[R] Read many cvs files

Thu Jan 3 20:49:27 CET 2013

This is what I do (a lot):

If all the files you want to read have the same structure, I  would suggest using dlply in package plyr to import them.

First set you working directory to the location of where you have your files ( use setwd()), then construct a vector of filenames you want to bring in:

library(plyr)
myfiles <- c("file1.csv", "file2.csv")

mydata <- dlply(myfiles, .progress="text")

HTH

James

James T. Durant, MSPH CIH
Environmental Health Scientist
US Agency for Toxic Substances and Disease Registry
Atlanta, GA 30341
770-488-0668

Message: 21
Date: Wed, 2 Jan 2013 16:14:57 +0100
From: Dominic Roye <dominic.roye at gmail.com>
To: R help <r-help at r-project.org>
Subject: [R] Read many cvs files
Message-ID:
	<CALvVS-EZHiMujH3aJnTMAEp60DVVnUnA7LTJdq0n6YiDMz2n8Q at mail.gmail.com>
Content-Type: text/plain

Hello R helpers,

I would like to automate this code for many files of the same type. But I
don?t know how to make it. In particular, i don?t know how to read many
files each one as an r object with the name of the file. Then a for loop
would be sufficient, right?

Many thanks and a happy new year.

Dominic

datos <- read.table('global2001.csv',head=T,sep=';',stringsAsFactors=F)

datos[datos==""] <- NA

temp <- datos[,19:53]

y <- split(temp,1:nrow(temp))
y2 <- lapply(y,function(x) paste(x[!is.na(x)],collapse=";"))

global2001 <- datos[,-19:-53]

global2001[1,"CODPA"] <- 1
global2001$CODPA <- y2
global2001$CODPA <- unlist(global2001$CODPA)

Example of a file:

> str(datos)
'data.frame':   112598 obs. of  53 variables:
 $ Identificaci?n.do.Paciente       : chr  "34" "41" "42" "46" ...
 $ N?mero.de.Historia               : int  3024659 3028931 3030905 3033514
3037754 3039062 3039851 3048020 3049659 3049659 ...
 $ TSI                              : chr  "580208NCEE0010"
"770802ROOR0019" "710720GEUS1015" "770319GLOO0011" ...
 $ Identificador.interno.de.episodio: int  2001033879 2001042319 2001036188
2001030007 2001039108 2001041196 2001063540 2001031533 2001031565
2001056967 ...
 $ Ano.Alta                         : int  2001 2001 2001 2001 2001 2001
2001 2001 2001 2001 ...
 $ Data.Ingreso                     : chr  "16/02/2001" "27/04/2001"
"09/03/2001" "18/01/2001" ...
 $ Data.Alta                        : chr  "20/02/2001" "30/04/2001"
"10/03/2001" "21/01/2001" ...
 $ Sexo                             : chr  "    MULLER" "    MULLER" "
HOME" "    MULLER" ...
 $ Idade.en.anos                    : int  43 23 29 23 48 27 80 42 42 42 ...
 $ C?digo.Concello                  : int  15030 15092 15030 15030 15019
15030 15032 15014 15005 15005 ...
 $ Concello                         : chr  "CORU?A, A" "VIMIANZO" "CORU?A,
A" "CORU?A, A" ...
 $ Hospital.abrev.                  : chr  "A CORU?A" "A CORU?A" "A CORU?A"
"A CORU?A" ...
 $ Motivo.de.Alta                   : chr  "DESTINO A DOMICILIO" "DESTINO A
DOMICILIO" "DESTINO A DOMICILIO" "DESTINO A DOMICILIO" ...
 $ C?d..Diagn?stico.Ppal.completo   : chr  "218.0 " "890.1 " "998.89" "650.
 " ...
 $ Diagn?stico.Ppal.completo        : chr  "LEIOMIOMA UTERINO SUBMUCOSO"
"HERIDA ABIERTA DE CADERA Y MUSLO-COMPLICADA" "OTRAS COMPLICACIONES
ESPECIFICADAS DE PROCEDIMIENTO" "PARTO NORMAL" ...
 $ GRD                              : int  359 443 453 373 796 372 14 758
450 450 ...
 $ Descrici?n..do.GRD               : chr  "PROC. SOBRE ?TERO E ANEXOS POR
CA.IN SITU E PROCESO NON MALIGNO SEN CC" "OUTROS PROCEDEMENTOS CIR?RXICOS
POR LESI?N TRAUM?TICA SEN CC" "COMPLICACI?NS DE TRATAMENTO SEN CC" "PARTO
SEN COMPLICACI?NS" ...
 $ Peso.GRD                         : num  1.098 0.948 0.601 0.58 3.846 ...
 $ Lista.de.c?digos.de.diagn?stico  : chr  "218.0" "890.1" "998.89" "650."
...
 $ X                                : chr  "" "E986" "780.2" "V27.0" ...
 $ X.1                              : chr  "" "" "780.4" "" ...
 $ X.2                              : chr  "" "" "381.3" "" ...
 $ X.3                              : chr  "" "" "" "" ...
 $ X.4                              : chr  "" "" "" "" ...
 $ X.5                              : chr  "" "" "" "" ...
 $ X.6                              : chr  "" "" "" "" ...
 $ X.7                              : chr  "" "" "" "" ...
 $ X.8                              : chr  "" "" "" "" ...
 $ X.9                              : chr  "" "" "" "" ...
 $ X.10                             : chr  "" "" "" "" ...
 $ X.11                             : chr  "" "" "" "" ...
 $ X.12                             : chr  "" "" "" "" ...
 $ X.13                             : chr  "" "" "" "" ...
 $ X.14                             : chr  "" "" "" "" ...
 $ X.15                             : chr  "" "" "" "" ...
 $ X.16                             : chr  "" "" "" "" ...
 $ X.17                             : chr  "" "" "" "" ...
 $ X.18                             : chr  "" "" "" "" ...
 $ X.19                             : chr  "" "" "" "" ...
 $ X.20                             : chr  "" "" "" "" ...
 $ X.21                             : chr  "" "" "" "" ...
 $ X.22                             : chr  "" "" "" "" ...
 $ X.23                             : num  NA NA NA NA NA NA NA NA NA NA ...
 $ X.24                             : chr  "" "" "" "" ...
 $ X.25                             : chr  "" "" "" "" ...
 $ X.26                             : num  NA NA NA NA NA NA NA NA NA NA ...
 $ X.27                             : chr  "" "" "" "" ...
 $ X.28                             : chr  "" "" "" "" ...
 $ X.29                             : num  NA NA NA NA NA NA NA NA NA NA ...
 $ X.30                             : num  NA NA NA NA NA NA NA NA NA NA ...
 $ X.31                             : num  NA NA NA NA NA NA NA NA NA NA ...
 $ X.32                             : num  NA NA NA NA NA NA NA NA NA NA ...
 $ X.33                             : logi  NA NA NA NA NA NA ...
>

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