Interactive Session 1B

File paths, {here}, project structure, code style

1. Setup

  • Fork and clone this repo
  • Check out the project structure & files

2. File path practice

  • We’ll run through each line in the toolik_airtemp_summary.qmd to understand where it’s pointing, what it’s doing, and add a few more tools to our coding toolkit (readr::read_csv(), janitor::clean_names(), %>%)

  • Similarly, we’ll create from scratch & work through one more example. We will:

    • Read in the chlorophyll data
    • Explore the imported data
    • Clean up the dataset names
    • Create a plot of chlorophyll concentration at varying measurement depth, do some customization
    • Export the graph to /figs
# read in data
toolik_chlorophyll <- read_csv(here::here("data", "data-raw", "toolik_chlorophyll.csv"))

# get data overview
skimr::skim(toolik_chlorophyll)

dim(toolik_chlorophyll)
names(toolik_chlorophyll)

# clean names
toolik_chlorophyll <- toolik_chlorophyll %>% clean_names() 

# make plot
toolik_chlorophyll_plot <- ggplot(data = toolik_chlorophyll, 
                                  aes(x = depth, y = as.numeric(active_chl_a_ug_l))) +
  geom_point() +
  theme_minimal() +
  labs(title = "Toolik Station Chlorophyll a concentration",
       x = "Depth (m)",
       y = "Chlorophyll a concentration (micrograms per liter)")

toolik_chlorophyll_plot

# save plot
ggsave(here::here("figs", "toolik_chlorophyll_plot.png"), height = 6, width = 7)
Data sources

All datasets are collected and provided by scientists with the Toolik Station Long Term Ecological Research (LTER) site, Alaska.

Toolik Station Meteorological Data: toolik_weather.csv Shaver, G. 2019. A multi-year DAILY weather file for the Toolik Field Station at Toolik Lake, AK starting 1988 to present. ver 4. Environmental Data Initiative. https://doi.org/10.6073/pasta/ce0f300cdf87ec002909012abefd9c5c (Accessed 2021-08-08).

Toolik Lake Chlorophyll: toolik_chlorophyll.csv Miller, M. 2014. Chlorophyll A, and primary productivity of Toolik lake , Arctic LTER 1975 to 1988, Toolik Filed Station, Alaska. ver 5. Environmental Data Initiative. https://doi.org/10.6073/pasta/6738024bf0174f73b3f74486f43d1059 (Accessed 2021-08-08).

Toolik fish: toolik_fish.csv Budy, P., C. Luecke, and M. McDonald. 2020. Fish captures in lakes of the Arctic LTER region Toolik Field Station Alaska from 1986 to present. ver 6. Environmental Data Initiative. https://doi.org/10.6073/pasta/d0a9358f783339821b82510eb8c61b45 (Accessed 2021-08-08).

End Interactive Session 1B