How do I use lapply to load files into the global environment? - r

I have the following working code:
############################################
###Read in all the wac gzip files###########
###Add some calculated fields ###########
############################################
library(readr)
setwd("N:/Dropbox/_BonesFirst/65_GIS_Raw/LODES/")
directory<-("N:/Dropbox/_BonesFirst/65_GIS_Raw/LODES/")
to.readin <- as.list(list.files(pattern="2002.csv"))
LEHD2002<-lapply(to.readin, function(x) {
read.table(gzfile(x), header = TRUE, sep = ",", colClasses = "numeric", stringsAsFactors = FALSE)
})
But I would like to load the things from lapply into the global environment, for debugging reasons.
This provides a way to do so.
# Load data sets
lapply(filenames, load, .GlobalEnv)
But when I attempt to use it, I get the following error:
Error in FUN(X[[i]], ...) : bad restore file magic number (file may be
corrupted) -- no data loaded In addition: Warning message: file
‘az_wac_S000_JT00_2004.csv.gz’ has magic number 'w_geo' Use of save
versions prior to 2 is deprecated
Am I doing something wrong, or is 'load' deprecated or the like?
The gzfile(x) converts the .gz (zipped) file to a .csv so that shouldn't be an issue...

load loads files in a binary format (e.g., .rda files). You're loading in files in a textual format, .csv files. This is why you're using read.table. When you try to read textual format files using load, you will get that error.
The usage: lapply(filenames, load, .GlobalEnv), passes .GlobalEnv to load, not to lapply. This is just a different way of reading in a list of files that are in a different format than yours. load can put the objects in a different environment as a way to protect you from overwriting objects in your current environment with the same name as the objects you're loading. Binary objects created using save (which you can load in with load) carry their names with them. When you load them in, you do not assign them to a name. They are accessible in the environment you choose to load them into with their original name.
Both methods load the objects into .GlobalEnv. So your code works the way you want it to. You can tell that your objects have not somehow been read into a different environment by trying to access them after you run the code. If you can access them using the object you named them with

Quick and dirty way is to load it into the global environment, with <<- rather than <-
LEHD2002<<-lapply(to.readin, function(x)
LEHD2002<-lapply(to.readin, function(x)
attach() can also be used; but is touchier, and attaching multiple files makes a mess. (ie, make sure you detach() any files you attach().

Related

Creating objects from all .xlsx documents in working directory

I am trying to create objects from all files in working directory with name of the original file. I tried to go the following way, but couldn't solve appearing problems.
# - SETTING WD
getwd()
setwd("PATH TO THE FILE")
library(readxl)
# - CREATING OBJECTS
file_objects <- list.files()
xlsx_objects <- unlist(grep(".xlsx",file_objects,value = T))
for (i in xlsx_objects) {
xlsx_objects[i] <- read_xlsx(xlsx_objects[i], header = T)
}
I tried to paste [i]item from "xlsx_objects" with path to WD but it only created a list of files names from docs in WD.
I also find information, that read.csv can read only one file at the time, but I guess that it should be the case with for loop, right? It is reading only one file at the time.
Using lapply (as described in this forum) I was able to get the data in the environment, but argument header didn't work, I lost names of my docs in that object which does not have desired structure. I am though looking for having these files in separated objects without calling every document exclusively.
IIUC, you could do something like:
files = list.files("PATH TO THE FILE", full.names = T, pattern = 'xlsx')
list_files = map(files, readxl::read_excel)
(You can't use read.csv to read excel files)
Also I recommend reading about R Projects so you don't have to use setwd() ever again, which makes your code harder to reproduce down the pipeline

Can convert a string to an object but can't save() it -- why? [duplicate]

