Individual back-calculated size-at-age based on otoliths from Pacific coral reef fish species

This repository contains code and data presented in the article:

Morat, F., Wicquart, J., Schiettekatte, N. M. D., de Synéty, G., Bienvenu, J., Casey, J. M., Brandl, S. J., Vii, J., Carlot, J., Degregori, S., Mercière, A., Fey, P., Galzin, R., Letourneur, Y., Sasal, P., Parravicini, V. Individual back-calculated size-at-age based on otoliths from Pacific coral reef fish species. Scientific Data, 7, 370 (2020).

1. How to download this project?

On the project main page on GitHub, click on the green button Code and then click on Download ZIP

2. Description of the project

2.1 Project organization

This project is divided in 4 folders:

• 📂 data folder contains 11 datasets (see part 2.2 Datasets description).
• 📂 R folder contains 3 R codes and a functions folder (see part 2.3 Code description).
• 📂 stan folder contains 2 stan codes used by the R codes for Bayesian analyses.
• 📂 output folder contains an HTML file including basic exploratory analyses. This file must be open in a browser and to zoom on the figure within the file, right click on the figure and open it in a new window.

2.2 Datasets description

The dataset 00_von-bertalanffy-literature.xlsx corresponds to values of Von Bertalanffy growth parameters extracted from scientific literature. The columns of the spreadsheet Data are described in the spreadsheet Metadata.

The dataset 01_coral_reef_fishes_data.csv (13 var. and 6,320 obs.) corresponds to the raw data used to generate the back-calculated size-at-age data (02_back-calculated-size-at-age_morat-et-al.csv), and contains the following variables:

• family Family
• genus Genus
• species Species
• id Unique code identifying each individual
• agei Age i (years)
• radi Otolith radius at age i (mm)
• agecap Age at capture (years)
• radcap Otolith radius at capture (mm)
• lencap Total length at capture (mm)
• l0p Total length at hatching (mm)
• weight Wet body mass at capture (g)
• location Island of the sampling
• observer Name of the person who realized the otolith reading

The dataset 02_back-calculated-size-at-age_morat-et-al.csv (18 var. and 6,320 obs.) corresponds to the dataset stored on figshare with the back-calculated size-at-age data, and contains the following variables:

• Family Family
• Genus Genus
• Species Species
• ID Unique code identifying each individual
• Agei Age i (years)
• Ri Otolith radius at age i (mm)
• Agecpt Age at capture (years)
• Rcpt Otolith radius at capture (mm)
• Lcpt Total length at capture (mm)
• L0p Total length at hatching (mm)
• R0p Otolith radius at hatching (mm)
• Li_sp_m Total length (mean, mm) at age i calculated by species
• Li_sp_sd Standard deviation around the value of Li_sp_m
• Li_sploc_m Total length (mean, mm) at age i calculated by species and location
• Li_sploc_sd Standard deviation around the value of Li_sploc_m
• Weight Wet body mass at capture (g)
• Location Island of the sampling
• Observer Name of the person who realized the otolith reading

The dataset 03_back-calculated_vbgf_fitted_sp.csv (8 var. and 5,474 obs.) corresponds to fitted values of Von Bertalanffy growth curve based on back-calculated data by species, and contains the following variables:

• age Age i (years)
• ypred_m Mean estimated value of total length at age i at population-level
• ypred_lq Lower 95% credible interval boundary of the ypred_m
• ypred_uq Upper 95% credible interval boundary of the ypred_m
• yrep_m Mean estimated value of total length at age i at individual-level
• yrep_lq Lower 95% credible interval boundary of the yrep_m
• yrep_uq Upper 95% credible interval boundary of the yrep_m
• Species Species

The dataset 03_back-calculated_vbgf_fitted_sploc.csv (9 var. and 5,016 obs.) corresponds to fitted values of Von Bertalanffy growth curve based on back-calculated data by species and location, and contains the following variables:

• age Age i (years)
• ypred_m Mean estimated value of total length at age i at population-level
• ypred_lq Lower 95% credible interval boundary of the ypred_m
• ypred_uq Upper 95% credible interval boundary of the ypred_m
• yrep_m Mean estimated value of total length at age i at individual-level
• yrep_lq Lower 95% credible interval boundary of the yrep_m
• yrep_uq Upper 95% credible interval boundary of the yrep_m
• Species Species
• Location Island of the sampling

