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4
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1answer
47 views

Speeding up nested for-loop analysis code

I have two matrices, the first one is mat 2000*500, the second one is 6000*500 ...
1
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1answer
28 views

Frequency form to case form - unexpected values in table

I'm taking count data on voting preferences by race and entering it into a table in frequency form, then expanding out to case form and using CrossTable to look at ...
3
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0answers
45 views

Finding the Cox regression coefficients in a mixed model for microarray data

I have written a code for a project which aims at finding the Cox regression coefficients in a mixed model for microarray data. The study was carried out on the Affymetrix Hgu133a platform. In the ...
5
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1answer
80 views

Vector comparison inside for-loop

The following code finds no-rain periods in a time series that were preceded by rain over a threshold (e.g. 10mm in 2 days [k=48]). ...
13
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2answers
108 views

Plot daily time spent on codereview.stackexchange.com

This draws an xyplot from csv data obtained from RescueTime API for activity time for "http://codereview.stackexchange.com". ...
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1answer
42 views

How I can generalise this code

I have this code and I want to generalize it and make it efficient. Each time I generate a number of random variables and I put it in the m equation to generate m. Can I get any help to simplify this ...
2
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0answers
19 views

Computing values with several large numeric vectors

I have several large numeric vectors (close to 1e6 entries each) and I need to make some computations with their values: ...
5
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1answer
83 views

Using Reddit API in R

I'm scraping some comments from Reddit using Reddit JSON API and R. Since the data does not have a flat structure, extracting it is a little tricky, but I've found a way. To give you a flavour of ...
4
votes
2answers
86 views

Calculation of mortgage repayments

I've just started learning R, but I feel that I'm using it only as a normal procedural language without taking advantage of some built-in functions and data structures. I wrote a function that ...
4
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0answers
50 views

Vectorize Fisher's Exact Test

I have two data frames/ lists of data, humanSplit and ratSplit, and they are of the form ...
6
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1answer
65 views

Generating Cartesian product of strings in R

Sometimes I need to create character vectors like this one: ...
5
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1answer
57 views

Mean of many subsets of a dataframe

I have large dataframe containing many replicates. The replicates are in groups of 3. So the first 3 replicates are in column 1, 2 and 3. The second set 4, 5 and 6... and so on. Now I create a new ...
2
votes
1answer
66 views

Data model code running too slowly

The model takes a long time to run. I have tried to vectorise it as far as I can, but it's still taking about a day to compute. I'm wondering if it's possible to speed it up. Maybe the problem isn't ...
5
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0answers
94 views

Merging overlapping/intersecting string vectors

I am trying to merge overlapping/intersecting sets given as a list of string vectors below in R (my actual data set has thousands of such sets). The overlap/intersection is based on the ...
3
votes
1answer
43 views

Calculating overlap of segments in chromosome data

I wrote an R code that basically performs 2 operations: For each segment in file A, find all segments in file B that lie in that segment. Find the percentage of overlap for each case in previous ...
2
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0answers
42 views

Speed up my backward model selection

I have implemented a quite long program in R and I have noticed that one block, concearning a backward model selection, is too slow and I would like to receive some suggestions in order to speed up ...
4
votes
2answers
61 views

Imperative code in R keeping track of state

A friend of mine has a spreadsheet where she coded a classroom video for various teaching events, which I needed to help her plot. For each recording, she used several video cassettes, and her time ...
3
votes
1answer
215 views

Replace for loop while with apply family function in R

I have trouble with for loop, my code runs very slowly. The thing I want to do is to use function from apply family to make my codes run faster (instead of using ...
2
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0answers
37 views

Merton default model with complex iterative approach

I am using Merton default model with complex iterative approach. I have already prepared my R codes but as I am quite new in R, they seem very inefficient, in sense that they runs almost 7 hours. My ...
0
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0answers
35 views

Create a simulation study using R to compare the accuracy (95% capture rate) and the lengths of the Chi-Squared confidence intervals

The minimum length confidence bounds for a normal population variance for chi-squared distribution is $$ g(a) = a ^\frac{n+1}{2} e^{-\frac a 2} - b^\frac{n+1}{2} e^{-\frac b 2} = 0. $$ Are they ...
2
votes
1answer
87 views

Backwards stepwise regression code in R (using cross-validation as criteria)

I want to write code that does backward stepwise selection using cross-validation as a criterion. I have only started learning R a month ago and I have almost zero programming experience prior to ...
0
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2answers
100 views

Optimizing the function in R by replacing for loop

I am trying to create a function that I want to use in my real data. Is there any way to optimize the following function? This is a function I created to filter the data. ...
3
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1answer
443 views

best way to apply across an xts object

As xts objects are arrays, getting apply functions to work is a little tricky if you want to preserve the dates. For example, take the ...
2
votes
1answer
48 views

finding names of un-named list elements

I have a naming problem: lists with un-named elements. I wish to get the names of the elements in the list, without going back upstream to where the list was created. An example is ...
3
votes
1answer
95 views

Simplifying loop for Incidence Matrix

I had to work in the Transport Problem and we're asked to try to make the fastest code for big matrices, so we're advised to try to avoid loops. And the only one I've got and I cannot imagine how to ...
2
votes
1answer
103 views

