Developing TFSA package for R


I have been writing R functions since 2009 as part of my PhD in Fisheries Management. Since then I was longing to pull out useful functions into an R package so others can use it. I named it TFSA (Tropical Fish Stock Assessment) since my intention is to make the functions available to students who work with tropical fisheries where length data is more reliable than age estimation. TFSA is in its very premature form and under development. A few reasons why I got inspired and motivated in developing TFSA (Tropical Fish Stock Assessment) is listed below.

1. There are a few R packages that are  useful (FLR project, FSA, fishmethods, fsap) to employ and evaluate fish stock assessments for research and teaching. However, from my understanding the utility of these packages in a tropical system (e.g. Indian fisheries context) is limited since age data is highly unreliable and difficult to standardise due to the lack of strong seasons. The only reliable data would be the size of the fish species in terms of length and weight.

2. The number of R users are increasing in the very recent years. However, the change is dramatic for marine biology. Perhaps people are realizing the power of R in terms of its flexibility (through seminars or social networking) and increase in number of R books. However, there is no R book made for fisheries research despite of the number of R packages in CRAN.

3. Learning R is not easy as compared to other user friendly statistical softwares like Excel or SPSS.  But it seems now fisheries biologists are showing more interests after realising its power and flexibility in modelling. However, the resources to learn R is very limited in the perspective of a biologist. I conducted a training program in India on April 2012 and all the participants (professors and researchers in biology) except one person were unaware about R. The person who knew about the existence of R couldn’t manage to make use of it for her research work.

I’m looking forward for people who can contribute and help towards developing this package. Ofcourse, they will be acknowledged in the package description.

TFSA package is available to download from here. At the moment, TFSA only have the following functions:

1. vbgf – Compute length of a fish species given the parameters (k,t0 and Linf). This is based on the Von Bertalanffy Growth Function equation.

2. freq.class – Build the frequency distribution table based on specified class intervals. Useful for building length frequency table. The function can also handle groupings (eg: length data from different months).

More ideas and suggestions are welcome. A tutorial on using these functions will be published soon.

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About Deepak George Pazhayamadom

I'm a fish biologist and a mathematical modeller. I have a wide range of research interests, mostly centered on fisheries resource management.

Posted on June 18, 2012, in TFSA and tagged . Bookmark the permalink. Leave a comment.

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