bt.caccavo.2019.RdComparisons between multi-disciplinary techniques based on integrated sampling designs that incorporate hydrography can enhance understanding of population structure and connectivity around the Southern Ocean.
bt.caccavo.2019The data frame 514 × 17 contains the following columns:
| order | integer | measurement order |
| type | character | MACS-3, blank or line/raster reading |
| day | character | date of analysis |
| sequence | integer | continuous runs on ICPMS |
| slide | integer | individual slides on which otoliths are mounted |
| ss_order | integer | order of individual sampling events in each session |
| sl_order | integer | order of individual sampling events on each slide |
| status | integer | type of sampling event, codes below: 1. MACS-3 reference; 2. Blank; 3. edge; 4. nucleus |
| treatment | integer | corresponding to area & size cohort, codes below: 1. West Filchner Trough, <13 cm (W-FT small); 2. West Filchner Trough, >13 cm (W-FT large); 3. East Filchner Trough, all sizes (E-FT); 4. Coats Land <13 cm (CL small); 5. Coats Land >13 cm (CL large); 6. Halley Bay <13 cm (HB small); 7. Halley Bay >13 cm (HB large); 8. Atka Bay, all sizes (AB) |
| id_series | character | region ID (i.e.EF, East Filchner)/ID number/otolith(R,right;L,left)/slide assignment (1–25) and slide position (A–H) |
| sl | numeric | fish standard length (cm) |
| mg25 | numeric | counts for Magnesium isotope |
| ca48 | numeric | counts for Calcium isotope |
| mn55 | numeric | counts for Manganese isotope |
| sr88 | numeric | counts for Strontium isotope |
| ba138 | numeric | counts for Barium isotope |
| pb208 | numeric | counts for Lead isotope |
The dataset contains intensity data from ICP-MS for all samples,MACS-3 standard readings,and blank readings (514 measurements of Antarctic silverfish).
Instrument: ICP-MS (inductively coupled plasma mass spectrometry)
Beam diameter: 20um
Scan speed: 6um/s
Reference materials: MACS-3 (United States Geological Survey microanalytical carbonate standard pressed pellet)
Caccavo, J. A., Ashford, J. R., Ryan, S., Papetti, C., Schröder, M., & Zane, L. (2019). Spatial structuring and life history connectivity of Antarctic silverfish along the southern continental shelf of the Weddell Sea. Marine Ecology Progress Series, 624, 195--212. https://doi.org/10.3354/MEPS13017
Data availability are available at https://doi.org/10.5061/dryad.h44j0zpgs
Traversing the paper's information via Semantic Scholar ID 20b1afcbe52f48d6dd34a64436562ff924eb6af3 using S2miner package
otolith, trace element, Sr/Ca, Mn/Ca, Mg/Ca, Ba/Ca, Pb/Ca
### copy data into 'dat'
dat <- bt.caccavo.2019
tibble::tibble(dat)
#> # A tibble: 514 × 17
#> order type day sequence slide ss_order sl_order status treatment id_series sl mg25 ca48
#> <int> <chr> <chr> <int> <int> <int> <int> <int> <int> <chr> <chr> <dbl> <dbl>
#> 1 1 MACS-3… 2017… 1 1 1 1 1 NA NA NA 2.21e5 2.32e6
#> 2 2 Blank1 2017… 1 1 2 2 2 NA NA NA 7.39e3 8.87e3
#> 3 3 Line2 2017… 1 1 3 3 3 3 EF / 161… 19 8.13e3 3.01e6
#> 4 4 Raster2 2017… 1 1 4 4 4 3 EF / 161… 19 5.13e3 2.64e6
#> 5 5 Line3 2017… 1 1 5 5 3 6 HB-S / 4… 11.2 7.24e3 3.36e6
#> 6 6 Raster3 2017… 1 1 6 6 4 6 HB-S / 4… 11.2 6.88e3 2.97e6
#> 7 7 Line4 2017… 1 1 7 7 3 5 CL-B / 1… 14.5 4.51e3 3.24e6
#> 8 8 Raster4 2017… 1 1 8 8 4 5 CL-B / 1… 14.5 6.89e3 2.98e6
#> 9 9 MACS-3… 2017… 1 1 9 9 1 NA NA NA 1.71e5 1.83e6
#> 10 10 Blank2 2017… 1 1 10 10 2 NA NA NA 2.53e3 8.89e3
#> # ℹ 504 more rows
#> # ℹ 4 more variables: mn55 <dbl>, sr88 <dbl>, ba138 <dbl>, pb208 <dbl>
if (FALSE) {
### loading packages
library(dplyr)
library(ggplot2)
### data cleaning
dat <- dat[which(dat$status >= 3), ]
dat$status <- ifelse(dat$status == 3, "Otolith edge", "Otolith nucleus")
dat$treatment <- ifelse(dat$treatment == 1, "WF-S",
ifelse(dat$treatment == 2, "WF-L",
ifelse(dat$treatment == 3, "EF",
ifelse(dat$treatment == 4, "CL-S",
ifelse(dat$treatment == 5, "CL-L",
ifelse(dat$treatment == 6, "HB-S",
ifelse(dat$treatment == 7, "HB-L", "AB")
)
)
)
)
)
)
### Sr/Ca profile figure
ggplot(data = dat, aes(status, sr88 / ca48)) +
geom_boxplot(aes(col = status), show.legend = F) +
facet_grid(treatment ~ ., scales = "free_y") +
ylab("Sr/Ca") +
xlab("") +
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")
)
### Mg/Ca profile figure
ggplot(data = dat, aes(status, mg25 / ca48)) +
geom_boxplot(aes(col = status), show.legend = F) +
facet_grid(treatment ~ ., scales = "free_y") +
ylab("Mg/Ca") +
xlab("") +
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")
)
### Mn/Ca profile figure
ggplot(data = dat, aes(status, mn55 / ca48)) +
geom_boxplot(aes(col = status), show.legend = F) +
facet_grid(treatment ~ ., scales = "free_y") +
ylab("Mn/Ca") +
xlab("") +
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")
)
### Ba/Ca profile figure
ggplot(data = dat, aes(status, ba138 / ca48)) +
geom_boxplot(aes(col = status), show.legend = F) +
facet_grid(treatment ~ ., scales = "free_y") +
ylab("Ba/Ca") +
xlab("") +
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")
)
### Pb/Ca profile figure
ggplot(data = dat, aes(status, pb208 / ca48)) +
geom_boxplot(aes(col = status), show.legend = F) +
facet_grid(treatment ~ ., scales = "free_y") +
ylab("Pb/Ca") +
xlab("") +
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")
)
}