John R. Morrongiello and Ronald E. Thresher. 2015. A statistical framework to explore ontogenetic growth variation among individuals and populations: a marine fish example. Ecological Monographs 85:93115. http://dx.doi.org/10.1890/13-2355.1


Supplement

Detailed worked tutorials of analyses performed in this paper, including R code for mixed effects models and example data.
Ecological Archives M085-005-S1.

Copyright


Authors
File list (downloads)
Description


Author(s)

John R. Morrongiello
CSIRO Marine and Atmospheric Research, Wealth from Oceans Flagship
GPO Box 1538, Hobart, TAS 7001, Australia
E-mail: jrmorrongiello@gmail.com

Ronald E. Thresher
CSIRO Marine and Atmospheric Research, Wealth from Oceans Flagship
GPO Box 1538, Hobart, TAS 7001, Australia


File list

S1_tutorial.pdf (MD5: b9ce89e5e69463afbfc055a2943824e6)  --  worked examples for the analysis of growth variation within and among individuals and populations

S2_R_code.txt (MD5: 6028e6cddbdf1473a4eef0faa8bd310a)  --  R code to perform analyses in S1

S3_within_zone_example_data.csv (MD5: ab86c1dd8ca7bcd2115f23a14b746bd8)  --  within-zone fish growth data

S4_among_zone_example_data.csv (MD5: d601bea4192d1f1c4c513fac34e39306)  --  among-zone fish growth data

S5_example_temperature.csv (MD5: f7ae18b64af07ec4b4d7ff94966bbf46)  --  temperature data used in among-zone analyses

Description

These supplements are designed to assist the reader to implement hierarchical growth models using the statistical software R. The first supplement (S1_tutorial.pdf) provides detailed model descriptions, formulations and analytical steps used in the paper, complementing models presented in Table 3. The second supplement (S2_R_code.txt) provides executable R code for analyses in S1. The third, fourth, and fifth supplements (S3_within_zone_example_data.csv, S4_among_zone_example_data.csv, and S5_example_temperature.csv) are example data sets.

Our analyses rely heavily on the R packages lme4, AICcmodavg, effects, lattice and plyr, all available on the comprehensive R archive network (CRAN; cran.r-project.org).

Each row in S3_within_zone_example_data.csv and S4_among_zone_example_data.csv represents a measurement of growth in mm (Increment). These observations are associated with an Age (in years) and belong to a fish (FishID) of a given sex (M or F). Each fish has an age-at-capture (ACC, in years). Associated with each Increment is its year of deposition (Year) and the annual bottom temperature (Temp) experienced by the individual at this time. In addition, the S4_among_zone_example_data.csv and S5_example_temperature.csv files contain a variable called zone that assigns each fish to a fictitious fishing area. See Table 2 for additional descriptions of these parameters.