Say I'm training models:
lm.1, lm.2, ... , lm.100
I would like to refer back to these later in my code for various purposes: say to inspect coefficients, run test data against them, etc.
What data structure should I use to store them in?
A list is what I've been using but lists for some reason seem a bit unwieldy of all the data structures in R
It is certainly a list.
A complete lm object is a list; the only thing in R that can hold a list is just a list. We have no other option.
In some cases, even if the return of a model is just a vector, we can not guarantee the resulting vectors are of equal length for all models we try, so we still have to use a list.
Related
I have run a GAM and obtained a summary output. I want to extract the output of summary into a table, so that I can use it in a document.
Let's say your gam model is called gamfit.
You can use l <- as.list(summary(gamfit)) to store this in a list.
Then access the parts with l[[1]], l[[2]], ...
The problem with this is that, depending on how many variables are used in the analysis, the data you want may move around and the list items aren't named. If the model isn't going to change, then it's fine.
Also note that all the information about the model is stored in gamfit.
Explore this in the Rstudio Environment window or at the command line with names(gamfit), followed by gamfit$name_of_interest.
I am playing a bit with text classification and SVM.
My understanding is that typically the way to pick up the features for the training matrix is essentially to use a "bag of words" where we essentially end up with a matrix with as many columns as different words are in our document and the values of such columns is the number of occurrences per word per document (of course each document is represented by a single row).
So that all works fine, I can train my algorithm and so on, but sometimes i get an error like
Error during wrapup: test data does not match model !
By digging it a bit, I found the answer in this question Error in predict.svm: test data does not match model which essentially says that if your model has features A, B and C, then your new data to be classified should contain columns A, B and C. Of course with text this is a bit tricky, my new documents to classify might contain words that have never been seen by the classifier with the training set.
More specifically I am using the RTextTools library whith uses SparseM and tm libraries internally, the object used to train the svm is of type "matrix.csr".
Regardless of the specifics of the library my question is, is there any technique in document classification to ensure that the fact that training documents and new documents have different words will not prevent new data from being classified?
UPDATE The solution suggested by #lejlot is very simple to achieve in RTextTools by simply making use of the originalMatrix optional parameter when using the create_matrix function. Essentially, originalMatrix should be the SAME matrix that one creates when one uses the create_matrix function for TRAINING the data. So after you have trained your data and have your models, keep also the original document matrix, when using new examples, make sure of using such object when creating the new matrix for your prediction set.
Regardless of the specifics of the library my question is, is there any technique in document classification to ensure that the fact that training documents and new documents have different words will not prevent new data from being classified?
Yes, and it is very trivial one. Before applying any training or classification you create a preprocessing object, which is supposed to map text to your vector representation. In particular - it stores whole vocabulary used for training. Later on you reuse the same preprocessing object on test documents, and you simply ignore words from outside of vocabulary stored before (OOV words, as they are often refered in the literature).
Obviously there are plenty other more "heuristic" approaches, where instead of discarding you try to map them to existing words (although it is less theoreticalyy justified). Rather - you should create intermediate representation, which will be your new "preprocessing" object which can handle OOV words (through some levenstein distance mapping etc.).
I would like to find out what the "R way" would be to let users the following with R: I have a file that can contain the data of one or more analysis runs of some other software. My R package should provide additional ways to calculate statistics or produce plots for those analyses. So the first step a user would have to do, is read in the file (with one or more analyses), then select the analysis and work with it.
An analysis is uniquely identified by two names (an analysis name and an analysis type where the type should later correspond to an S3 class).
What I am not sure about is how to best represent the collection of analyses that is returned when reading in the file: should this be an object or simply a list of lists (since there are two ids for identifying an analysis, the first list could be indexed by name and the second by type). Using a list feels very low-level and clumsy though.
If the read function returns a special kind of container object what would be a good method to access one of the contained objects based on name and type?
There are probably many ways how to do this, but since I only started to work with R in a way where others should eventually use my code, I am not sure how to best follow existing R-conventions for how to design this.
I am working on developing and optimizing a linear model using the lm() function and subsequently the step() function for optimization. I have added a variable to my dataframe by using a random generator of 0s and 1s (50% chance each). I use this variable to subset the dataframe into a training set and a validation set If a record is not assigned to the training set it is assigned to the validation set. By using these subsets I am able to estimate how good the fit of the model is (by using the predict function for the records in the validation set and comparing them to the original values). I am interested in the coefficients of the optimized model and in the results of the KS-test between the distributions of the predicted and actual results.
All of my code was working fine, but when I wanted to test whether my model is sensitive to the subset that I chose I ran into some problems. To do this I wanted to create a for (i in 1:10) loop, each time using a different random subset. This turned out to be quite a challenge for me (I have never used a for loop in R before).
Here's the problem (well actually there are many problems, but here is one of them):
I would like to have separate dataframes for each run in the loop with a unique name (for example: Run1, Run2, Run3). I have been able to create a variable with different strings using paste(("Run",1:10,sep=""), but that just gives you a list of strings. How do I use these strings as names for my (subsetted) dataframes?
Another problem that I expect to encounter:
Subsequently I want to use the fitted coefficients for each run and export these to Excel. By using coef(function) I have been able to retrieve the coefficients, however the number of coefficients included in the model may change per simulation run because of the optimization algorithm. This will almost certainly give me some trouble with pasting them into the same dataframe, any thoughts on that?
Thanks for helping me out.
For your first question:
You can create the strings as before, using
df.names <- paste(("Run",1:10,sep="")
Then, create your for loop and do the following to give the data frames the names you want:
for (i in 1:10){
d.frame <- # create your data frame here
assign(df.name[i], d.frame)
}
Now you will end up with ten data frames with ten different names.
For your second question about the coefficients:
As far as I can tell, these don't naturally fit into your data frame structure. You should consider using lists, as they allow different classes - in other words, for each run, create a list containing a data frame and a numeric vector with your coefficients.
Don't create objects with numbers in their names, and then try and access them in a loop later, using get and paste and assign. The right way to do this is to store your elements in an R list object.
I am trying to build a data processing program. Currently I use a double matrix to represent the data table, each row is an instance, each column represents a feature. I also have an extra vector as the target value for each instance, it is of double type for regression, it is of integer for classification.
I want to make it more general. I am wondering what kind of structure R uses to store a dataset, i.e. the internal implementation in R.
Maybe if you inspect the rpy2 package, you can learn something about how data structures are represented (and can be accessed).
The internal data structures are `data.frame', a detailed introduction to the data frame can be found here.
http://cran.r-project.org/doc/manuals/R-intro.html#Data-frames