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Ekkehardt.Altpeter@bag.admin.ch

2003-Feb-13 13:02 UTC

[R] ESRI shape file import and time-space models

Dear R user,

I am running R under Windows 2000.

 

I am looking for a routine for importing

 

-        shape files (ESRI) into R

-        dbase files (FOXPRO) into R

 

and I am looking for time-space models for description and prediction of
Bernoulli-, Binomial- and Poissonvaraibles.

 

Thank's a lot for a reply. 

 

Sincerely yours,

Ekkehardt Altpeter

Swiss Federal Office of Public Health.

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Stephane Dray

2003-Feb-13 14:19 UTC

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[R] ESRI shape file import and time-space models

See the Rmap project for importing shapefiles:

http://www.maths.lancs.ac.uk/Software/Rmap
>Dear R user,
>
>I am running R under Windows 2000.
>
>
>
>I am looking for a routine for importing
>
>
>
>-        shape files (ESRI) into R
>
>-        dbase files (FOXPRO) into R
>
>
>
>and I am looking for time-space models for description and
>prediction of Bernoulli-, Binomial- and Poissonvaraibles.
>
>
>
>Thank''s a lot for a reply.
>
>
>
>Sincerely yours,
>
>Ekkehardt Altpeter
>
>Swiss Federal Office of Public Health.
--
Stéphane DRAY
---------------------------------------------------------------
Biométrie et Biologie évolutive - Equipe "Écologie Statistique"
Universite Lyon 1 - Bat 711 - 69622 Villeurbanne CEDEX - France

Tel : 04 72 43 27 56			   Fax : 04 78 89 27 19
       04 72 43 27 57 	   E-mail : dray@biomserv.univ-lyon1.fr
---------------------------------------------------------------
ADE-4               http://pbil.univ-lyon1.fr/ADE-4/ADE-4F.html
---------------------------------------------------------------
	[[alternate HTML version deleted]]

david.whiting@ncl.ac.uk

2003-Feb-14 05:20 UTC

head link

[R] ESRI shape file import and time-space models

On Thu, Feb 13, 2003 at 12:36:51PM +0100, Ekkehardt.Altpeter at bag.admin.ch
wrote:> Dear R user,
> 
> I am running R under Windows 2000.
> 
> I am looking for a routine for importing
> 
> -        shape files (ESRI) into R
> 
> -        dbase files (FOXPRO) into R
I assume that as you say dbase (Foxpro) you mean Foxpro version < 3.0,
e.g. 2.x.  I don't know of a way of opening dbase/foxpro files from
within R (I think I saw once that RODBC can connect with dbase files,
and if it does I'm sure you'll hear from someone else who knows more
about it than me). 

If you have Foxpro and don't need an elegant solution, but just need to
get the job done then you can export files from foxpro as tab-delimited
files (COPY TO foxdata.txt DELIM WITH TAB) which you can then read into
R with:

dta <- read.delim("foxdata.txt", header=FALSE, sep="\t",
strip.white TRUE)

This gets the data in, but does not give you the field names.  I have
written a little foxpro program that creates a tab-delimited file with
the headers (field names) that seems to work.  Again, I read the data
into R with read.delim(). Let me know if you want me to send you the
Foxpro program.

HTH,

Dave
 
-- 
Dave Whiting
Dar es Salaam, Tanzania

Benjamin.STABLER@odot.state.or.us

2003-Feb-14 17:30 UTC

head link

[R] ESRI shape file import and time-space models

Attached are some functions that I wrote to read and write shapefiles and
dbfs easily from within R.  You do not need any additional libraries or C
code.  I am still working out a few bugs but I have tested it with quite a
few different files and it seems to be working pretty well.  There is little
documentation at this point though.  I'd appreciate any comments about the
code.  Thanks.

Benjamin Stabler
Transportation Planning Analysis Unit
Oregon Department of Transportation
555 13th Street NE, Suite 2
Salem, OR 97301  Ph: 503-986-4104


>Dear R user,
>I am running R under Windows 2000.
>I am looking for a routine for importing
 
>        shape files (ESRI) into R
>        dbase files (FOXPRO) into R
>and I am looking for time-space models for description and prediction of
>Bernoulli-, Binomial- and Poissonvaraibles.
>Thank's a lot for a reply. 
>Sincerely yours,
>Ekkehardt Altpeter
>Swiss Federal Office of Public Health.
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R. Herold

2003-Feb-16 17:51 UTC

head link

[R] ESRI shape file import and time-space models

Thanks for providing your functions, especially those for 
reading and writing dBase files (read.dbf and write.dbf), 
which presumably are of general interest because there is 
no other implementation for reading and writing these 
formats (apart from ODBC), as far as I know. 

