #set working directory
>
> library(psych)
> library(xtable)
> library(tools)
>
> #Create example data frame with many variables
> df <- as.data.frame(matrix( rnorm(1000), ncol=100))
>
> df <- describe(df) #describe from lib psych
>
> #How Can I create a text file with the output of "describe"?
> #The "save as" function from the GUI saves
> #only last part of the output to a text file (the first part is cut)
>
>
> #delete some variables. Or can I exclude variables from
> #beeing analyzed by "describe" to reduce the numer of cols?
> df$kurtosis <- df$skew <- df$se <- NULL
>
> x.df <- xtable(df) #Create an xtable object
> print(x.df, tabular.environment = "longtable", , floating =
FALSE,
>      file="c:\\temp\\descript.tex") #create latex file
>
> # produce dvi file in working directory (from tools)
> texi2dvi("c:\\temp\\descript.tex")  #the lines below have to be
added
>
> #Problem: these lines have to be added "manually" to the latex
> #before calling "texi2dvi":
>
> #\documentclass{article}
> #\usepackage{longtable}
> # Latex code
> #\end{document
>
>
> #Can I prodcuce a PDF file within R?
>
>
> Thanks a lot in advance!
> Udo
>
> ______________________________________________
> 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.


Dr. Hank Stevens, Associate Professor
338 Pearson Hall
Botany Department
Miami University
Oxford, OH 45056

Office: (513) 529-4206
Lab: (513) 529-4262
FAX: (513) 529-4243
http://www.cas.muohio.edu/~stevenmh/
http://www.cas.muohio.edu/ecology
http://www.muohio.edu/botany/

"If the stars should appear one night in a thousand years, how would men
believe and adore." -Ralph Waldo Emerson, writer and philosopher  
(1803-1882)

#How Can I create a text file with the output of
"describe"?

?sink
?write.table
?write.csv

#delete some variables. 

?Extract
df[,-(10:12)]
df[, 1:9]


--- ukoenig at med.uni-marburg.de wrote:
> Dear list readers,
> I want to:
> 
> 1. Get a table of basic descriptive statistics for
> my variables
> with the variable names one below the other
> like SPSS descriptive statistics:
> 
> Varname N Min Max Mean SD
> xxxx    x  x  x    x   x
> xxx     x  x  x    x   x
> ....
> 
> 2. Delete some variables from a data frame or
> exclude variables
> from beeing analyzed.
> 
> 3. Create a text file / redirect the terminal output
> to a
> file (it is supposed to be easy, but I could not
> find a solution)?
> 
> 4. Create a latex/dvi file
> 
> 5. Create a PDF file (can that be done within R?)
> 
> This code took me some ours (I am new to R). What do
> you think about
> my solution? Are there easier ones? Comments
> welcome! Sorry if
> my questions look very basic and I hope they are
> understandable.
> 
> 
> #here is my code
> setwd("c:\\temp") #set working directory
> 
> library(psych)
> library(xtable)
> library(tools)
> 
> #Create example data frame with many variables
> df <- as.data.frame(matrix( rnorm(1000), ncol=100))
> 
> df <- describe(df) #describe from lib psych
> 
> #How Can I create a text file with the output of
> "describe"?
> #The "save as" function from the GUI saves
> #only last part of the output to a text file (the
> first part is cut)
> 
> 
> #delete some variables. Or can I exclude variables
> from
> #beeing analyzed by "describe" to reduce the numer
> of cols?
> df$kurtosis <- df$skew <- df$se <- NULL
> 
> x.df <- xtable(df) #Create an xtable object
> print(x.df, tabular.environment = "longtable", ,
> floating = FALSE,
>       file="c:\\temp\\descript.tex") #create latex
> file
> 
> # produce dvi file in working directory (from tools)
> texi2dvi("c:\\temp\\descript.tex")  #the lines below
> have to be added
> 
> #Problem: these lines have to be added "manually" to
> the latex
> #before calling "texi2dvi":
> 
> #\documentclass{article}
> #\usepackage{longtable}
> # Latex code
> #\end{document
> 
> 
> #Can I prodcuce a PDF file within R?
> 
> 
> Thanks a lot in advance!
> Udo
> 
> ______________________________________________
> 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.
> 


[[elided Yahoo spam]]

On Mon, Mar 17, 2008 at 7:05 PM,  <ukoenig at med.uni-marburg.de>
wrote:
>  1. Get a table of basic descriptive statistics for my variables
>  with the variable names one below the other
>  like SPSS descriptive statistics:
[trimmed]
>  2. Delete some variables from a data frame or exclude variables
>  from beeing analyzed.
Rcmdr can help you perform these; hence you could learn a correct syntax.
>  4. Create a latex/dvi file
There is also xtable() that can export objects to LaTeX. Soon this
will be possible graphically from Rcmdr, too.

