Phytoplankton.Rmd

---
title: "Phytoplankton dynamics"
author: "Jens Daniel Müller"
date:  "`r format(Sys.time(), '%d %B, %Y')`"
output: 
  workflowr::wflow_html:
    number_sections: true
    toc_depth: 3
    toc_float:
      collapsed: false
editor_options:
  chunk_output_type: console
---


```{r global_options, include = FALSE}
knitr::opts_chunk$set(warning=FALSE, message=FALSE)
```

```{r packages}
library(tidyverse)
```

```{r ggplot_theme, include = FALSE}
theme_set(theme_bw())
```

```{r read_parameters, include = FALSE}
parameters <-
  read_rds(here::here("data",
                       "parameters.rds"))
```


# Phytoplankton cell counts

## Data preparation


```{r read_prepare_sensor_data}

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)

```

```{r convert_biomass_unit}

tp_ID_grid <- tp_ID_grid


```



```{r phytoplankton_time_series, fig.asp=0.8}

tp_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)))) +
  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"
)

```