However, I suggest changing one byte character readBin to 
readChar as the latter does not expect zero-terminated
strings which were not present in my dBase-III-files' headers.
One such header entry for example was (hex): 

4B 4C 49 4e 00 00 00 00 00 00 00 43 2B 00 00 00
02 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 

(field "KLIN", type "C" [note "43" followed by
"2B",
 not "00"], width/length 2, padded to size 32)

## ---------------------------------------------------
## From read.dbf: 
## Field Descriptions (32 bytes each)
for (i in 1:num.fields) {
  field.name.test <- readBin (infile, character(), 1, size=10,
endian="little")
  field.name      <- c (field.name, field.name.test)
  if (nchar (field.name.test)!=10) {
    file.temp <- readBin (infile,integer(), 10 - (nchar
(field.name.test)), 1, endian="little")
  }
  ## RH 2003-02-16: replaced readBin by readChar in next line 
  field.type   <- c (field.type, readChar (infile, 1))  
  ## RH 2003-02-16: incremented by 1 to 4 items in next line 
  ## to compensate for above change 
  file.temp    <- readBin (infile, integer(),  4, 1,
endian="little")
  field.length <- c (field.length, readBin (infile, integer(), 1, 1,
endian="little")) 
  file.temp    <- readBin (infile, integer(), 15, 1,
endian="little")
}
## ---------------------------------------------------

An enhancement might be to also set the appropriate type for 
date fields, maybe like this (although I don't know internals
of dBase date and time storage variants): 

## ---------------------------------------------------
## From read.dbf: 
## Set the numeric fields to numeric
for (i in 1:ncol(dbf)) {
  ## RH 2003-02-16: added next line for date type setting 
  if(fields$TYPE[i]=="D") {dbf[,i] <- strptime (as.character
(dbf[,i]),
format="%Y%m%d")}
  if(fields$TYPE[i]=="C") {dbf[,i] <- as.character (dbf[,i])}
  if(fields$TYPE[i]=="N") {dbf[,i] <- as.numeric (as.character
(dbf[,i]))}
  if(fields$TYPE[i]=="F") {dbf[,i] <- as.numeric (as.character
(dbf[,i]))
                           warning("Possible trouble converting numeric
field in the DBF\n") 
                          } 
} 
## ---------------------------------------------------

Thanks and greetings - Ralf Herold 

-- Dr. med. Ralf Herold  
| Koordinationszentrale Kompetenznetz
| P?diatrische Onkologie und H?matologie  
| http://www.kinderkrebsinfo.de/   
| Charit? Campus Virchow-Klinikum  
| Medizinische Fakult?t Humboldt-Universit?t  
| D-13353 Berlin, Augustenburger Platz 1  
| Raum 4.3425 4. Etage Mittelallee 8  
| Tel. +49 (30) 450-566834 Fax -566906  
| mailto:ralf.herold at charite.de  
> ----- Original Message ----- 
> From: Benjamin.STABLER at odot.state.or.us
> To: Ekkehardt.Altpeter at bag.admin.ch
> Cc: r-help at stat.math.ethz.ch
> Subject: Re: [R] ESRI shape file import and time-space models
> Date: Fri, 14 Feb 2003 08:29:12 -0800
[...]> Attached are some functions that I wrote to read and write 
> shapefiles and
> dbfs easily from within R.  You do not need any additional 
> libraries or C
> code.  I am still working out a few bugs but I have tested it 
[...]> Benjamin Stabler
> Transportation Planning Analysis Unit
> Oregon Department of Transportation
> 555 13th Street NE, Suite 2
> Salem, OR 97301  Ph: 503-986-4104[...]

Benjamin.STABLER@odot.state.or.us

2003-Feb-18 23:13 UTC

head link

[R] ESRI shape file import and time-space models

Thanks to R. Herold for the suggested change from readBin to readChar for
the field type in the field header descriptions.  The code below is the
revised read.dbf function.  Fan's odbc.dbase function is much faster than my
read.dbf() function, and it is defintely better for large files.  Thanks
also to Fan for the comments.  Finally, I am working on putting together a
package to read and write shapefiles.  

