data-raw/plot_data.R

In beanumber/macleish: Retrieve Data from MacLeish Field Station

library(readxl)
library(tidyverse)
library(janitor)
library(lubridate)
library(stringr)
library(usethis)
library(devtools)
library(dplyr)


# Uploading data into R
tree_diameter1 <- read_excel("data-raw/MacLeish Data_Plot MC-01.xlsx")
tree_diameter2 <- read_excel("data-raw/MacLeish Data_Plot MC-02.xlsx")


# Plot Data 1
# Creating year and height column 
tree_diameter1 <- tree_diameter1 %>%
  pivot_longer(c(`Fall'15`, `Fall'14`,`Fall'13`,`Fall'12`,`Fall'11`,`Fall'10`), names_to = "year", values_to = "diameter")

# Separating fall and year into new columns 
tree_diameter1 <- tree_diameter1 %>%
  separate(year, c("semester", "year"), sep = 4)

# Changing abbreviated year into full year 
tree_diameter1$year[tree_diameter1$year == "'15"] <- "2015"
tree_diameter1$year[tree_diameter1$year == "'14"] <- "2014"
tree_diameter1$year[tree_diameter1$year == "'13"] <- "2013"
tree_diameter1$year[tree_diameter1$year == "'12"] <- "2012"
tree_diameter1$year[tree_diameter1$year == "'11"] <- "2011"
tree_diameter1$year[tree_diameter1$year == "'10"] <- "2010"

# Changing value "DEAD" to NA for diameter
# Tree diameter didn't increase or decrease over time when dead
tree_diameter1$`diameter`[tree_diameter1$`diameter` == "DEAD"] <- "NA"

# Changing variable names to lowercase and removing numerical units 
tree_diameter1 <- tree_diameter1 %>%
  rename(notes = `Notes:`, module = `Module#`, tag = `Tag#`) %>% 
  rename_with(tolower) 

# Moved notes to final column
tree_diameter1 <- tree_diameter1 %>% 
  select(module, tag, species, position, semester, year, diameter, notes)

# Change value "sub-canopy" to "subcanopy"
tree_diameter1$position[tree_diameter1$position == "sub-canopy"] <- "subcanopy"

# Changing year and diameter from character to numeric variables 
tree_diameter1$year <- as.numeric(tree_diameter1$year)
tree_diameter1$diameter <- as.numeric(tree_diameter1$diameter)

# Changing species name from scientific to common name
tree_diameter1$species[tree_diameter1$species == "Acer rubrum"] <- "Red Maple"
tree_diameter1$species[tree_diameter1$species == "Betula lenta"] <- "Sweet Birch"
tree_diameter1$species[tree_diameter1$species == "Betula papyrifera"] <- "Paper Birch"
tree_diameter1$species[tree_diameter1$species == "Fagus grandifolia"] <- "American Beech"
tree_diameter1$species[tree_diameter1$species == "Hamamelis virginiana"] <- "American Witch-hazel"
tree_diameter1$species[tree_diameter1$species == "Pinus strobus"] <- "Eastern White Pine"
tree_diameter1$species[tree_diameter1$species == "Quercus rubra"] <- "Northern Red Oak"
tree_diameter1$species[tree_diameter1$species == "Tsuga canadensis"] <- "Eastern Hemlock"

# Plot Data 2
# Creating year and height column 
tree_diameter2 <- tree_diameter2 %>%
  pivot_longer(c(`FALL 2016`, `Fall'12`,`Fall'11`,`Fall'10`,`Fall'09`), names_to = "year", values_to = "diameter")

# Separating fall and year into new columns 
tree_diameter2 <- tree_diameter2 %>%
  separate(year, c("semester", "year"), sep = 4)

# Changing abbreviated year into full year 
tree_diameter2$year[tree_diameter2$year == "'09"] <- "2009"
tree_diameter2$year[tree_diameter2$year == "'10"] <- "2010"
tree_diameter2$year[tree_diameter2$year == "'11"] <- "2011"
tree_diameter2$year[tree_diameter2$year == "'12"] <- "2012"

# Changing fall to lowercase
tree_diameter2$semester[tree_diameter2$semester == "FALL"] <- "Fall"

# Changing value "DEAD" to NA for height 
tree_diameter2$diameter[tree_diameter2$diameter == "DEAD"] <- "NA"

# Changing variable names to lowercase and removing numerical units
tree_diameter2 <- tree_diameter2 %>%
  rename(notes = `Notes:`, module = `Module#`, tag = `Tag#`) %>% 
  rename_with(tolower)

# Replace species listed as "???" with NA
tree_diameter2$species[tree_diameter2$species == "???"] <- "NA"

# Moved notes to final column
tree_diameter2 <- tree_diameter2 %>% 
  select(module, tag, species, semester, year, diameter, notes)

# Changing year and diameter from character to numeric variables 
tree_diameter2$year <- as.numeric(tree_diameter2$year)
tree_diameter2$diameter <- as.numeric(tree_diameter2$diameter)

# Changing species name from scientific to common name
tree_diameter2$species[tree_diameter2$species == "Acer rubrum"] <- "Red Maple"
tree_diameter2$species[tree_diameter2$species == "Betula lenta"] <- "Sweet Birch"
tree_diameter2$species[tree_diameter2$species == "Fagus grandifolia"] <- "American Beech"
tree_diameter2$species[tree_diameter2$species == "Pinus strobus"] <- "Eastern White Pine"
tree_diameter2$species[tree_diameter2$species == "Quercus rubra"] <- "Northern Red Oak"
tree_diameter2$species[tree_diameter2$species == "Tsuga canadensis"] <- "Eastern Hemlock"

# Write both to package
usethis::use_data(tree_diameter1, overwrite = TRUE)
usethis::use_data(tree_diameter2, overwrite = TRUE)