Phytoplankton dynamics
Jens Daniel Müller
28 September, 2020
Last updated: 2020-09-28
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Knit directory: BloomSail/
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library(tidyverse)1 Phytoplankton cell counts
1.1 Data preparation
max_dep <- 25
surface_dep <- 6
stations_in <- c("P07", "P10")
class_in <- "t" # using total biomass per Species class onlytp <- read_csv(here::here("Data/_summarized_data_files",
"tp.csv"),
col_types = cols(ID = col_character()))
cruise_dates <- read_csv(here::here("Data/_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% stations_in,
class == class_in,
Species != "Nodulariadead") %>%
mutate(ID = if_else(ID == "180722", "180723", ID))
tp <- tp %>%
mutate(dep_grid = cut(dep,
breaks = c(-1,surface_dep,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 %>%
filter(Species != "total") %>%
ggplot(aes(date_time_ID, value, col=dep_grid))+
geom_point()+
geom_line()+
facet_grid(Species~.)+
scale_color_brewer(palette = "Set1", name= "Depth (m)")+
scale_x_datetime(breaks = "week", date_labels = "%d %b")+
labs(y=expression(Biomass~(mg/m^3)))+
theme(axis.title.x = element_blank())
ggsave(here::here("output/Plots/Figures_publication/appendix", "Phytoplankton_mean_total_biomass.pdf"),
width = 180, height = 120, dpi = 300, units = "mm")
ggsave(here::here("output/Plots/Figures_publication/appendix", "Phytoplankton_mean_total_biomass.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_1.29 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