Regards,
Benjamin Stabler
Transportation Planning Analysis Unit
Oregon Department of Transportation
555 13th Street NE, Suite 2
Salem, OR 97301  Ph: 503-986-4104

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
~~~~~~~~~~~~~
#Read DBF format
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
~~~~~~~~~~~~~

read.dbf <- function(dbf.name) {
	
	infile<-file(dbf.name,"rb")
	
	#Header
	file.version <- readBin(infile,integer(), 1, size=1,
endian="little")
	file.year <- readBin(infile,integer(), 1, size=1, endian="little")
	file.month <- readBin(infile,integer(), 1, size=1,
endian="little")
	file.day <- readBin(infile,integer(), 1, size=1, endian="little")
	num.records <- readBin(infile,integer(), 1, size=4,
endian="little")
	header.length <- readBin(infile,integer(), 1, size=2,
endian="little")
	record.length <- readBin(infile,integer(), 1, size=2,
endian="little")
	file.temp <- readBin(infile,integer(), 20, size=1,
endian="little")
	header <- list(file.version,file.year, file.month, file.day,
num.records, header.length, record.length)
	names(header) <-
c("file.version","file.year","file.month","file.day","num.records","header.l
ength","record.length")
	rm(file.version,file.year, file.month, file.day, num.records,
header.length, record.length)
		
	#Calculate the number of fields
	num.fields <- (header$header.length-32-1)/32
	field.name <- NULL
	field.type <- NULL
	field.length <- NULL
	
	#Field Descriptions (32 bytes each)
	for (i in 1:num.fields) {
		field.name.test <- readBin(infile,character(), 1, size=10,
endian="little")
		field.name <- c(field.name,field.name.test)
		if (nchar(field.name.test)!=10) {
			file.temp <- readBin(infile,integer(),
10-(nchar(field.name.test)), 1, endian="little")
		}	
		field.type <- c(field.type,readChar(infile, 1))
		file.temp <- readBin(infile,integer(), 4, 1,
endian="little")
		field.length <- c(field.length,readBin(infile,integer(), 1,
1, endian="little"))
		file.temp <- readBin(infile,integer(), 15, 1,
endian="little")
	}
	
	#Create a table of the field info
	fields <-
data.frame(NAME=field.name,TYPE=field.type,LENGTH=field.length)
	#Set all fields with length<0 equal to correct number of characters
	fields$LENGTH[fields$LENGTH<0]<-(256+fields$LENGTH[fields$LENGTH<0])
	#Read in end of attribute descriptions terminator - should be
integer value 13
	file.temp <- readBin(infile,integer(), 1, 1, endian="little")
	#Increase the length of field 1 by one to account for the space at
the beginning of each record	
	fields$LENGTH[1]<-fields$LENGTH[1]+1
	#Add fields to the header list
	header <- c(header,fields=NULL)
	header$fields <- fields
	
	#Read in all the records data and the end of file value - should be
value 26
	all.records <- readBin(infile, integer(),
header$num.records*header$record.length, size=1, endian="little")
	file.temp <- readBin(infile,integer(), 1, 1, endian="little")
	close(infile)
	
	#Compress the binary values using run length encoding
	all.records <- rle(all.records)
	#Swap ASCII decimal codes for ASCII character codes
	ascii <-
c(32,46,48,49,50,51,52,53,54,55,56,57,65,66,67,68,69,70,71,72,73,74,75,76,77
,78,79,80,81,82,83,84,85,86,87,88,89,90,97,98,99,100,101,102,103,104,105,106
,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,33,35,36,37
,38,39,40,41,42,43,44,45,47,58,59,60,61,62,63,64,91,92,93,94,95,123,124,125,
126)
	ascii.values <- c("
",".","0","1","2","3","4","5","6","7","8","9","A","B","C","D","E","F","G","H
","I","J","K","L","M","N","O","P","Q","R","S","T","U","V","W","X","Y","Z","a
","b","c","d","e","f","g","h","i","j","k","l","m","n","o","p","q","r","s","t
","u","v","w","x","y","z","!","#","$","%","&","'","(",")","*","+","\,","-","
/",":",";","<","=",">","?","@","[","
","]","^","_","{","|","}","~")
	all.records$values <-
ascii.values[match(as.character(all.records$values),as.character(ascii),
nomatch=1)]
	all.records <- inverse.rle(all.records)
	
	#Create a matrix of the ASCII data by record
	base.data <-
t(matrix(all.records,header$record.length,header$num.records))
	rm(all.records)
	