Hope this is of help,
Liviu

ukoenig at med.uni-marburg.de wrote:
> Dear list readers,
> I want to:
> 
> 1. Get a table of basic descriptive statistics for my variables
> with the variable names one below the other
> like SPSS descriptive statistics:
> 
> Varname N Min Max Mean SD
> xxxx    x  x  x    x   x
> xxx     x  x  x    x   x
> ....
> 
This looks very much like the output of the "describe" function in the
prettyR package. You can specify which summary stats you want (even roll 
your own).
> 2. Delete some variables from a data frame or exclude variables
> from beeing analyzed.
> 
> 3. Create a text file / redirect the terminal output to a
> file (it is supposed to be easy, but I could not find a solution)?
>
sink("myoutputfile.txt")
do.your.stuff(...)
sink()
OR
maybe you would enjoy "htmlize" or "R2html" in the prettyR
package.
> 4. Create a latex/dvi file
> 
You do this with Sweave, I think.
> 5. Create a PDF file (can that be done within R?)
> 
For plots, the pdf device.
Jim

At 7:05 PM +0100 3/17/08, ukoenig at med.uni-marburg.de
wrote:
>Dear list readers,
>I want to:
>
>1. Get a table of basic descriptive statistics for my variables
>with the variable names one below the other
>like SPSS descriptive statistics:
>
>Varname N Min Max Mean SD
>xxxx    x  x  x    x   x
>xxx     x  x  x    x   x
>....
Udo,
   To limit the number of columns of describe,  set   skew=FALSE

to delete variables from the description, do so in the call to describe

e.g.,
df <- as.data.frame(matrix( rnorm(1000), ncol=100))
describe(df[c(1:10,20:30)],skew=FALSE)
describe(df[-c(10:98)],range=FALSE,skew=FALSE)

to print the output  into LaTeX,  look at the the Sweave package.


Bill
>2. Delete some variables from a data frame or exclude variables
>from beeing analyzed.
>
>3. Create a text file / redirect the terminal output to a
>file (it is supposed to be easy, but I could not find a solution)?
>
>4. Create a latex/dvi file
>
>5. Create a PDF file (can that be done within R?)
>
>This code took me some ours (I am new to R). What do you think about
>my solution? Are there easier ones? Comments welcome! Sorry if
>my questions look very basic and I hope they are understandable.
>
>
>#here is my code
>setwd("c:\\temp") #set working directory
>
>library(psych)
>library(xtable)
>library(tools)
>
>#Create example data frame with many variables
>df <- as.data.frame(matrix( rnorm(1000), ncol=100))
>
>df <- describe(df) #describe from lib psych
>
>#How Can I create a text file with the output of "describe"?
>#The "save as" function from the GUI saves
>#only last part of the output to a text file (the first part is cut)
>
>
>#delete some variables. Or can I exclude variables from
>#beeing analyzed by "describe" to reduce the numer of cols?
>df$kurtosis <- df$skew <- df$se <- NULL
>
>x.df <- xtable(df) #Create an xtable object
>print(x.df, tabular.environment = "longtable", , floating = FALSE,
>       file="c:\\temp\\descript.tex") #create latex file
>
># produce dvi file in working directory (from tools)
>texi2dvi("c:\\temp\\descript.tex")  #the lines below have to be
added
>
>#Problem: these lines have to be added "manually" to the latex
>#before calling "texi2dvi":
>
>#\documentclass{article}
>#\usepackage{longtable}
># Latex code
>#\end{document
>
>
>#Can I prodcuce a PDF file within R?
>
>
>Thanks a lot in advance!
>Udo
>
>______________________________________________
>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.

-- 
William Revelle		http://personality-project.org/revelle.html
Professor			http://personality-project.org/personality.html
Department of Psychology             http://www.wcas.northwestern.edu/psych/
Northwestern University	http://www.northwestern.edu/
Use R for statistics:                          http://personality-project.org/r

William Revelle wrote:
> At 7:05 PM +0100 3/17/08, ukoenig at med.uni-marburg.de wrote:
>> Dear list readers,
>> I want to:
>>
>> 1. Get a table of basic descriptive statistics for my variables
>> with the variable names one below the other
>> like SPSS descriptive statistics:
>>
>> Varname N Min Max Mean SD
>> xxxx    x  x  x    x   x
>> xxx     x  x  x    x   x
>> ....
> 
> Udo,
>    To limit the number of columns of describe,  set   skew=FALSE
The describe function in the Hmisc package does not have a skew option. 
  Please list the relevant package when talking about describe.

