Supplement 1. Detailed worked tutorials of analyses performed in this paper, including R code for mixed effects models and example data.
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
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.