I am repeatedly applying a function to read and process a bunch of csv files. Each time it runs, the function creates a data frame (this.csv.data) and uses save() to write it to a .RData file with a unique name. Problem is, later when I read these .RData files using load(), the loaded variable names are not unique, because each one loads with the name this.csv.data....
I'd like to save them with unique tags so that they come out properly named when I load() them. I've created the following code to illustrate .
this.csv.data = list(data=c(1:9), unique_tag = "some_unique_tag")
assign(this.csv.data$unique_tag,this.csv.data$data)
# I want to save the data,
# with variable name of <unique_tag>,
# at a file named <unique_tag>.dat
saved_file_name <- paste(this.csv.data$unique_tag,"RData",sep=".")
save(get(this.csv.data$unique_tag), saved_file_name)
but the last line returns:
"Error in save(get(this_unique_tag), file = data_tag) :
object ‘get(this_unique_tag)’ not found"
even though the following returns the data just fine:
get(this.csv.data$unique_tag)
Just name the arguments you use. With your code the following works fine:
save(list = this.csv.data$unique_tag, file=saved_file_name)
My preference is to avoid the name in the RData file on load:
obj = local(get(load('myfile.RData')))
This way you can load various RData files and name the objects whatever you want, or store them in a list etc.
You really should use saveRDS/readRDS to serialize your objects.
save and load are for saving whole environments.
saveRDS(this.csv.data, saved_file_name)
# later
mydata <- readRDS(saved_file_name)
you can use
save.image("myfile.RData")
This worked for me:
env <- new.env()
env[[varname]] <- object_to_save
save(list=c(varname), envir=env, file='out.Rda')
You could probably do it without a new env (but I didn't try this):
.GlobalEnv[[varname]] <- object_to_save
save(list=c(varname), envir=.GlobalEnv, file='out.Rda')
You might even be able to remove the envir variable.

readxl::read_xls returns "libxls error: Unable to open file"