Thanks
Frank
> 
> to delete variables from the description, do so in the call to describe
> 
> e.g.,
> df <- as.data.frame(matrix( rnorm(1000), ncol=100))
> describe(df[c(1:10,20:30)],skew=FALSE)
> describe(df[-c(10:98)],range=FALSE,skew=FALSE)
> 
> to print the output  into LaTeX,  look at the the Sweave package.
> 
> 
> Bill
> 
>> 2. Delete some variables from a data frame or exclude variables
>>from beeing analyzed.
>> 3. Create a text file / redirect the terminal output to a
>> file (it is supposed to be easy, but I could not find a solution)?
>>
>> 4. Create a latex/dvi file
>>
>> 5. Create a PDF file (can that be done within R?)
>>
>> This code took me some ours (I am new to R). What do you think about
>> my solution? Are there easier ones? Comments welcome! Sorry if
>> my questions look very basic and I hope they are understandable.
>>
>>
>> #here is my code
>> setwd("c:\\temp") #set working directory
>>
>> library(psych)
>> library(xtable)
>> library(tools)
>>
>> #Create example data frame with many variables
>> df <- as.data.frame(matrix( rnorm(1000), ncol=100))
>>
>> df <- describe(df) #describe from lib psych
>>
>> #How Can I create a text file with the output of "describe"?
>> #The "save as" function from the GUI saves
>> #only last part of the output to a text file (the first part is cut)
>>
>>
>> #delete some variables. Or can I exclude variables from
>> #beeing analyzed by "describe" to reduce the numer of cols?
>> df$kurtosis <- df$skew <- df$se <- NULL
>>
>> x.df <- xtable(df) #Create an xtable object
>> print(x.df, tabular.environment = "longtable", , floating =
FALSE,
>>       file="c:\\temp\\descript.tex") #create latex file
>>
>> # produce dvi file in working directory (from tools)
>> texi2dvi("c:\\temp\\descript.tex")  #the lines below have to
be added
>>
>> #Problem: these lines have to be added "manually" to the
latex
>> #before calling "texi2dvi":
>>
>> #\documentclass{article}
>> #\usepackage{longtable}
>> # Latex code
>> #\end{document
>>
>>
>> #Can I prodcuce a PDF file within R?
>>
>>
>> Thanks a lot in advance!
>> Udo
>>
>> ______________________________________________
>> 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.
> 
> 

-- 
Frank E Harrell Jr   Professor and Chair           School of Medicine
                      Department of Biostatistics   Vanderbilt University

Ben Fairbank wrote:
> "tiny high-resolution histograms"
> 
> Could you say a bit more on that topic?  How achieved?  Where
latex(describe()) uses LaTeX's picture environment after binning into 
101 bins.
> documented?  Similar to Tufte's sparklines?  
yes, a bit

See the link from http://biostat.mc.vanderbilt.edu/Hmisc

Frank
> 
> Maybe the list as a whole would be interested.
> 
> Thank you,
> 
> Ben 
> 
> If you use LaTeX you'll get more (and better) output including tiny 
> high-resolution histograms of continuous variables.
> 
> Frank
> 
> 

-- 
Frank E Harrell Jr   Professor and Chair           School of Medicine
                      Department of Biostatistics   Vanderbilt University

Just to forestall confusion amongst those who would like to use one of 
the functions called "describe"...

Hmisc package - describe
numeric
  name
  count of observations
  count of missing values
  count of unique values
  mean
  seven quantiles
  five lowest and highest values
discrete (factor or numeric with <= 10 unique values) -
  as for numeric, but
  no mean, quantiles or low/high values and
  including a frequency/percent display for each value.

psych package - describe
  item name
  item number
  number of valid cases
  mean
  standard deviation
  median
  mad: median absolute deviation (from the median)
  minimum
  maximum
  skew	(optional)
  kurtosis	(optional)
  standard error

prettyR package - describe
numeric
  name
  mean
  median
  var
  sd
  valid.n
the above are the defaults - the user can specify the name(s) of any 
function(s) as an argument to the function to customize the display.
factor
  name
  count for each value
  percent for each value
  modal value
  count of missing values
logical
  name
  count of FALSE
  count of TRUE
  percent of TRUE
  count of missing values

Have fun

Jim