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Questions tagged [reproducible-research]

Reproducible research is the idea that the result of scientific research should be published with data and code in order to make it possible for other researchers to verify the results.

Reproducible research is the idea that the result of scientific research should be published with data and code in order to make it possible for other researchers to verify the results.

Reproducible research may be especially important to you if your investigation involves large amount of data or very complex calculations.

One possible set of tools for reproducible research is using with or .

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How to add code from an R variable into a Quarto Code Block

I have some code stored as a character. I would like to dynamically add this code to a Quarto Code Block (Not a Code Chunk or executable Code Cell). I know I can add code into an executable code cell stored in an r variable, say, MyCode with the…
StatsStudent
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Is there a Julia equivalent of the targets R package?

The targets R package lets the user define an execution pipeline with minimal extra syntax and automatically handles things like cache and random seeds. It would be nice to have a similar tool in Julia. Closest thing I have found so far is…
Luna
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How to use `SpaDES.project::setupProject` to create new project using modules from GitHub repo?

I'm trying to use setupProjector setupModules to download/source .R files from github. I'm clearly doing something wrong as the following is not adding any modules to the simPath$modulePath as I would expect it to? Or is it not supposed to do…
Ceres
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How can I use `SpaDES.project::setupProject` and `SpaDES.experiment::experiment2`?

I've setup my project, but my goal is to create two simList objects that I want to pass to experiment2. This fails because I'm passing an object needed in the simulation via .... Am I using ... incorrectly? If not, how can I pass additional…
Ceres
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Inconsistent results trying to reproduce the variables selected by LASSO ran using enet(lambda = 0) with lars(type = "lasso")

The scripts which are referenced and from which the lines of code included came from can all be found at my GitHub Repository for this project, along with mini practice datasets (called ten, top 50, and last 50) so that you can replicate my…
Marlen
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larger train/val loss at initial epoch and slower decreasing compared to the paper's result

I am working on reproducing the results reported in this paper. A UNET based network is used for estimating sound speed map from raw Ultrasound channel data. I have been stuck in further reducing the train/val loss for a long time. Basically, I…
Margie Shi
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Counting the number of correct regression models selected by FS Stepwise Regression in R ran on N datasets

I need to count how many times the Models selected by a Forward Selection Stepwise Regression I have run on 58,500 different datasets are correctly specified (are the true underlying/structural regression models for their corresponding dataset). The…
Marlen
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Can I use snakemake with humans-in-the-loop?

I am very curious about snakemake but I'm not sure it fits my use case, because I have humans in the loop. My process is something like this: Start with a baseline binary classification model Generate 100 examples near the margin (predicted…
Joseph Turian
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How to write reproducible comment in rmarkdown

Can anyone help in how to write a reproducible comment in Rmarkdown? For example, we have the data set as shown below: age fnlwgt education_num 39 77516 13 50 83311 13 38 215646 9 53 234721 7 In Rmarkdown report comments are typed…
Farhan
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How could one use either an lapply or a For Loop combined with an IF in R to return just the names of LASSO IVs with coefficients > 0?

I have via lots of legwork and previous helpful answers to previous Stackoverflow questions successfully ran a uniquely fit LASSO Regression to each of my 47,000 individual 500 row by 31 columns (30 IVs & 1 DV columns) datasets for a research…
Marlen
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Is there a simple way to generalize code which successfully fits a LASSO Regression to a single csv to n csvs in a file folder?

My goal/task is to fit a LASSO Regression function using the enet() function from the elastic net package in R to each of the 47,000 individual csv file formatted datasets which are all located in the same large file folder called "sample_obs". Each…
Marlen
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YAML Header for R Markdown file - Adding LaTeX packages with options throws errors (sometimes)

Following the R Markdown Cookbook (along with a number of the posts here) and I'm trying to insert a collection of LaTeX packages in the YAML header for my R Markdown file. When I copy/paste the header from that website into my file: output: …
Karl Wolfschtagg
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Problem while implementating of “Continual Learning Through Synaptic Intelligence” paper

I am trying to reproduce the results of “Continual Learning Through Synaptic Intelligence” paper [1]. I tried implementing the algorithm as best as I could understand after going through paper many times. I also looked at it’s official…
Sudhir Yadav
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Reproducible issues with Python statsmodel and Docker

I'm running some Python statsmodel code in a Docker container. When I run this code on two different computers (using the same Docker container pulled from DockerHub, not built locally 2x), I am getting different results. The differences are tiny -…
mankoff
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Inconsistent performance each time I run a neural network

Is each run of a Neural Network different? I would like to mention I have a documented really good performance, and now the model is not performing the same each time I run it. Is there a seed command to use? I am writing a computer science research…
EnlightenedFunky
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