Phytoplankton dynamics
Jens Daniel Müller
06 November, 2020
Last updated: 2020-11-06
Checks: 7 0
Knit directory: BloomSail/
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library(tidyverse)1 Phytoplankton cell counts
1.1 Data preparation
tp <- read_csv(
here::here("data/intermediate/_summarized_data_files",
"tp.csv"),
col_types = cols(ID = col_character())
)
cruise_dates <-
read_csv(
here::here(
"data/intermediate/_summarized_data_files",
"cruise_date.csv"
),
col_types = cols(ID = col_character())
)
#### calculate mean total phytoplanton biomass in different water depth intervals
tp <- tp %>%
filter(
station %in% parameters$stations_in_phytoplankton,
class == parameters$class_in_phytoplankton,
Species != "Nodulariadead"
) %>%
mutate(ID = if_else(ID == "180722", "180723", ID))
tp <- tp %>%
mutate(dep_grid = cut(
dep,
breaks = c(-1, parameters$surface_dep, parameters$max_dep),
labels = c("0-6", "6-25")
)) %>%
drop_na()
tp_ID_grid <- tp %>%
group_by(ID, dep_grid, Species) %>%
summarise(value = mean(value, na.rm = TRUE)) %>%
ungroup()
tp_ID_grid <- full_join(cruise_dates, tp_ID_grid)tp_ID_grid <- tp_ID_gridtp_ID_grid %>%
filter(Species != "total") %>%
ggplot(aes(date_time_ID, value, col = dep_grid)) +
geom_point() +
geom_line() +
facet_wrap(~ Species, ncol=1) +
scale_color_brewer(palette = "Set1", name = "Depth (m)") +
scale_x_datetime(breaks = "week", date_labels = "%d %b") +
# scale_y_continuous(sec.axis = sec_axis(~ . * 0.16 / 12,
# name = expression(Biomass ~ (mu~mol-C~kg^-1)))) +
labs(y = expression(Biomass ~ (mg~m^-3))) +
theme(axis.title.x = element_blank())
ggsave(
here::here(
"output/Plots/Figures_publication/appendix",
"Fig_S5.pdf"
),
width = 180,
height = 120,
dpi = 300,
units = "mm"
)
ggsave(
here::here(
"output/Plots/Figures_publication/appendix",
"Fig_S5.png"
),
width = 180,
height = 120,
dpi = 300,
units = "mm"
)
sessionInfo()R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
Matrix products: default
locale:
[1] LC_COLLATE=English_Germany.1252 LC_CTYPE=English_Germany.1252
[3] LC_MONETARY=English_Germany.1252 LC_NUMERIC=C
[5] LC_TIME=English_Germany.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] forcats_0.5.0 stringr_1.4.0 dplyr_1.0.0 purrr_0.3.4
[5] readr_1.3.1 tidyr_1.1.0 tibble_3.0.3 ggplot2_3.3.2
[9] tidyverse_1.3.0 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] tidyselect_1.1.0 xfun_0.16 haven_2.3.1 colorspace_1.4-1
[5] vctrs_0.3.2 generics_0.0.2 htmltools_0.5.0 yaml_2.2.1
[9] blob_1.2.1 rlang_0.4.7 later_1.1.0.1 pillar_1.4.6
[13] withr_2.2.0 glue_1.4.1 DBI_1.1.0 RColorBrewer_1.1-2
[17] dbplyr_1.4.4 modelr_0.1.8 readxl_1.3.1 lifecycle_0.2.0
[21] munsell_0.5.0 gtable_0.3.0 cellranger_1.1.0 rvest_0.3.6
[25] evaluate_0.14 labeling_0.3 knitr_1.30 httpuv_1.5.4
[29] fansi_0.4.1 broom_0.7.0 Rcpp_1.0.5 promises_1.1.1
[33] backports_1.1.8 scales_1.1.1 jsonlite_1.7.0 farver_2.0.3
[37] fs_1.4.2 hms_0.5.3 digest_0.6.25 stringi_1.4.6
[41] rprojroot_1.3-2 grid_4.0.2 here_0.1 cli_2.0.2
[45] tools_4.0.2 magrittr_1.5 crayon_1.3.4 whisker_0.4
[49] pkgconfig_2.0.3 ellipsis_0.3.1 xml2_1.3.2 reprex_0.3.0
[53] lubridate_1.7.9 assertthat_0.2.1 rmarkdown_2.3 httr_1.4.2
[57] rstudioapi_0.11 R6_2.4.1 git2r_0.27.1 compiler_4.0.2