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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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How to run a single regression function in R using a single function on each of a large number of datasets within a folder

I need to run the enet() function from the elasticnet library in RStudio on each of these 47,000 datasets individually because they have been created in such a way that we know what the real underlying population for each dataset is and want to see…
Marlen
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Where does R store the markdown templates?

I have an R markdown template (skeleton.Rmd and template.yaml) that I would like to use. The various documents that describe the creation of templates (e.g., here, here, and here) all say that templates are either created in the working directory…
Karl Wolfschtagg
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How to make PDF output and code output look right in Rmarkdown

I'm working with a large collection of R Markdown files that are collectively used to create a book (PDF output) using bookdown. For long lines of code (that will show up in the book), I've been writing it out close to column 80, at which point I…
Karl Wolfschtagg
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How to make the training using Tensorflow 2 Object Detection API deterministic i.e. achieve Reproducibility?

I am using TF2 Object Detection API to train a ssd_resnet50. Each time I train it I get different losses and evaluation scores (tensorboard logs -- graphs). I am using VOC2012 dataset to retrain a pretrained ssd_resnet50_v1_fpn_640x640_coco17_tpu-8…
Rohit Mundra
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Span-Aste with allennlp - testing against new unseen and unlabeled data

I am trying to use this colab of this github page to extract the triplet [term, opinion, value] from a sentence from my custom dataset. Here is an overview of the system architecture: While I can use the sample offered in the colab and also train…
KeyPi
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Implementation of multitask "nested" neural network

I am trying to implement a multitask neural network used by a paper but am quite unsure how I should code the multitask network because the authors did not provide code for that part. The network architecture looks like (paper): To make it simpler,…
user48867
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Trying to find correlation between events and covid positivity rates

I'm looking to test for correlation between specific events (mostly holidays) and a university's covid positivity rates. I've been using ggplot2 but am not sure of how I should look at the actual correlation values between the data, and how I could…
maccoons
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Problems with reproducibility although setting a fix set.seed() in R

I'm using the package and function lpsymphony::lpsymphony_solve_LP(obj, mat, dir, rhs, types, max) to solve my linear programming problem. And now I want to show that the restrictions in the argument mat matter and therefore I solved this problem…
tueftla
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How to reproduce a graph from "Visualizing The Beatles" in ggplot2

With the Spotify API in R, you can get datasets like this, identifying: album name, key and mode of the key: data <- tibble::tribble(~track_name,~key_name,~mode_name, "willow","G","major", "champagne…
Paula
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Comsol Multiphysics Research Papers

I am currently attempting to model the absorption of Carbon Dioxide by different solutions. I found this paper that does this. They used Comsol Multiphysics but show almost no images of them modeling things in Comsol. They only show the differential…
Tariq S.
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Why do I have different results for the same model?

I use Skopt to find the best hyper-parameters for my model. I fix all the seed with the following code: import random from tensorflow.compat.v1.keras.backend import set_session from tensorflow.compat.v1.keras.backend import clear_session from…
isaaccs
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What changes invalidate snakemake pipeline

It is not clear what changes will invalidate the pipeline and prompt snakemake to re-run the workflow. Does change in input, intermediate output or custom script re-run the pipeline? In my experience changing intermediate output and custom script…
leo
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OpenMP, random variables, and reproducibility

I'm writing an R code, which calls C++, and C++ functions use a lot of parallel computing based on openMP. This is my first code using openMP and what I saw is that even setting the same C++ random seed, the code never gives the same results. I read…
niandra82
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How Do I Write Different Matrix Produced by a `Loop` into One-Single Matrix

I have an R function as below: ## Load packages and prepare multicore process library(forecast) library(future.apply) plan(multisession) library(parallel) library(foreach) library(doParallel) n_cores <- detectCores() cl <-…
Daniel James
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Image augmentation reproducibility

How can I reproduce the same image augmentation results when I'm using the following data pipeline for an image segmentation task? I want to compare different models, so data augmentation needs to be deterministic. class data_loader(object): def…
ae5n
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