The dataset 03_back-calculated_vbgf_predictions_sp.csv (6 var. and 120 obs.) corresponds to estimated values of Von Bertalanffy growth parameters based on back-calculated data by species, and contains the following variables:

• Species Family
• Agei Age i (years)
• Estimate Mean estimated value of total length at age i
• Est.Error Standard deviation around the Estimate
• Q2.5 Lower 95% credible interval boundary of the Estimate
• Q97.5 Upper 95% credible interval boundary of the Estimate

The dataset 03_back-calculated_vbgf_predictions_sploc.csv (7 var. and 159 obs.) corresponds to estimated values of Von Bertalanffy growth parameters based on back-calculated data by species and location, and contains the following variables:

• Species Family
• Location Island of the sampling
• Agei Age i (years)
• Estimate Mean estimated value of total length at age i
• Est.Error Standard deviation around the Estimate
• Q2.5 Lower 95% credible interval boundary of the Estimate
• Q97.5 Upper 95% credible interval boundary of the Estimate

The dataset 03_raw_vbgf_fitted_sp.csv (6 var. and 5,196 obs.) corresponds to fitted values of Von Bertalanffy growth curve based on raw data (age estimated and length at capture) by species, and contains the following variables:

• Species Species
• Agei Age i (years)
• Estimate Mean estimated value of total length at age i
• Est.Error Standard deviation around the Estimate
• Q2.5 Lower 95% credible interval boundary of the Estimate
• Q97.5 Upper 95% credible interval boundary of the Estimate

The dataset 03_raw_vbgf_fitted_sploc.csv (7 var. and 4,828 obs.) corresponds to fitted values of Von Bertalanffy growth curve based on raw data (age estimated and length at capture) by species, and contains the following variables:

• Species Species
• Location Island of the sampling
• Agei Age i (years)
• Estimate Mean estimated value of total length at age i
• Est.Error Standard deviation around the Estimate
• Q2.5 Lower 95% credible interval boundary of the Estimate
• Q97.5 Upper 95% credible interval boundary of the Estimate

The dataset 03_back-calculated_vbgf_predictions_sp.csv (6 var. and 108 obs.) corresponds to estimated values of Von Bertalanffy growth parameters based on raw data (age estimated and length at capture) by species, and contains the following variables:

• Species Species
• Agei Age i (years)
• Estimate Mean estimated value of total length at age i
• Est.Error Standard deviation around the Estimate
• Q2.5 Lower 95% credible interval boundary of the Estimate
• Q97.5 Upper 95% credible interval boundary of the Estimate

The dataset 03_back-calculated_vbgf_predictions_sploc.csv (7 var. and 114 obs.) corresponds to estimated values of Von Bertalanffy growth parameters based on raw data (age estimated and length at capture) by species and location, and contains the following variables:

• Species Species
• Location Island of the sampling
• Agei Age i (years)
• Estimate Mean estimated value of total length at age i
• Est.Error Standard deviation around the Estimate
• Q2.5 Lower 95% credible interval boundary of the Estimate
• Q97.5 Upper 95% credible interval boundary of the Estimate

2.3 Code description

• The 02_back_calculation.R code is used to obtain the back-calculated size-at-age.

• The codes 03_vbgf_back_calculated_sp.R, 03_vbgf_back_calculated_sploc.R, 03_vbgf_raw_sp.R and 03_vbgf_raw_sploc.R are respectively used to obtain Von Bertalanffy growth parameters and fitted values with back-calculated data by species, by species and location, with raw data by species, and by species and location.

• The functions folder contains the function graphical_par.R and theme_graph.R which are functions dedicated to graphical representations. The function bcalc_bayes.R is used to fit Von Bertalanffy growth model, the function growthreg.R is used to extract growth parameters from back-calculated data and the function pred_vbgf.R is used to fit Von Bertalanffy growth curves from values of the three parameters.

2.4 How to reproduce the final datasets?

To reproduce the 8 final datasets (i.e. those starting by 03), open and run successively the R codes 02_back_calculation.R, and all the R codes starting by 03. Make sure that all required packages were previously installed. Due to the elevated number of iterations from the Bayesian model, the codes necessitate an important amount of time to run. Please note that a full reproduction of the results is not possible, as Bayesian estimations are different at each run.

