Quantifying habitat use of migratory fish across riverscapes

The authors construct a novel space-time isotope model of provenance (STIMP) that determines the habitat use through time of migratory fish across river basins.

bt.brennan.2019b

Format

The data frame 60,690 × 10 contains the following columns:

file_id	character	file identifier
smp_id	character	sample identifier
date_collected	character	date sample collected
size	integer	body mass
age	numeric	age of captured
oto_sr8786	numeric	sr isotopes
oto_sr8786_se	numeric	process error of sr isotopes
proportion_growth	numeric	proportion growth (body mass)
derivative	numeric	derivative of isotope state

Details

The otolith Sr isotopes dataset from chinook salmon (Oncorhynchus tshawytscha) harvested in 2011 during a coastal fishery in Bristol Bay.

Instrument: LA-MC-ICP-MS (laser ablation–multicollector–inductively coupled plasma–mass spectrometry)

Source

Brennan, S. R., Cline, T. J., & Schindler, D. E. (2019). Quantifying habitat use of migratory fish across riverscapes using space-time isotope models. Methods in Ecology and Evolution,10(7), 1036--1047. https://doi.org/10.1111/2041-210X.13191

Code and Data availability are available at https://doi.org/10.5061/dryad.6f462d4

Traversing the paper's information via Semantic Scholar ID 82783367d82b43c20edf5721e3c26f978948cd34 using S2miner package

Author

Liuyong Ding, ly_ding@126.com

Concepts

otolith, stable isotope, Sr8786

Examples

### copy data into 'dat'
dat <- bt.brennan.2019b
tibble::tibble(dat)
#> # A tibble: 60,690 × 10
#>    fileID  smpID dateCollected  size sex     age oto_sr8786 oto_sr8786_se proportion_growth derivative
#>    <chr>   <chr> <chr>         <int> <chr> <dbl>      <dbl>         <dbl>             <dbl>      <dbl>
#>  1 NBK_1.… NB_K1 6/27/11          NA ""      1.2      0.705      0.000204     0.00000000824       1.06
#>  2 NBK_1.… NB_K1 6/27/11          NA ""      1.2      0.705      0.000184     0.000000223         1.02
#>  3 NBK_1.… NB_K1 6/27/11          NA ""      1.2      0.705      0.000172     0.00000103          1.16
#>  4 NBK_1.… NB_K1 6/27/11          NA ""      1.2      0.705      0.000165     0.00000283          1.06
#>  5 NBK_1.… NB_K1 6/27/11          NA ""      1.2      0.705      0.000159     0.00000601          1.01
#>  6 NBK_1.… NB_K1 6/27/11          NA ""      1.2      0.705      0.000154     0.0000110           1.01
#>  7 NBK_1.… NB_K1 6/27/11          NA ""      1.2      0.705      0.000152     0.0000181           1.04
#>  8 NBK_1.… NB_K1 6/27/11          NA ""      1.2      0.705      0.000153     0.0000278           1.06
#>  9 NBK_1.… NB_K1 6/27/11          NA ""      1.2      0.705      0.000157     0.0000405           1.02
#> 10 NBK_1.… NB_K1 6/27/11          NA ""      1.2      0.705      0.000164     0.0000566           1.01
#> # ℹ 60,680 more rows

if (FALSE) {
### sulfur profile figure
library(dplyr)
library(ggplot2)

### Sr isotopes
ggplot(data = dat, aes(proportion_growth, oto_sr8786)) +
  geom_line(aes(group = smp_id, colour = sex), show.legend = F) +
  facet_grid(sex ~ ., scales = "free_y") +
  xlab("Proportion of growth (um in otolith)") +
  ylab(expression(paste(
    {}^"87",
    "Sr/",
    {}^"86",
    "Sr"
  ))) +
  theme_bw() +
  theme(
    panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
    panel.background = element_blank(), axis.line = element_line(colour = "black"),
    text = element_text(size = 10), legend.title = element_blank(),
    plot.title = element_text(face = "bold")
  )
}