Percent Cover

Percent cover box plot at four sites

Setting up

#read in data
alldata<-read.csv(
      "https://raw.githubusercontent.com/Cmwegener/thesis/master/data/field/CB_field_data_plus.csv",
    header = TRUE
  )
alldata$date<-as.Date(alldata$date, format = c("%Y-%m-%d"))

Subset

HS<-subset(alldata, alldata$site.old == "HS")
BY<-subset(alldata, alldata$site.old == "BY")
ND<-subset(alldata, alldata$site.old == "ND")
PC<-subset(alldata, alldata$site.old == "PC")

Graph

a <-
  ggplot(data = HS,
         mapping = aes(x = date, y = cover, group = date)) + geom_boxplot(alpha=0.3) +
  ggtitle("Horseshoe Bay") +
  scale_x_date(date_breaks = "2 month", date_labels = "%b %Y")+
  geom_jitter(position=position_jitter(0.5),
              size=1,
              alpha = 0.3) + theme(
    plot.title = element_text(size = 20, face = "plain"),
    axis.text.x = element_text(angle = 60, hjust = 1),
    axis.text = element_text(size = 20),
    axis.title = element_text(size = 20, face = "plain"),
    panel.grid.major = element_blank(),
    panel.grid.minor = element_blank(),
    panel.background = element_blank(),
    axis.line = element_line(colour = "black")
  ) +
  ylab(" ") +
  xlab(" ")

b <-
  ggplot(data = BY,
         mapping = aes(x = date, y = cover, group = date)) + geom_boxplot(alpha=0.3) +
  ggtitle("Brickyard Park") +
  scale_x_date(date_breaks = "2 month", date_labels = "%b %Y") +
  geom_jitter(position=position_jitter(0.5),
              size=1,
              alpha = 0.3)+ theme(
    plot.title = element_text(size = 20, face = "plain"),
    axis.text.x = element_text(angle = 60, hjust = 1),
    axis.text = element_text(size = 20),
    axis.title = element_text(size = 20, face = "plain"),
    panel.grid.major = element_blank(),
    panel.grid.minor = element_blank(),
    panel.background = element_blank(),
    axis.line = element_line(colour = "black")
  ) +
  ylab(" ") +
  xlab(" ")

c <-
  ggplot(data = ND,
         mapping = aes(x = date, y = cover, group = date)) + geom_boxplot(alpha=0.3) +
  ggtitle("Point Chauncy") +
  scale_x_date(date_breaks = "2 month", date_labels = "%b %Y") +
  geom_jitter(position=position_jitter(0.5),
              size=1,
              alpha = 0.3)+ theme(
    plot.title = element_text(size = 20, face = "plain"),
    axis.text.x = element_text(angle = 60, hjust = 1),
    axis.text = element_text(size = 20),
    axis.title = element_text(size = 20, face = "plain"),
    panel.grid.major = element_blank(),
    panel.grid.minor = element_blank(),
    panel.background = element_blank(),
    axis.line = element_line(colour = "black")
  ) +
  ylab(" ") +
  xlab(" ")

d <-
  ggplot(data = PC,
         mapping = aes(x = date, y = cover, group = date)) + geom_boxplot(alpha=0.3) +
  ggtitle("Paradise Cay") +
  scale_x_date(date_breaks = "2 month", date_labels = "%b %Y") +
  geom_jitter(position=position_jitter(0.5),
              size=1,
              alpha = 0.3)+ theme(
    plot.title = element_text(size = 20, face = "plain"),
    axis.text.x = element_text(angle = 60, hjust = 1),
    axis.text = element_text(size = 20),
    axis.title = element_text(size = 20, face = "plain"),
    panel.grid.major = element_blank(),
    panel.grid.minor = element_blank(),
    panel.background = element_blank(),
    axis.line = element_line(colour = "black")
  ) +
  ylab(" ") +
  xlab(" ")

Stack and annotate

pcfigure<-ggarrange(d, c, b, a, ncol = 4, nrow = 1)

## Warning: Removed 20 rows containing non-finite values (stat_boxplot).

## Warning: Removed 20 rows containing missing values (geom_point).

## Warning: Removed 10 rows containing non-finite values (stat_boxplot).

## Warning: Removed 10 rows containing missing values (geom_point).

annotate_figure(pcfigure,
                top = text_grob("", color = "black", face = "plain", size = 25), left = text_grob("Percent Cover", color = "black", rot = 90, size=25, face="bold"))