bt.sturrock.2015.RdThe authors used otolith 87Sr/86Sr in adult chinook salmon (Oncorhynchus tshawytcha) returning to the Stanislaus River in the California Central Valley (USA) to reconstruct the sizes at which they outmigrated as juveniles in a wetter (2000) and drier (2003) year.
bt.sturrock.2015The data frame 3,654 × 11 contains the following columns:
| sample_id | character | sample identifier |
| collection_date | character | sample collection date |
| length | integer | length at collection (cm) |
| age | integer | age at collection (years) |
| sex | integer | sex (female or male) |
| outmigration_year | integer | outmigration year |
| distance | numeric | distance from otolith core (um) |
| oto_sr8786 | numeric | otolith 87Sr/86Sr value (spot analysis) |
| oto_sr8786_2se | numeric | instrument error |
| oto_srV | numeric | strontium signal |
| laser_properties | character | laser properties (spot size, power, repetition rate, dwell time, spacing) |
The dataset contains 87Sr/86Sr values measured in the otoliths of adult chinook salmon sampled in the Stanislaus River, California, between 2001 and 2006. Fish age was estimated using scale annuli, and individuals that outmigrated in 2000 and 2003 were retained for the current analysis (see "outmigration year"). Each otolith contains multiple 87Sr/86Sr values, representing spot analyses sampled along a standardized 90° transect from the otolith core towards the otolith edge.
Instrument: LA-MC-ICP-MS (laser ablation multi-collector inductively coupled plasma mass spectrometry)
Sturrock, A. M., Wikert, J. D., Heyne, T., Mesick, C., Hubbard, A. E., Hinkelman, T. M., ... & Johnson, R. C. (2015). Reconstructing the migratory behavior and long-term survivorship of juvenile Chinook salmon under contrasting hydrologic regimes. PLoS One, 10(5), e0122380. https://doi.org/10.1371/journal.pone.0122380
Data availability are available at https://doi.org/10.5061/dryad.c56rk
Traversing the paper's information via Semantic Scholar ID bd4c80e8eef6f81369f81af5c12016f30ffde72e using S2miner package
otolith, stable isotope, Sr8786
### copy data into 'dat'
dat <- bt.sturrock.2015
tibble::tibble(dat)
#> # A tibble: 3,654 × 11
#> sample_id collection_date length age sex outmigration_year distance oto_sr8786 oto_sr8786_2se
#> <chr> <chr> <int> <int> <chr> <int> <dbl> <dbl> <dbl>
#> 1 SR11234 2001-11-30 58 2 F 2000 30.7 0.708 0.0003
#> 2 SR11234 2001-11-30 58 2 F 2000 75.3 0.708 0.000178
#> 3 SR11234 2001-11-30 58 2 F 2000 125. 0.708 0.000108
#> 4 SR11234 2001-11-30 58 2 F 2000 177. 0.707 0.000088
#> 5 SR11234 2001-11-30 58 2 F 2000 229. 0.707 0.000116
#> 6 SR11234 2001-11-30 58 2 F 2000 276. 0.707 0.00007
#> 7 SR11234 2001-11-30 58 2 F 2000 324. 0.707 0.000078
#> 8 SR11234 2001-11-30 58 2 F 2000 376. 0.708 0.000188
#> 9 SR11234 2001-11-30 58 2 F 2000 423. 0.708 0.000196
#> 10 SR11234 2001-11-30 58 2 F 2000 470. 0.709 0.00017
#> # ℹ 3,644 more rows
#> # ℹ 2 more variables: oto_sr_v <dbl>, laser_properties <chr>
if (FALSE) {
### loading packages
library(dplyr)
library(ggplot2)
### Sr8786 profile figure
ggplot(data = dat,aes(distance, oto_sr8786))+
geom_line(aes(col = sex),show.legend = F,linewidth = 0.02, na.rm = T)+
facet_grid(.~ sex)+
labs(
x = expression(paste("Distance from core (", mu, "m)", sep = "")),
y = 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")
)
}