I have multiple .xls (~100MB) files from which I would like to load multiple sheets (from each) into R as a dataframe. I have tried various functions, such as xlsx::xlsx2 and XLConnect::readWorksheetFromFile, both of which always run for a very long time (>15 mins) and never finish and I have to force-quit RStudio to keep working.
I also tried gdata::read.xls, which does finish, but it takes more than 3 minutes per one sheet and it cannot extract multiple sheets at once (which would be very helpful to speed up my pipeline) like XLConnect::loadWorkbook can.
The time it takes these functions to execute (and I am not even sure the first two would ever finish if I let them go longer) is way too long for my pipeline, where I need to work with many files at once. Is there a way to get these to go/finish faster?
In several places, I have seen a recommendation to use the function readxl::read_xls, which seems to be widely recommended for this task and should be faster per sheet. This one, however, gives me an error:
> # Minimal reproducible example:
> setwd("/Users/USER/Desktop")
> library(readxl)
> data <- read_xls(path="test_file.xls")
Error:
filepath: /Users/USER/Desktop/test_file.xls
libxls error: Unable to open file
I also did some elementary testing to make sure the file exists and is in the correct format:
> # Testing existence & format of the file
> file.exists("test_file.xls")
[1] TRUE
> format_from_ext("test_file.xls")
[1] "xls"
> format_from_signature("test_file.xls")
[1] "xls"
The test_file.xls used above is available here.
Any advice would be appreciated in terms of making the first functions run faster or the read_xls run at all - thank you!
UPDATE:
It seems that some users are able to open the file above using the readxl::read_xls function, while others are not, both on Mac and Windows, using the most up to date versions of R, Rstudio, and readxl. The issue has been posted on the readxl GitHub and has not been resolved yet.
I downloaded your dataset and read each excel sheet in this way (for example, for sheets "Overall" and "Area"):
install.packages("readxl")
library(readxl)
library(data.table)
dt_overall <- as.data.table(read_excel("test_file.xls", sheet = "Overall"))
area_sheet <- as.data.table(read_excel("test_file.xls", sheet = "Area"))
Finally, I get dt like this (for example, only part of the dataset for the "Area" sheet):
Just as well, you can use the read_xls function instead read_excel.
I checked, it also works correctly and even a little faster, since read_excel is a wrapper over read_xls and read_xlsx functions from readxl package.
Also, you can use excel_sheets function from readxl package to read all sheets of your Excel file.
UPDATE
Benchmarking is done with microbenchmark package for the following packages/functions: gdata::read.xls, XLConnect::readWorksheetFromFile and readxl::read_excel.
But XLConnect it's a Java-based solution, so it requires a lot of RAM.
I found that I was unable to open the file with read_xl immediately after downloading it, but if I opened the file in Excel, saved it, and closed it again, then read_xl was able to open it without issue.
My suggested workaround for handling hundreds of files is to build a little C# command line utility that opens, saves, and closes an Excel file. Source code is below, the utility can be compiled with visual studio community edition.
using System.IO;
using Excel = Microsoft.Office.Interop.Excel;
namespace resaver
{
class Program
{
static void Main(string[] args)
{
string srcFile = Path.GetFullPath(args[0]);
Excel.Application excelApplication = new Excel.Application();
excelApplication.Application.DisplayAlerts = false;
Excel.Workbook srcworkBook = excelApplication.Workbooks.Open(srcFile);
srcworkBook.Save();
srcworkBook.Close();
excelApplication.Quit();
}
}
}
Once compiled, the utility can be called from R using e.g. system2().
I will propose a different workflow. If you happen to have LibreOffice installed, then you can convert your excel files to csv programatically. I have Linux, so I do it in bash, but I'm sure it can be possible in macOS.
So open a terminal and navigate to the folder with your excel files and run in terminal:
for i in *.xls
do soffice --headless --convert-to csv "$i"
done
Now in R you can use data.table::fread to read your files with a loop:
Scenario 1: the structure of files is different
If the structure of files is different, then you wouldn't want to rbind them together. You could run in R:
files <- dir("path/to/files", pattern = ".csv")
all_files <- list()
for (i in 1:length(files)){
fileName <- gsub("(^.*/)(.*)(.csv$)", "\\2", files[i])
all_files[[fileName]] <- fread(files[i])
}
If you want to extract your named elements within the list into the global environment, so that they can be converted into objects, you can use list2env:
list2env(all_files, envir = .GlobalEnv)
Please be aware of two things: First, in the gsub call, the direction of the slash. And second, list2env may overwrite objects in your Global Environment if they have the same name as the named elements within the list.
Scenario 2: the structure of files is the same
In that case it's likely you want to rbind them all together. You could run in R:
files <- dir("path/to/files", pattern = ".csv")
joined <- list()
for (i in 1:length(files)){
joined <- rbindlist(joined, fread(files[i]), fill = TRUE)
}
On my system, i had to use path.expand.
R> file = "~/blah.xls"
R> read_xls(file)
Error:
filepath: ~/Dropbox/signal/aud/rba/balsheet/data/a03.xls
libxls error: Unable to open file
R> read_xls(path.expand(file)) # fixed
Resaving your file and you can solve your problem easily.
I also find this problem before but I get the answer from your discussion.
I used the read_excel() to open those files.
I was seeing a similar error and wanted to share a short-term solution.
library(readxl)
download.file("https://mjwebster.github.io/DataJ/spreadsheets/MLBpayrolls.xls", "MLBPayrolls.xls")
MLBpayrolls <- read_excel("MLBpayrolls.xls", sheet = "MLB Payrolls", na = "n/a")
Yields (on some systems in my classroom but not others):
Error: filepath: MLBPayrolls.xls libxls error: Unable to open file
The temporary solution was to paste the URL of the xls file into Firefox and download it via the browser. Once this was done we could run the read_excel line without error.
This was happening today on Windows 10, with R 3.6.2 and R Studio 1.2.5033.
If you have downloaded the .xls data from the internet, even if you are opening it in Ms.Excel, it will open a prompt first asking to confirm if you trust the source, see below screenshot, I am guessing this is the reason R (read_xls) also can't open it, as it's considered unsafe. Save it as .xlsx file and then use read_xlsx() or read_excel().
Even thought this is not a code-based solution, I just changed the type file. For instance, instead of xls I saved as csv or xlsx. Then I opened it as regular one.
I worked it for me, because when I opened my xlsfile, I popped up the message: "The file format and extension of 'file.xls'' don't match. The file could be corrupted or unsafe..."

