Hmisc (version 2.2-0)

sasxport.get: Enhanced Importing of SAS Transport Files using read.xport

Description

Uses the read.xport and lookup.xport functions in the foreign library to import SAS datasets. SAS date, time, and date/time variables are converted to the appropriate Date or POSIX objects in R, variable names are converted to lower case, SAS labels are associated with variables, and (by default) integer-valued variables are converted from storage mode double to integer. If the user ran PROC FORMAT CNTLOUT= in SAS and included the resulting dataset in the SAS version 5 transport file, variables having customized formats that do not include any ranges (i.e., variables having standard PROC FORMAT; VALUE label formats) will have their format labels looked up, and these variables are converted to S factors.

For those users having access to SAS, method='csv' is preferred when importing several SAS datasets. Run SAS macro exportlib.sas available from http://biostat.mc.vanderbilt.edu/twiki/pub/Main/Hmisc/exportlib.sas to convert all SAS datasets in a SAS data library (from any engine supported by your system) into CSV files. If any customized formats are used, it is assumed that the PROC FORMAT CNTLOUT= dataset is in the data library as a regular SAS dataset, as above.

SASdsLabels reads a file containing PROC CONTENTS printed output to parse dataset labels, assuming that PROC CONTENTS was run on an entire library.

Usage

sasxport.get(file, force.single = TRUE,
             method=c('read.xport','dataload','csv'), formats=NULL, allow=NULL)
sasdsLabels(file)

Arguments

file

name of a file containing the SAS transport file. file may be a URL beginning with http://. For sasdsLabels, file is the name of a file containing a PROC CONTENTS output listing. For

force.single

set to FALSE to keep integer-valued variables not exceeding $2^31-1$ in value from being converted to integer storage mode

method

set to "dataload" if you have the dataload executable installed and want to use it instead of read.xport. This seems to correct some errors in which rarely some factor variables are always missing when read by <

formats

a data frame or list (like that created by read.xport) containing PROC FORMAT output, if such output is not stored in the main transport file.

allow

a vector of characters allowed by Rthat should not be converted to periods in variable names. By default, underscores in variable names are converted to periods as with Rbefore version 1.9.

Value

• If there is more than one dataset in the transport file other than the PROC FORMAT file, the result is a list of data frames containing all the non-PROC FORMAT datasets. Otherwise the result is the single data frame. sasdsLabels returns a named vector of dataset labels, with names equal to the dataset names.

Details

See contents.list for a way to print the directory of SAS datasets when more than one was imported.

See Also

read.xport,label,sas.get, DateTimeClasses,lookup.xport, contents,describe

Examples

# SAS code to generate test dataset:
# libname y SASV5XPT "test2.xpt";
#
# PROC FORMAT; VALUE race 1=green 2=blue 3=purple; RUN;
# PROC FORMAT CNTLOUT=format;RUN;  * Name, e.g. 'format', unimportant;
# data test;
# LENGTH race 3 age 4;
# age=30; label age="Age at Beginning of Study";
# race=2;
# d1='3mar2002'd ;
# dt1='3mar2002 9:31:02'dt;
# t1='11:13:45't;
# output;
#
# age=31;
# race=4;
# d1='3jun2002'd ;
# dt1='3jun2002 9:42:07'dt;
# t1='11:14:13't;
# output;
# format d1 mmddyy10. dt1 datetime. t1 time. race race.;
# run;
# data z; LENGTH x3 3 x4 4 x5 5 x6 6 x7 7 x8 8;
#    DO i=1 TO 100;
#        x3=ranuni(3);
#        x4=ranuni(5);
#        x5=ranuni(7);
#        x6=ranuni(9);
#        x7=ranuni(11);
#        x8=ranuni(13);
#        output;
#        END;
#    DROP i;
#    RUN;
# PROC MEANS; RUN;
# PROC COPY IN=work OUT=y;SELECT test format z;RUN; *Creates test2.xpt;
w <- sasxport.get('test2.xpt')
# To use an existing copy of test2.xpt available on the web:
w <- sasxport.get('http://hesweb1.med.virginia.edu/biostat/s/data/sas/test2.xpt')

describe(w$test)   # see labels, format names for dataset test
# Note: if only one dataset (other than format) had been exported,
# just do describe(w) as sasxport.get would not create a list for that
lapply(w, describe)# see descriptive stats for both datasets
contents(w$test)   # another way to see variable attributes
lapply(w, contents)# show contents of both datasets
options(digits=7)  # compare the following matrix with PROC MEANS output
t(sapply(w$z, function(x)
 c(Mean=mean(x),SD=sqrt(var(x)),Min=min(x),Max=max(x))))