Blog Archives

R package “fishdynr”

February 1, 2015
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R package “fishdynr”

The fishdynr package allows for the construction of some basic population dynamics models commonly used in fisheries science. Included are models of a single cohort, cohortSim, and a more complex iterative model that incorporates a stock-recruitment re...

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Data point locator function

December 5, 2014
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Data point locator function

Here's a little function to select data points in an open graphical device (ptlocator()). The function does a scaling of the x and y axes in order to give them equal weighting and remove the influence of differing units or ranges. The function then cal...

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Additional tips for structuring an individual-based model in R

September 30, 2014
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Additional tips for structuring an individual-based model in R

 I had a reader ask me recently to help understand how to modify the code of an individual-based model (IBM) that I posted a while back. It was my first attempt at an IBM in R, and I realized that I have made some significant changes to the way th...

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Maximal Information Coefficient (Part II)

September 17, 2014
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Maximal Information Coefficient (Part II)

A while back, I wrote a post simply announcing a recent paper that described a new statistic called the "Maximal Information Coefficient" (MIC), which is able to describe the correlation between paired variables regardless of linear or nonlinear relationship. This turned out to be quite a popular post, and included a lively discussion...

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PCA / EOF for data with missing values – a comparison of accuracy

September 15, 2014
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PCA / EOF for data with missing values – a comparison of accuracy

Not all Principal Component Analysis (PCA) (also called Empirical Orthogonal Function analysis, EOF) approaches are equal when it comes to dealing with a data field that contain missing values (i.e. "gappy"). The following post compares several methods by assessing the accuracy of the derived PCs to reconstruct the "true" data set, as was similarly...

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“sinkr” – a collection of functions featured on “me nugget”

September 2, 2014
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“sinkr” – a collection of functions featured on “me nugget”

The R package sinkr (version 1.0) has now been released:  https://github.com/menugget/sinkrI have finally gotten around to learning how to create an R package and decided to start by bundling functions that I have featured on the blog. Thanks to the R Studio team for making this so easy (in combination with...

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Rotated axis labels in R plots

August 5, 2014
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Rotated axis labels in R plots

It's somehow amazing to me that the option for slanted or rotated axes labels is not an option within the basic plot() or axis() functions in R.  The advantage is mainly in saving plot area space when long labels are needed (rather than as a means...

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Flood fill a region of an active device in R

July 23, 2014
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Flood fill a region of an active device in R

The following is a function to "flood fill" a region on the active plotting device. Once called, the user will be asked to click on the desired target region. The flood fill algorithm then searches neighbors in 4 directions of the target cell (down, le...

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Automated determination of distribution groupings – A StackOverflow collaboration

May 18, 2014
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Automated determination of distribution groupings – A StackOverflow collaboration

For those of you not familiar with StackOverflow (SO), it's a coder's help forum on the StackExchange website. It's one of the best resources for R-coding tips that I know of, due entirely to the community of users that routinely give expert advise (as...

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Evaluating model performance – A practical example of the effects of overfitting and data size on prediction

May 3, 2014
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Evaluating model performance – A practical example of the effects of overfitting and data size on prediction

Following my last post on decision making trees and machine learning, where I presented some tips gathered from the "Pragmatic Programming Techniques" blog, I have again been impressed by its clear presentation of strategies regarding the evaluation of model performance. I have seen some of these topics presented elsewhere -...

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