3. How to report issues?

Please report any bugs or issues HERE.

4. Reproducibility parameters

R version 3.6.3 (2020-02-29)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252    LC_MONETARY=French_France.1252
[4] LC_NUMERIC=C                   LC_TIME=French_France.1252    

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] formattable_0.2.0.1  kableExtra_1.1.0     plotly_4.9.2.1       readxl_1.3.1        
 [5] brms_2.13.0          Rcpp_1.0.4.6         bayesplot_1.7.2      rstan_2.19.3        
 [9] StanHeaders_2.21.0-5 plyr_1.8.6           rfishbase_3.0.4      forcats_0.5.0       
[13] stringr_1.4.0        dplyr_1.0.0          purrr_0.3.4          readr_1.3.1         
[17] tidyr_1.1.0          tibble_3.0.1         ggplot2_3.3.2        tidyverse_1.3.0     

loaded via a namespace (and not attached):
  [1] colorspace_1.4-1     ellipsis_0.3.1       ggridges_0.5.2       rsconnect_0.8.16    
  [5] estimability_1.3     htmlTable_2.0.1      markdown_1.1         base64enc_0.1-3     
  [9] fs_1.4.1             rstudioapi_0.11      DT_0.13              gh_1.1.0            
 [13] fansi_0.4.1          mvtnorm_1.1-1        lubridate_1.7.9      xml2_1.3.2          
 [17] bridgesampling_1.0-0 splines_4.0.1        knitr_1.28           shinythemes_1.1.2   
 [21] Formula_1.2-3        jsonlite_1.6.1       packrat_0.5.0        broom_0.5.6         
 [25] cluster_2.1.0        dbplyr_1.4.4         png_0.1-7            shiny_1.5.0         
 [29] compiler_4.0.1       httr_1.4.1           emmeans_1.5.0        backports_1.1.7     
 [33] lazyeval_0.2.2       assertthat_0.2.1     Matrix_1.2-18        fastmap_1.0.1       
 [37] cli_2.0.2            later_1.1.0.1        acepack_1.4.1        htmltools_0.5.0     
 [41] prettyunits_1.1.1    tools_4.0.1          igraph_1.2.5         coda_0.19-3         
 [45] gtable_0.3.0         glue_1.4.1           reshape2_1.4.4       cellranger_1.1.0    
 [49] vctrs_0.3.1          nlme_3.1-148         crosstalk_1.1.0.1    xfun_0.14           
 [53] ps_1.3.3             rvest_0.3.6          miniUI_0.1.1.1       mime_0.9            
 [57] lifecycle_0.2.0      gtools_3.8.2         zoo_1.8-8            scales_1.1.1        
 [61] colourpicker_1.0     hms_0.5.3            promises_1.1.1       Brobdingnag_1.2-6   
 [65] inline_0.3.15        shinystan_2.5.0      RColorBrewer_1.1-2   yaml_2.2.1          
 [69] memoise_1.1.0        gridExtra_2.3        loo_2.2.0            rpart_4.1-15        
 [73] latticeExtra_0.6-29  stringi_1.4.6        dygraphs_1.1.1.6     checkmate_2.0.0     
 [77] pkgbuild_1.0.8       rlang_0.4.6          pkgconfig_2.0.3      matrixStats_0.56.0  
 [81] evaluate_0.14        lattice_0.20-41      rstantools_2.0.0     htmlwidgets_1.5.1   
 [85] processx_3.4.2       tidyselect_1.1.0     magrittr_1.5         R6_2.4.1            
 [89] generics_0.0.2       Hmisc_4.4-0          DBI_1.1.0            pillar_1.4.4        
 [93] haven_2.3.1          foreign_0.8-80       withr_2.2.0          xts_0.12-0          
 [97] survival_3.1-12      abind_1.4-5          nnet_7.3-14          modelr_0.1.8        
[101] crayon_1.3.4         rmarkdown_2.3        jpeg_0.1-8.1         grid_4.0.1          
[105] data.table_1.12.8    blob_1.2.1           callr_3.4.3          threejs_0.3.3       
[109] webshot_0.5.2        reprex_0.3.0         digest_0.6.25        xtable_1.8-4        
[113] httpuv_1.5.4         RcppParallel_5.0.1   stats4_4.0.1         munsell_0.5.0       
[117] viridisLite_0.3.0    shinyjs_1.1