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... [Read more...]

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... [Read more...]

 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... [Read more...]

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 ... [Read more...]

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" ... [Read more...]

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 ... [Read more...]

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... [Read more...]

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... [Read more...]

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... [Read more...]

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 - ... [Read more...]

I have recently come across Ricky Ho's blog "Pragmatic Programming Techniques", which seems to be excellent resource for all sorts of aspects regarding data exploration and predictive modelling. The post "Six steps in data science" provides a nice overview to some of the topics covered in the blog. For some ... [Read more...]

After noticing some frustrating inaccuracies with the high-resolution world coastlines and national boundaries database found in worldHires from the package mapdata (based on CIA World Data Bank II data), I decided to look into other options. Although listed as "depreciated", the data found in NOAAs online "Coastline Extractor" is a ... [Read more...]

GMT (Generic Mapping Tools) (http://gmt.soest.hawaii.edu/) is a great mapping tool. I'm hoping to use it more in the future, but for the meantime I wanted to recreate some of the it's standard color palettes in R. Unfortunately, I couldn't find documen... [Read more...]

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Following  a question that I posted on stackoverflow.com, I recieved the great advice to use the Bioconductor rhdf5 package to work with HDF5 files. The package is not located on CRAN, but can be sourced from the Bioconductor website: source("http://bioconductor.org/biocLite.R")biocLite("rhdf5") Created by ... [Read more...]

I have been curious for a while as to how R might be used for the construction of an individually-based model (IBM), or agent-based model (ABM). In particular, what R objects lend themselves best to storing information on individuals, and allow for new... [Read more...]

Word cloud of DOMA hearing transcriptsI must admit, there is something appealing about the word cloud - that is, until you try to understand what it actually means...Word clouds are pervasive - even in the science world. I was somewhat spurred to wri... [Read more...]

The following is a template that I usually start with when producing figures for publication. It allows me to control:The overall size of the figure (in inches) (WIDTH, HEIGHT)The layout of figure subplots (using the layout() function) (LO)The resoluti... [Read more...]

When plotting, I am constantly defaulting to the "main" colors in R - In other words, the colors that one can quickly call by number (1="black", 2="red", 3="green", 4="blue", ... etc.) . In my opinion, these colors do not lend themselves well to compelling graphics. I imagine this is the reason for ... [Read more...]