Articles by Francisco Lima

Bayesian models in R

May 1, 2019 | Francisco Lima

If there was something that always frustrated me was not fully understanding Bayesian inference. Sometime last year, I came across an article about a TensorFlow-supported R package for Bayesian analysis, called greta. Back then, I searched for greta tutorials and stumbled on this blog post that praised a textbook called ...
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The tidy caret interface in R

November 16, 2018 | Francisco Lima

Among most popular off-the-shelf machine learning packages available to R, caret ought to stand out for its consistency. It reaches out to a wide range of dependencies that deploy and support model building using a uniform, simple syntax. I have been using caret extensively for the past three years, with ...
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Convolutional Neural Networks in R

July 8, 2018 | Francisco Lima

Last time I promised to cover the graph-guided fused LASSO (GFLASSO) in a subsequent post. In the meantime, I wrote a GFLASSO R tutorial for DataCamp that you can freely access here, so give it a try! The plan here is to experiment with convolutional neural networks (CNNs), a form ...
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Linear mixed-effect models in R

December 11, 2017 | Francisco Lima

Statistical models generally assume that All observations are independent from each other The distribution of the residuals follows , irrespective of the values taken by the dependent variable y When any of the two is not observed, more sophisticated modelling approaches are necessary. Let’s consider two hypothetical problems that violate ...
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Genome-wide association studies in R

October 9, 2017 | Francisco Lima

This time I elaborate on a much more specific subject that will mostly concern biologists and geneticists. I will try my best to outline the approach as to ensure non-experts will still have a basic understanding. This tutorial illustrates the power of genome-wide association (GWA) studies by mapping the genetic ...
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Partial least squares in R

June 17, 2017 | Francisco Lima

My last entry introduces principal component analysis (PCA), one of many unsupervised learning tools. I concluded the post with a demonstration of principal component regression (PCR), which essentially is a ordinary least squares (OLS) fit using the first principal components (PCs) from the predictors. This brings about many advantages: There ...
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Principal Component Analysis in R

January 23, 2017 | Francisco Lima

Principal component analysis (PCA) is routinely employed on a wide range of problems. From the detection of outliers to predictive modeling, PCA has the ability of projecting the observations described by variables into few orthogonal components defined at where the data ‘stretch’ the most, rendering a simplified overview. PCA is ...
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Probability distributions in R

December 4, 2016 | Francisco Lima

Some of the most fundamental functions in R, in my opinion, are those that deal with probability distributions. Whenever you compute a P-value you rely on a probability distribution, and there are many types out there. In this exercise I will cover four: Bernoulli, Binomial, Poisson, and Normal distributions. Let ...
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