Basic graphical R code draws an ellipse instead of a circle

I wrote some very basic R code. This has at least two problems. It uses a very basic imperative-programming style instead of good R style. It draws the result as an ellipse, not a circle. This ...
2
votes
2answers
152 views

Should I be trying to imitate the control flow in this example R code? [closed]

I have heard that some patterns in R code are really anti-patterns and thus I am trying to imitate superior examples of R code. I am confused about control flow. I have been reviewing some R code ...
2
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1answer
63 views

Check column values are in different sets

I have a data frame called data with lots of columns, and Country is one of them. I created a new logical column called ...
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2answers
151 views

Learning R – repeated measures simulator optimisation

I am learning to program in R and to do that and create something useful in the process, I have decided to rewrite this Java applet for repeated measures simulation and to implement some new ...
3
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1answer
140 views

Vectorize or otherwise speed up a double for loop

I have this function containing some loops and a double for loop. What it does is set up a matrix first to store results in (the task at hand is comparing genomes) and then with sliding window, ...
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1answer
77 views

Which components of this r loop are inefficient?

I realize that there is a surfeit of posts on SE/SO about optimizing one's R for() loops. I'm afraid, though, that I don't understand all of the guidance in the answers there, or how to apply their ...
3
votes
1answer
135 views

More elegant filter script in R

I'm very new both to programming and to R so please bear with me :-) I've written the following bit of code, which works perfectly well and runs through a data file with 17446 rows in about 35 ...
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vote
2answers
104 views

Is this correct R? remove first duplicate dataframe

I have a dataframe with several columns. One of them is an user id column, in this column, I have several ids that can be repeated several times. What I want to do is remove the first id, for ...
4
votes
0answers
224 views

Speed up a monte carlo simulation with nested loop

I would like to know if there is a more efficiency way to speed up below code. It uses a procedure where subsampling is required in the nested loop (which a previous answer helped to make more ...
3
votes
1answer
455 views

Compute intersections of all combinations of vectors in a list of vectors in R

My goal is to compute the intersections of several vectors (sets of identifiers, gene-names to be specific). I start with a list of vectors and run the function below, which loops through 1:n where n ...
2
votes
1answer
171 views

Increase efficiency for an R simulator of the Monty Hall Puzzle

The Monty Hall Problem is a simple puzzle involving probability that even stumps professionals in careers dealing with some heavy-duty math. Here's the basic problem: Suppose you're on a game show, ...
3
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2answers
61 views

Speeding up for-loop over a list

I have two lists with ca. 4000 elements where each each element have two columns. These are being fed into a function. Besides the function they are being fed into, is it possible to speed it up ...
3
votes
1answer
144 views

R code is slow on filling a matrix

I am running an R code, which is implementing a Markov Chain Monte Carlo algorithm for updating a density distribution There is a specific section of my code which tries to fill a very large matrix ...
2
votes
1answer
129 views

Speed up a sampling function

I have the following dataset kkk<-data.frame(days=1:100,positive=rbinom(100,1,0.05)) Over the monitoring period of 100 days, if an event occurs then for that ...
2
votes
1answer
105 views

Looping through rows of data sets in files

I have files containing data sets which contain 11,000 rows. I have to run a loop through each row, which is taking me 25 minutes for each file. ...
1
vote
1answer
158 views

increase speed for 'for loop'

I have files containing data set which contain 11,000 rows. I have to run a loop through each row, this is taking me 25minutes for each file. I am using following code: ...
3
votes
2answers
171 views

Returning an existing data frame with four new columns

I'm trying to implement a function that given a data frame returns the same data frame with four columns added. These new four columns are: for each row, I get the maximum element and its index and ...
1
vote
1answer
476 views

Visualizing simulation results of a project

I am having some performance problems with a little R script of mine that I use to visualize simulation results of a project of mine. It now takes longer on my machine to run the R script than the ...
3
votes
2answers
122 views

Calculating calendar year for a student based on DOB

I've written this brief function for calculating which calendar year a student would be in Year 1 based on their DOB (date of birth). In 1998 there was a change in the DOB cut points for starting Year ...
-1
votes
1answer
379 views

Optimize C++ Code

I have the following C++ function which I'd like to speed up, if possible. This program will have many different users, so parallelization is not really an option. The C++ function is wrapped by C ...
5
votes
2answers
798 views

Converting dataframe columns to binary columns

I basically want to convert all categorical column in an R dataframe to several binary columns: For example, a categorical column like ...
2
votes
1answer
208 views

Script for fetching a list of “end-positions” from a MySQL database

This script fetches a list of "end-positions" from a MySQL database. The positions are array positions that are the same in both MySQL and R. Next, the script takes the previous 34 elements for each ...
3
votes
1answer
573 views

Generate graph in Matlab

I use this Matlab code: ...
2
votes
1answer
57 views

Is there a more efficient way to simulate in R, by exposition factor, gender and disease profile?

I started working with R recently and need to do a simulation for 100 000 people that divides them in exposition factor for a disease, gender and presence or absence of disease. My background info is ...
3
votes
1answer
127 views

What is the best approach to use in R and why?

I'm starting working with R, and found some tutorials and exercises online. I want to divide one variable in two, bigger and equal 79 and smaller 79. Perhaps because I'm used to python, my first ...