I successfully wrote a for loop in R. That is okay and I am very happy that it works. But I also want to understand what I've done exactly because I will have to work with loops later on in my analysis as well.
I work with Raster Data (DEMs). I load them into the environment as rasters and then I use the getValues function in the loop as I want to do some calculations. Looks as follows:
list <- dir(pattern=".tif", full.names=T)
tif.files <- list()
tif.files.values <- tif.files
for (i in 1: length(list)){
tif.files[[i]] <- raster (list[[i]])
tif.files.values[[i]] <- getValues(tif.files[[i]])
}
Okay, so far so good. I don't get why I have to specify tif.files and tif.files.values before I use them in the loop and I don't know why to specify them exactly how I did that. For the first part, the raster operation, I had a pattern. Maybe someone can explain the context. I really want to understand R.
When you do:
tif.files[[i]] <- raster (list[[i]])
then tif.files[[i]] is the result of running raster(list[[i]]), so that is storing the raster object. This object contains the metadata (extent, number of rows, cols etc) and the data, although if the tiff is huge it doesn't actually read it in at the time.
tif.files.values[[i]] <- getValues(tif.files[[i]])
that line calls getValues on the raster object, which reads the values from the raster and returns a vector. The values of the grid cells are now in tif.files.values[[i]].
Experiment by printing tif.files[[1]] and tif.files.values[[1]] at the R prompt.
Note
This is R, not RStudio, which is the interface you are using that has all the buttons and menus. The R language exists quite happily without it, and your question is just a language question. I've edited and tagged it now for you.
I have some r code that I've used in the past to produce topic models. Everything was working fine until I updated all of my r packages in the hopes of fixing a slightly unrelated problem. Now, code which had previously worked seems to be broken and I can't figure out what to do.
I read this post and found it very helpful in setting this up originally. It describes a method of cleaning blank rows after sparse terms have been removed to set up subsequent analysis. Here is what happens when I enter the same code with my current packages:
> rowTotals <- apply(a.dtm.t, 1, sum) #Find the sum of words in each Document
> a.dtm.t.rt <- a.dtm.t[rowTotals>0]
Error in `[.simple_triplet_matrix`(a.dtm.t, rowTotals > 0) :
Logical vector subscripting disabled for this object.
Does anyone know how I can go about locating the problem, and roll back to a working solution? Thanks.
Try a.dtm.t.rt <- a.dtm.t[which(rowTotals>0)]
If that doesn't work then you need to show a reproducible example. We have no idea what anything you're doing here is.
I find the same problem as yours. I use slam package to solve this issue.
library(slam)
# take tdm as a large term-document matrix
freq <- rowapply_simple_triplet_matrix(tdm,sum)
Also the colapply_simple_triplet_matrix will help to handle the sparse matrix
I have a dataset(300MB) on which I wish to run k means clustering using Mahout. The data is in a form of csv which contains only numerical values. Is it still necessary to input the file in vectorized format for the mahout k means command? If not, how can i run the k means command directly on my csv file without converting it to a vector format?
If your data is 300 MB, the answer is don't use Mahout at all.
Really ONLY EVER use Mahout when your data no longer fits into memory. Map Reduce is expensive, you only want to use it when you can't solve the problem without.
Being a programmer I occasionally find the need to analyze large amounts of data such as performance logs or memory usage data, and I am always frustrated by how much time it takes me to do something that I expect to be easier.
As an example to put the question in context, let me quickly show you an example from a CSV file I received today (heavily filtered for brevity):
date,time,PS Eden Space used,PS Old Gen Used, PS Perm Gen Used
2011-06-28,00:00:03,45004472,184177208,94048296
2011-06-28,00:00:18,45292232,184177208,94048296
I have about 100,000 data points like this with different variables that I want to plot in a scatter plot in order to look for correlations. Usually the data needs to be processed in some way for presentation purposes (such as converting nanoseconds to milliseconds and rounding fractional values), some columns may need to be added or inverted, or combined (like the date/time columns).
The usual recommendation for this kind of work is R and I have recently made a serious effort to use it, but after a few days of work my experience has been that most tasks that I expect to be simple seem to require many steps and have special cases; solutions are often non-generic (for example, adding a data set to an existing plot). It just seems to be one of those languages that people love because of all the powerful libraries that have accumulated over the years rather than the quality and usefulness of the core language.
