An R package for the book Using R for Modelling and Quantitative Methods in Fisheries (2021). ISBN: 9780367469894 due to be made available in September 2020 but formally published in 2021.

Hardback and softback versions are available from www.routledge.com, but is also available for pre-order from Amazon (best to use one’s local Amazon site). A gitbook version is under development and once completed will at least be available on gitpages. I will annouce here when it is ready.

The release version of the MQMF package (commit 88bc002499), is available on CRAN, but to install this development version from GitHub you can use:

# install.packages("devtools") #  remove the first hash to install devtools
devtools::install_github("https://github.com/haddonm/MQMF/")

The development version differs from having more details put into the help pages, plus various typos and obscure text fixed. No changes have been made to the code base yet, though various developments are now in mind to increase robustness and generality of a number of the functions.

There are currently no vignettes, although the example code-chunks from the book are all available as the help pages of functions chapter2, chapter3, …, and chapter7.

I have now put together the full GitBook version so that anyone can read the material on-line at: https://haddonm.github.io/URMQMF/, where URMQMF is an abbreviation of Using R for Modelling and Quantitative Methods in Fisheries. The book itself has been published by Chapman & Hall/CRC in its R-Series, and is available from booksellers, including from Routledge.

This new book is an evolution and adaptation of my book Modelling and Quantitative Methods in Fisheries (Haddon, 2011). It is designed to introduce materials needed to understand the use of R in fisheries and ecology. The book is not really for total beginners to R, and only a brief introduction to a few less commonly used aspects of R is provided. In terms of fisheries and population ecology, because it covers a wide array of subjects, and hence is limited in the depth in which each can be treated, it should probably be considered an introductory text. Even so, sufficient detail and worked examples are given that anyone should be able to make a good start with simple model fitting, characterizing uncertainty, and other basic fisheries model fitting. Subjects such as maximum likelihood, simple and dynamic model fitting, and the estimation of uncertainty do receive relatively detailed attention. For example, there is a sufficient development around the use of MCMC that anyone should be able to develop a better understanding of its strengths and weaknesses. More advanced subjects such as age- and size-structured models are not included here as they are not really suited to brief treatments.

The primary objective of this book is that it be useful to workers in the field. Hopefully, this R package will assist with that objective.

Malcolm Haddon

Hobart, September 6, 2023

Haddon, M. (2011) Modelling and Quantitative Methods in Fisheries. 2nd Ed. CRC/Chapman & Hall. 449p.

Haddon, M. (2021) Using R for Modelling and Quantitative Methods in Fisheries. CRC/Chapman & Hall. 337p.