	#Function to collapse the ASCII codes, string split them and replace
" " with ""
	format.record <- function(record) {
		record <- paste(record,collapse="")
		record <- substring(record,
c(1,cumsum(fields$LENGTH)[1:length(cumsum(fields$LENGTH))-1]+1),cumsum(field
s$LENGTH))
		record <- gsub(" + ","", record)
		record
	}
	#Format the base.data ASCII record stream
	dbf <- as.data.frame(t(apply(base.data,1,format.record)))
	#Set the numeric fields to numeric
	for (i in 1:ncol(dbf)) {
		if(fields$TYPE[i]=="C") { dbf[[i]] <- as.character(dbf[[i]])
}
		if(fields$TYPE[i]=="N") { dbf[[i]] <-
as.numeric(as.character(dbf[[i]])) }
		if(fields$TYPE[i]=="F") { dbf[[i]] <-
as.numeric(as.character(dbf[[i]])) 
			warning("Possible trouble converting numeric field
in the DBF\n")
		}
	}
	colnames(dbf) <- as.character(fields$NAME)
	list(dbf=dbf, header=header)
}
>-----Original Message-----
>From: R. Herold [mailto:ralf.herold at charite.de]
>Sent: Sunday, February 16, 2003 8:49 AM
>To: r-help at stat.math.ethz.ch
>Cc: STABLER Benjamin
>Subject: Re: Re: [R] ESRI shape file import and time-space models
>
>
>Thanks for providing your functions, especially those for 
>reading and writing dBase files (read.dbf and write.dbf), 
>which presumably are of general interest because there is 
>no other implementation for reading and writing these 
>formats (apart from ODBC), as far as I know. 
>
>However, I suggest changing one byte character readBin to 
>readChar as the latter does not expect zero-terminated
>strings which were not present in my dBase-III-files' headers.
>One such header entry for example was (hex): 
>
>4B 4C 49 4e 00 00 00 00 00 00 00 43 2B 00 00 00
>02 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
>
>(field "KLIN", type "C" [note "43" followed by
"2B",
> not "00"], width/length 2, padded to size 32)
>
>## ---------------------------------------------------
>## From read.dbf: 
>## Field Descriptions (32 bytes each)
>for (i in 1:num.fields) {
>  field.name.test <- readBin (infile, character(), 1, size=10,
>endian="little")
>  field.name      <- c (field.name, field.name.test)
>  if (nchar (field.name.test)!=10) {
>    file.temp <- readBin (infile,integer(), 10 - (nchar
>(field.name.test)), 1, endian="little")
>  }
>  ## RH 2003-02-16: replaced readBin by readChar in next line 
>  field.type   <- c (field.type, readChar (infile, 1))  
>  ## RH 2003-02-16: incremented by 1 to 4 items in next line 
>  ## to compensate for above change 
>  file.temp    <- readBin (infile, integer(),  4, 1,
endian="little")
>  field.length <- c (field.length, readBin (infile, integer(), 1, 1,
>endian="little")) 
>  file.temp    <- readBin (infile, integer(), 15, 1,
endian="little")
>}
>## ---------------------------------------------------
>
>An enhancement might be to also set the appropriate type for 
>date fields, maybe like this (although I don't know internals
>of dBase date and time storage variants): 
>
>## ---------------------------------------------------
>## From read.dbf: 
>## Set the numeric fields to numeric
>for (i in 1:ncol(dbf)) {
>  ## RH 2003-02-16: added next line for date type setting 
>  if(fields$TYPE[i]=="D") {dbf[,i] <- strptime (as.character
(dbf[,i]),
>format="%Y%m%d")}
>  if(fields$TYPE[i]=="C") {dbf[,i] <- as.character (dbf[,i])}
>  if(fields$TYPE[i]=="N") {dbf[,i] <- as.numeric (as.character
>(dbf[,i]))}
>  if(fields$TYPE[i]=="F") {dbf[,i] <- as.numeric (as.character
>(dbf[,i]))
>                           warning("Possible trouble converting numeric
>field in the DBF\n") 
>                          } 
>} 
>## ---------------------------------------------------
>
>Thanks and greetings - Ralf Herold 
>
>-- Dr. med. Ralf Herold  
>| Koordinationszentrale Kompetenznetz
>| P?diatrische Onkologie und H?matologie  
>| http://www.kinderkrebsinfo.de/   
>| Charit? Campus Virchow-Klinikum  
>| Medizinische Fakult?t Humboldt-Universit?t  
>| D-13353 Berlin, Augustenburger Platz 1  
>| Raum 4.3425 4. Etage Mittelallee 8  
>| Tel. +49 (30) 450-566834 Fax -566906  
>| mailto:ralf.herold at charite.de  
>
>> ----- Original Message ----- 
>> From: Benjamin.STABLER at odot.state.or.us
>> To: Ekkehardt.Altpeter at bag.admin.ch
>> Cc: r-help at stat.math.ethz.ch
>> Subject: Re: [R] ESRI shape file import and time-space models
>> Date: Fri, 14 Feb 2003 08:29:12 -0800
>[...]
>> Attached are some functions that I wrote to read and write 
>> shapefiles and
>> dbfs easily from within R.  You do not need any additional 
>> libraries or C
>> code.  I am still working out a few bugs but I have tested it 
>[...]
>> Benjamin Stabler
>> Transportation Planning Analysis Unit
>> Oregon Department of Transportation
>> 555 13th Street NE, Suite 2
>> Salem, OR 97301  Ph: 503-986-4104
>[...]
>

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