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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 can I use my Ipython notebook code and output to within Latex (specifically in the Lyx GUI)

I have an Ipython notebook here and want to use it within the Lyx GUI so I can make a Latex document http://nbviewer.ipython.org/gist/decisionstats/4142e98375445c5e4174 import pandas as pd #importing packages import os as os #pd.describe_option()…
Ajay Ohri
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Loading a dput into R using a script

When creating a reproducible example I often want to output a data.frame or similar using put(): my_data <- structure(list(pr_id = c("X1626", "X1689", "X1818", "X2044", "X1572"), t1 = c("PID", "WRC", "PID", "PID", "PID"), t2 = c("PRO", "DEC",…
histelheim
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knitr templating - Dynamic chunks issue

The following code is a very simplified MRE for an issue I'm experiencing. I'm trying to avoid R template packages, such as brew, and only use knit_expand() to achieve my goals. The issue is twofold: generated chunks don't get parsed (this is not…
Aleksandr Blekh
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How can I automatically combine matplotlib graphs with Adobe Illustrator vector illustrations?

I'm currently writing a scientific paper and am generating most of the figures using matplotlib. I have a pipeline set up using a makefile that regenerates all of my plots whenever I update the data. My problem is that the figures are made up…
R_Beagrie
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R code evaluated by rmarkdown but not when file is sources

I write my R scripts in RStudio. I have also started using the Rmarkdown notebook feature of RStudio. As part of my workflow, I would like to have R scripts that include some R code evaluated when I source the code and when I render a notebook, and…
wmmurrah
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Getting a command to re-create an object that is simpler than with dput()

The output of dput is usually much more complex than what a user would have typed to create the same object. I understand that this might be necessary to guarantee a 100% reproducibility (including for instance when different users use different…
nassimhddd
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Transitioning research project to knitr-based setup

Finally, I've decided to move my dissertation research closer toward the goal of making it as good reproducible research as it can be, given my circumstances. Since currently I don't use LaTeX for my dissertation report (though I'm considering this…
Aleksandr Blekh
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Reproducible Research: Convert sas7bdat data files to csv files by invoking statTransfer using GNU make

QUESTION: I'm very new to GNU Make. Is there a better way to programmatically convert statistical datasets from sas7bdat to csv files and keep them in sync with each other using GNU Make to promote reproducible research? Would you approach this…
penguinv22
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Linking/importing externalized source code in org-mode

This paper inspired me to check out Emac's org-mode a bit and currently I try to assess what's more suitable for writing my documents: knitr/Sweave (I'm mainly using R to do my programming) or org-mode. What I really like about knitr is the option…
Rappster
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Include source code to function from external file in R

I have a standard data analysis procedure that I need to run on various (~50 datasets). I have been developing it for some time and now I got to the point where I would like to turn it into a function which takes a dataset and spits out some…
krhlk
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What is a simple to use library besides elastic net which can fit LASSO Regressions for output verification

I have run a series of LASSO Regressions in RStudio sequentially, one on each csv-formatted dataset within a file folder using the enet() function from the elastic net package in R with its lambda argument set to 0. However, as an important sanity…
Marlen
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How to extract object orientation from video stream (Webcam) - Python

I found this guide which teaches how to refine the orientation of objects from images. I would love to know if it can and should be used to analyze the orientation of objects displayed in video streams. The basis for the work is from the scientific…
Nave Achia
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How to best visualise gender/sexuality data about humans and robots?

I want to make a simple barchart using data from Döring & Poeschl 2019 paper about how sexual relationships between humans and robots are represented in fictions, but I can't figure it out - I think I am missing something really obvious - or perhaps…
Jill Walker Rettberg
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What are common sources of randomness in Machine Learning projects with Keras?

Reproducibility is important. In a closed-source machine learning project I'm currently working on it is hard to achieve it. What are the parts to look at?
Martin Thoma
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Using a build system for reproducible research?

I am doing a research project that involves a pipeline of programs, each generating an output file that becomes the input for the next program. I would like to make it easy to repeat the series of commands that I used to create the desired output.…
Ryan C. Thompson
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