Can I know what is in my .Rdata file without opening it [duplicate]

I sometimes use print( load( "myDataFile.RData" ) ) to list the contents of a data file when I load it. Is there a way to list the contents without loading the objects contained in the data file?
I do not think you could do that without loading the object.
A solution could be to save the R objects with a wrapper to save, which function would save the object AND the structure of the object to a special Rdata file. Later you could load the special binary file with a wrapper to load, where you could specify to only list the structure of the data.
I have done something like this in a very basic package, named saves, can be found on CRAN.
Update: I made up a very simple metadata solution
save.ls <- function(x, file) {
save(list=x, file=file)
l <- ls()
save(l, file=paste(file, 'ls', sep=''))
}
load.ls <- function(file) {
attach(paste(file, 'ls', sep=''));
return(l)
detach(pos=2)
}
Save with save.ls instead of save and load with load.ls to test. Meta information is saved in separate file (ending in "ls"), but the mechanism could be improved easily e.g. making a tar archive (like I do in the package linked above) of the Rdata object and the file containing the metadata.
attach(file);ls(pos=2);detach(pos=2)
That'll do it. Probably. #untested
In R v3.0.1 the load() function got a new argument. Loading an RData file with
load("mydata.RData", verbose=TRUE)
will show you the objects that are loaded. Of course, it still means you have to load the object.
Maybe,
load( "myDataFile.RData",ex<-new.env() )
content=ls.str(ex)

How to save() with a particular variable name

I am repeatedly applying a function to read and process a bunch of csv files. Each time it runs, the function creates a data frame (this.csv.data) and uses save() to write it to a .RData file with a unique name. Problem is, later when I read these .RData files using load(), the loaded variable names are not unique, because each one loads with the name this.csv.data....
I'd like to save them with unique tags so that they come out properly named when I load() them. I've created the following code to illustrate .
this.csv.data = list(data=c(1:9), unique_tag = "some_unique_tag")
assign(this.csv.data$unique_tag,this.csv.data$data)
# I want to save the data,
# with variable name of <unique_tag>,
# at a file named <unique_tag>.dat
saved_file_name <- paste(this.csv.data$unique_tag,"RData",sep=".")
save(get(this.csv.data$unique_tag), saved_file_name)
but the last line returns:
"Error in save(get(this_unique_tag), file = data_tag) :
object ‘get(this_unique_tag)’ not found"
even though the following returns the data just fine:
get(this.csv.data$unique_tag)
Just name the arguments you use. With your code the following works fine:
save(list = this.csv.data$unique_tag, file=saved_file_name)
My preference is to avoid the name in the RData file on load:
obj = local(get(load('myfile.RData')))
This way you can load various RData files and name the objects whatever you want, or store them in a list etc.
You really should use saveRDS/readRDS to serialize your objects.
save and load are for saving whole environments.
saveRDS(this.csv.data, saved_file_name)
# later
mydata <- readRDS(saved_file_name)
you can use
save.image("myfile.RData")
This worked for me:
env <- new.env()
env[[varname]] <- object_to_save
save(list=c(varname), envir=env, file='out.Rda')
You could probably do it without a new env (but I didn't try this):
.GlobalEnv[[varname]] <- object_to_save
save(list=c(varname), envir=.GlobalEnv, file='out.Rda')
You might even be able to remove the envir variable.

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