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:
$ Identificación.do.Paciente : chr "34" "41"
"42" "46" ...
$ Número.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 ...
$ Código.Concello : int 15030 15092 15030 15030 15019
15030 15032 15014 15005 15005 ...
$ Concello : chr "CORUÑA, A"
"VIMIANZO" "CORUÑA,
A" "CORUÑA, A" ...
$ Hospital.abrev. : chr "A CORUÑA" "A
CORUÑA" "A CORUÑA"
"A CORUÑA" ...
$ Motivo.de.Alta : chr "DESTINO A DOMICILIO"
"DESTINO A
DOMICILIO" "DESTINO A DOMICILIO" "DESTINO A DOMICILIO"
...
$ Cód..Diagnóstico.Ppal.completo : chr "218.0 " "890.1 "
"998.89" "650.
" ...
$ Diagnóstico.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 ...
$ Descrición..do.GRD : chr "PROC. SOBRE ÚTERO E ANEXOS POR
CA.IN SITU E PROCESO NON MALIGNO SEN CC" "OUTROS PROCEDEMENTOS
CIRÚRXICOS
POR LESIÓN TRAUMÁTICA SEN CC" "COMPLICACIÓNS DE TRATAMENTO SEN
CC" "PARTO
SEN COMPLICACIÓNS" ...
$ Peso.GRD : num 1.098 0.948 0.601 0.58 3.846 ...
$ Lista.de.códigos.de.diagnóstico : 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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You can read the files into a "list" -- you don't want to create unique object names for each one. files <- list.files(..pattern to match files..) results <- lapply(files, read.table, header = TRUE) On Wed, Jan 2, 2013 at 10:14 AM, Dominic Roye <dominic.roye at gmail.com> wrote:> 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 ... >> > > [[alternative HTML version deleted]] > > > ______________________________________________ > 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. >-- Jim Holtman Data Munger Guru What is the problem that you are trying to solve? Tell me what you want to do, not how you want to do it.
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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