inst/extdata/vignettePlots.R

In shaughnessyar/driftR: Drift Correcting Water Quality Data

library(ggplot2)
library(dplyr)
library(tidyr)
library(stringr)
library(scales)

df <- dr_readSonde(system.file("extdata", "rawData.csv", package = "driftR"), defineVar = TRUE)
df <- dr_factor(df, corrFactor = corrFac, dateVar = Date, timeVar = Time, format = "MDY")
df <- dr_correctOne(df, sourceVar = SpCond, cleanVar = SpCond_Corr, calVal = 1.07, calStd = 1,
                    factorVar = corrFac)
df <- dr_correctTwo(df, sourceVar = pH, cleanVar = pH_Corr, calValLow = 7.01, calStdLow = 7,
                    calValHigh = 11.8, calStdHigh =  10, factorVar = corrFac)
df <- dr_correctTwo(df, sourceVar = Chloride, cleanVar = Chloride_Corr,
                    calValLow = 11.6, calStdLow = 10, calValHigh = 1411,
                    calStdHigh =  1000, factorVar = corrFac)
df <- dr_drop(df, head=10, tail=5)


ggplot(data = df) +
  geom_histogram(mapping = aes(x = pH), bins = 10)

ggsave("vignettes/pH_hist.png", width = 200, height = 150, units = "mm", dpi = 100)

df %>%
  mutate(dateTime = stringr::str_c(Date, Time, sep = " ", collapse = NULL)) %>%
  mutate(dateTime = base::as.POSIXct(dateTime, format = "%m/%d/%Y %H:%M:%S")) %>%
  ggplot() +
  geom_line(mapping = aes(x = dateTime, y = SpCond))

ggsave("vignettes/SpCond_line.png", width = 200, height = 150, units = "mm", dpi = 100)

df %>%
  mutate(dateTime = str_c(Date, Time, sep = " ", collapse = NULL)) %>%
  mutate(dateTime = as.POSIXct(dateTime, format = "%m/%d/%Y %H:%M:%S")) %>%
  select(dateTime, SpCond, SpCond_Corr) %>%
  gather(key = "measure", value = "value", SpCond, SpCond_Corr) %>%
  arrange(dateTime) %>%
  ggplot() +
    geom_line(mapping = aes(x = dateTime, y = value, group = measure, color = measure))

ggsave("vignettes/SpCond_corrLine.png", width = 200, height = 150, units = "mm", dpi = 100)

df %>%
  mutate(dateTime = str_c(Date, Time, sep = " ", collapse = NULL)) %>%
  mutate(dateTime = as.POSIXct(dateTime, format = "%m/%d/%Y %H:%M:%S")) %>%
  select(dateTime, SpCond, SpCond_Corr) %>%
  gather(key = "measure", value = "value", SpCond, SpCond_Corr) %>%
  ggplot() +
    geom_smooth(mapping = aes(x = dateTime, y = value, group = measure, color = measure))

ggsave("vignettes/SpCond_corrSmooth.png", width = 200, height = 150, units = "mm", dpi = 100)


df %>%
  mutate(dateTime = str_c(Date, Time, sep = " ", collapse = NULL)) %>%
  mutate(dateTime = as.POSIXct(dateTime, format = "%m/%d/%Y %H:%M:%S")) %>%
  select(dateTime, pH, pH_Corr) %>%
  gather(key = "measure", value = "value", pH, pH_Corr) %>%
  ggplot() +
    geom_line(mapping = aes(x = dateTime, y = value, group = measure, color = measure))

ggsave("vignettes/pH_corrLine.png", width = 200, height = 150, units = "mm", dpi = 100)

df %>%
  mutate(dateTime = str_c(Date, Time, sep = " ", collapse = NULL)) %>%
  mutate(dateTime = as.POSIXct(dateTime, format = "%m/%d/%Y %H:%M:%S")) %>%
  select(dateTime, pH, pH_Corr) %>%
  gather(key = "measure", value = "value", pH, pH_Corr) %>%
  ggplot() +
  geom_smooth(mapping = aes(x = dateTime, y = value, group = measure, color = measure))

ggsave("vignettes/pH_corrSmooth.png", width = 200, height = 150, units = "mm", dpi = 100)

ggplot(data = df) +
  geom_point(mapping = aes(x = SpCond_Corr, y = Chloride_Corr))

ggsave("vignettes/spCondChlor.png", width = 200, height = 150, units = "mm", dpi = 100)

ggplot(data = df) +
  geom_point(mapping = aes(x = SpCond_Corr, y = Chloride_Corr, color = Date))

ggsave("vignettes/spCondChlorDate.png", width = 200, height = 150, units = "mm", dpi = 100)

ggplot(data = df, mapping = aes(x = SpCond_Corr, y = Chloride_Corr, color = Date)) +
  geom_point() +
  facet_wrap(~ Date) +
  theme(legend.position="none")

ggsave("vignettes/spCondChlorByDate.png", width = 200, height = 150, units = "mm", dpi = 100)

ggplot(data = df, mapping = aes(x = SpCond_Corr, y = Chloride_Corr, color = Date)) +
  geom_point(color = "#cccccc") +
  geom_smooth() +
  facet_wrap(~ Date) +
  theme(legend.position="none")

ggsave("vignettes/spCondChlorByDate_smooth.png", width = 200, height = 150, units = "mm", dpi = 100)

df %>%
  mutate(secondHalf = ifelse(Date == "9/21/2015" | Date == "9/22/2015" | Date == "9/23/2015", TRUE, FALSE)) %>%
  ggplot() +
  geom_boxplot(mapping = aes(x = secondHalf, y = pH_Corr))

ggsave("vignettes/pHTempByDate_box.png", width = 200, height = 150, units = "mm", dpi = 100)

df %>%
  mutate(dateTime = str_c(Date, Time, sep = " ", collapse = NULL)) %>%
  mutate(dateTime = as.POSIXct(dateTime, format = "%m/%d/%Y %H:%M:%S")) %>%
  select(dateTime, SpCond, SpCond_Corr) %>%
  gather(key = "measure", value = "value", SpCond, SpCond_Corr) %>%
  ggplot() +
  geom_smooth(mapping = aes(x = dateTime, y = value, group = measure, color = measure)) +
  scale_x_datetime(labels = date_format("%m-%d-%Y"), date_breaks = "1 day") +
  labs(
    title = "Comparison of Corrected and Uncorrected Specific Conductance Values",
    subtitle = "Example Creek, Eastern Missouri",
    x = "Date",
    y = "Specific Conductance",
    caption = "Smoothed using a generalized additive model; \nPlot produced by the Saint Louis University Hydrology and Geochemistry Research Lab",
    color = "Series"
  ) +
  scale_colour_discrete(labels=c("Raw Conductivity", "Corrected Conductivity"))

ggsave("vignettes/disseminationPlot.png", width = 200, height = 150, units = "mm", dpi = 100)