The internal implementation of R's dataset - r

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

Related

Comparison of good vs bad dataset using R

Stuck in a problem. There are two datasets A and B. Say they're datasets of two factories. Factory A is performing really well whereas Factory B is not. I have the data-set of Factory A (data being output from the manufacturing units) as well as Factory B, both having the same variables. How can I identify the problematic variable in Factory B which needs to be fixed so that Factory B starts performing well too? Therefore, I need to identify the problematic variable which needs immediate attention.
Looking forward to your response.
p.s: coding language being used is R
Well this is shameless plug for the dataMaid package which I helped write and which sort of does what you are asking. The idea of the dataMaid package is to run a battery of tests on the variables in a data frame and produce a report that a human investigator (preferably someone with knowledge about the context) can look through in order to identify potential problems.
A super simple way to get started is to load the package and use the
clean function on a data frame (if you try to clean the same data
frame several times then it may be necessary to add the replace=TRUE
argument to overwrite the existing report).
devtools::install_github("ekstroem/dataMaid")
library(dataMaid)
data(trees)
clean(trees)
This will create a report with summaries and error checks for each
variable in the trees data frame. A summary of all the variables is provided and for the trees data it looks like this
while the information from each variable may look like this
Here we get a status about the variable type, summary statistics, a plot and - in this case - an indicator that there might be a problem with outliers.
The dataMaid package can also be used interactively by running checks for the individual variables or for all variables in the dataset
data(toyData)
check(toyData$var2) # Individual check of var2
check(toyData) # Check all variables at once
By default the standard battery of tests is run depending on the
variable type, but it is possible to extend the package by providing your own checks.
In your case I would run the package on both datasets to get two reports, and any major differences in those would raise a flag about what could be problematic.

rangedummarizedexperiment for deseq2

I'm trying to use the DESeq2 package in R for differential gene expression, but I'm having trouble creating the required RangedSummarizedExperiment object from my input data. I have found several tutorials and vignettes for doing this, but they all seem to apply to a raw data set that is different from mine. My data has gene names as row names and patient id as column names, and the data is simply integer count data. There has to be a simple way to create the RangedSummarizedExperiment object from this type of input data, but I haven't yet found a way. Can anybody help? Thanks.
I had a similar problem understanding how to use this data structure. I eventually managed to do without it by using DESeqDataSetFromMatrix. You can see an example in the first code block of Modify r object with rpy2 (this code is pure R, rpy2 stuff comes after). In this example, I have genes as rows and samples as columns, so it is likely you will be able to adopt the same approach.

Text classification with R and SVM. Matrix features

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.).

Convention for R function to read a file and return a collection of objects

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.

decision trees with forced structure

I have been using decision trees (CART) in R using the rpart package to look at the relationship between SST (predictor variables) and climate (predictand variable).
I would like to "force" the tree into a particular structure - i.e. split on predictor variable 1, then on variable 2.
I've been using R for a while so I thought I'd be able to look at the code behind the rpart function and modify it to search for 'best splits' in a particular predictor variable first. However the rpart function calls C routines and not having any experience with C I get lost here...
I could write a function from scratch but would like to avoid it if possible! So my questions are:
Is there another decision tree technique (implemented in R
preferably) in which you can force the structure of the tree?
If not - is there some way I could convert the C code to R?
Any other ideas?
Thanks in advance, and help is much appreciated.
When your data indicates a tree with a known structure, present that structure to R using either a newick or nexus file format. Then you can read in the structure using either read.tree or read.nexus from Package Phylo.
Maybe you should look at the method formal parameter of rpart
In the documentation :
... ‘method’ can be a list of functions named ‘init’, ‘split’ and ‘eval’. Examples are given in the file ‘tests/usersplits.R’ in the sources.

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