Don't get me wrong, I understand the value of R to people who are using it, it's just that given how rarely I spend time on this kind of thing I think that I will never become an expert on it, and to a non-expert every single task just becomes too cumbersome.
Microsoft Excel is great in terms of usability but it just isn't powerful enough to handle large data sets. Also, both R and Excel tend to freeze completely (!) with no way out other than waiting or killing the process if you accidentally make the wrong kind of plot over too much data.
So, stack overflow, can you recommend something that is better suited for me? I'd hate to have to give up and develop my own tool, I have enough projects already. I'd love something interactive that could use hardware acceleration for the plot and/or culling to avoid spending too much time on rendering.
#flodin It would have been useful for you to provide an example of the code you use to read in such a file to R. I regularly work with data sets of the size you mention and do not have the problems you mention. One thing that might be biting you if you don't use R often is that if you don't tell R what the column-types R, it has to do some snooping on the file first and that all takes time. Look at argument colClasses in ?read.table.
For your example file, I would do:
dat <- read.csv("foo.csv", colClasses = c(rep("character",2), rep("integer", 3)))
then post process the date and time variables into an R date-time object class such as POSIXct, with something like:
dat <- transform(dat, dateTime = as.POSIXct(paste(date, time)))
As an example, let's read in your example data set, replicate it 50,000 times and write it out, then time different ways of reading it in, with foo containing your data:
> foo <- read.csv("log.csv")
> foo
date time PS.Eden.Space.used PS.Old.Gen.Used
1 2011-06-28 00:00:03 45004472 184177208
2 2011-06-28 00:00:18 45292232 184177208
PS.Perm.Gen.Used
1 94048296
2 94048296
Replicate that, 50000 times:
out <- data.frame(matrix(nrow = nrow(foo) * 50000, ncol = ncol(foo)))
out[, 1] <- rep(foo[,1], times = 50000)
out[, 2] <- rep(foo[,2], times = 50000)
out[, 3] <- rep(foo[,3], times = 50000)
out[, 4] <- rep(foo[,4], times = 50000)
out[, 5] <- rep(foo[,5], times = 50000)
names(out) <- names(foo)
Write it out
write.csv(out, file = "bigLog.csv", row.names = FALSE)
Time loading the naive way and the proper way:
system.time(in1 <- read.csv("bigLog.csv"))
system.time(in2 <- read.csv("bigLog.csv",
colClasses = c(rep("character",2),
rep("integer", 3))))
Which is very quick on my modest laptop:
> system.time(in1 <- read.csv("bigLog.csv"))
user system elapsed
0.355 0.008 0.366
> system.time(in2 <- read.csv("bigLog.csv",
colClasses = c(rep("character",2),
rep("integer", 3))))
user system elapsed
0.282 0.003 0.287
For both ways of reading in.
As for plotting, the graphics can be a bit slow, but depending on your OS this can be sped up a bit by altering the device you plot - on Linux for example, don't use the default X11() device, which uses Cairo, instead try the old X window without anti-aliasing. Also, what are you hoping to see with a data set as large as 100,000 observations on a graphics device with not many pixels? Perhaps try to rethink your strategy for data analysis --- no stats software will be able to save you from doing something ill-advised.
It sounds as if you are developing code/analysis as you go along, on the full data set. It would be far more sensible to just work with a small subset of the data when developing new code or new ways of looking at your data, say with a random sample of 1000 rows, and work with that object instead of the whole data object. That way you guard against accidentally doing something that is slow:
working <- out[sample(nrow(out), 1000), ]
for example. Then use working instead of out. Alternatively, whilst testing and writing a script, set argument nrows to say 1000 in the call to load the data into R (see ?read.csv). That way whilst testing you only read in a subset of the data, but one simple change will allow you to run your script against the full data set.
For data sets of the size you are talking about, I see no problem whatsoever in using R. Your point, about not becoming expert enough to use R, will more than likely apply to other scripting languages that might be suggested, such as python. There is a barrier to entry, but that is to be expected if you want the power of a language such as python or R. If you write scripts that are well commented (instead of just plugging away at the command line), and focus on a few key data import/manipulations, a bit of plotting and some simple analysis, it shouldn't take long to masters that small subset of the language.
