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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 .

Related links:

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Alternative approach to reproducible research where source code is the primary medium

TL;DR: The common dynamic document (IPython notebook style) approach to reproducible research usually does not result in reusable source code modules. Are there tools/approaches that use the source code as the primary medium and include text within…
Ondřej Grover
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Extracting git information in rstudio

I'm trying my hand at some reproducible research in RStudio and with Rmarkdown. Mostly because I'm too lazy to paste figures into powerpoint or word over and over. grin One thing that I think is very important with reproducible research is…
namelessjon
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Set seed parallel random forest in caret for reproducible result

I wish to run random forest in parallel using caret package, and I wish to set the seeds for reproducible result as in Fully reproducible parallel models using caret. However, I don't understand line 9 in the following code taken from caret help:…
HadiITC
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Include a text representation of an object (like dput) in a function call for reproducible research

I have created a shiny app in which a user can load a file and use the object as a function argument. I also print the code to run the function locally (so that I or anyone else could copy and paste to reproduce the result). What I would like to do…
Andy
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How to make a latex table for 3d-array in R

I have a 3d-array "arr" in R: > v1 <- c("100", "75", "31", "41", "1000", "69") > v2 <- c("10m", "6h", "5d", "11m", "6h", "5d") > arr <- array(c(v1, v2), dim=c(3, 2, 2), dimnames=list(c("d1", "d2", "d3"), c("m1", "m2"), c("v1", "v2"))) > arr , , v1 …
Simon
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Validating successful execution of R scripts from top to bottom in a clean session without errors

I teach multiple R Courses where students have to submit an analysis they did on a specific dataset. As a first, (small) step towards reproducibility, I want to make sure the script they are submitting ran at least once on their local computer with…
Ratnanil
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Tensorflow-Keras how to get reproducible results across different machines

I am trying to get exact reproducibility when running the training of a very simple model with tf-keras over different machines. For instance I have mahcine A, and B, and I would like the weights I get when calling model.fit() to be exactly…
ClonedOne
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keras.Model.save changes binary every time model saved

Why does keras.Model.save() produce different binaries with every run, when, AFAIU, I have taken all the necessary steps for complete reproducibility of the results and even binaries? You can verify this by simply executing the following script…
thomasarvanitidis
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How to get reproducible weights initializaiton in Keras?

I set both numpy and tensorflow random seeds as suggested Generate some data - this part is reproducible, gives same results always Create a simple network and make a prediction (without training, just with random weights) - prediction is…
Dmitry Toda
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Networkx maximal_independent_set reproducibility

How can I get reproducible results in a Jupyter Notebook (Python3)? Defining a seed for the main random generators seems to be not enough, see MWE below: import numpy as np import random import os…
simon
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dput a long list - shorten list but preserve structure

If we want to make a reproducible question on a complex/large dataset for SO, we can use dput(head(df)) to reduce the size. Is there a similar approach to reduce the size of complex nested lists with varying list lengths? I'm thinking an approach…
user63230
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Different behaviors between a Docker image and the same image imported in singularity

I have recently started using Docker to secure the computational reproducibility of my research. Since the HPC service at my institution only supports singularity, I want to import a Docker image within singularity when I perform part of my analysis…
Akira Murakami
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How do I ensure repeatability of Julia code and assoicated dependencies?

Say I have a project where I am performing analysis (ie not looking to develop a sharable package) but I want to ensure that others could clone the repository and instantiate the dependencies and run the code as written. Steps I have taken so…
Alec
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How can I create an executable research compendium (erc)?

I have a manuscript for a scientific publication, the data, and the scripts used to generate the result figures and tables. How can I wrap these three in an executable research compendium, so that others can easily reproduce the computational steps…
Edzer Pebesma
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Can we create saliency maps from image segmentation tasks?

I also know the fact that saliency map is also a form of image segmentation task. But it has been used very widely for interpretable deep learning ( Read GradCam etc ) . I also came across this paper…
Sayantan Das
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