R is a great tool, but I never had to resort to use it. Instead I find python to be more than adequate for my needs when I need to pull data out of huge logs. Python really comes with "batteries included" with built-in support for working with csv-files
The simplest example of reading a CSV file:
import csv
with open('some.csv', 'rb') as f:
reader = csv.reader(f)
for row in reader:
print row
To use another separator, e.g. tab and extract n-th column, use
spamReader = csv.reader(open('spam.csv', 'rb'), delimiter='\t')
for row in spamReader:
print row[n]
To operate on columns use the built-in list data-type, it's extremely versatile!
To create beautiful plots I use matplotlib
code
The python tutorial is a great way to get started! If you get stuck, there is always stackoverflow ;-)
There seem to be several questions mixed together:
Can you draw plots quicker and more easily?
Can you do things in R with less learning effort?
Are there other tools which require less learning effort than R?
I'll answer these in turn.
There are three plotting systems in R, namely base, lattice and ggplot2 graphics. Base graphics will render quickest, but making them look pretty can involve pathological coding. ggplot2 is the opposite, and lattice is somewhere in between.
Reading in CSV data, cleaning it and drawing a scatterplot sounds like a pretty straightforward task, and the tools are definitely there in R for solving such problems. Try asking a question here about specific bits of code that feel clunky, and we'll see if we can fix it for you. If your datasets all look similar, then you can probably reuse most of your code over and over. You could also give the ggplot2 web app a try.
The two obvious alternative languages for data processing are MATLAB (and its derivatives: Octave, Scilab, AcslX) and Python. Either of these will be suitable for your needs, and MATLAB in particular has a pretty shallow learning curve. Finally, you could pick a graph-specific tool like gnuplot or Prism.
SAS can handle larger data sets than R or Excel, however many (if not most) people--myself included--find it a lot harder to learn. Depending on exactly what you need to do, it might be worthwhile to load the CSV into an RDBMS and do some of the computations (eg correlations, rounding) there, and then export only what you need to R to generate graphics.
ETA: There's also SPSS, and Revolution; the former might not be able to handle the size of data that you've got, and the latter is, from what I've heard, a distributed version of R (that, unlike R, is not free).
I can't find something to the effect of an undo command in R (neither on An Introduction to R nor in R in a Nutshell). I am particularly interested in undoing/deleting when dealing with interactive graphs.
What approaches do you suggest?
You should consider a different approach which leads to reproducible work:
Pick an editor you like and which has R support
Write your code in 'snippets', ie short files for functions, and then use the facilities of the editor / R integration to send the code to the R interpreter
If you make a mistake, re-edit your snippet and run it again
You will always have a log of what you did
All this works tremendously well in ESS which is why many experienced R users like this environment. But editors are a subjective and personal choice; other people like Eclipse with StatET better. There are other solutions for Mac OS X and Windows too, and all this has been discussed countless times before here on SO and on other places like the R lists.
In general I do adopt Dirk's strategy. You should aim for your code to be a completely reproducible record of how you have transformed your raw data into output.
However, if you have complex code it can take a long time to re-run it all. I've had code that takes over 30 minutes to process the data (i.e., import, transform, merge, etc.).
In these cases, a single data-destroying line of code would require me to wait 30 minutes to restore my workspace.
By data destroying code I mean things like:
x <- merge(x, y)
df$x <- df$x^2
e.g., merges, replacing an existing variable with a transformation, removing rows or columns, and so on. In these cases, it's easy, especially when first learning R to make a mistake.
To avoid having to wait this 30 minutes, I adopt several strategies:
If I'm about to do something where there's a risk of destroying my active objects, I'll first copy the result into a temporary object. I'll then check that it worked with the temporary object and then rerun replacing it with the proper object.
E.g., first run temp <- merge(x, y); check that it worked str(temp); head(temp); tail(temp) and if everything looks good x <- merge(x, y)
As is common in psychological research, I often have large data frames with hundreds of variables and different subsets of cases. For a given analysis (e.g., a table, a figure, some results text), I'll often extract just the subset of cases and variables that I need into a separate object for the analysis and work with that object when preparing and finalising my analysis code. That way, I'm less likely to accidentally damage my main data frame. This assumes that the results of the analysis does not need to be fed back into the main data frame.
If I have finished performing a large number of complex data transformations, I may save a copy of the core workspace objects. E.g., save(x, y, z , file = 'backup.Rdata') That way, If I make a mistake, I only have to reload these objects.
df$x <- NULL is a handy way of removing a variable in a data frame that you did not want to create
However, in the end I still run all the code from scratch to check that the result is reproducible.