Code to summarise and visualise quality codes in hydrologic data

Qcode

# see  https://tonyladson.wordpress.com/2015/02/17/quality-codes-in-hydrologic-data/

library(treemap)
library(RColorBrewer)
library(ggplot2)
library(grid)
library(lubridate)

# Generate some data

# dates
set.seed(2015)

xdate <- seq(as.Date('2000-01-01'),as.Date('2002-12-31'), by = '1 day' )

# generate some flow data, usually this would come from a stream gauging record
flow <- rlnorm(n= length(xdate), meanlog = 1, sdlog=0.5)

qcodes <- c(1, 2, 15, 50, 151, 240, 255)
qcode.seq <- sample(qcodes, length(xdate), replace = TRUE, prob = 1/qcodes)

my.data <- data.frame(xdate = xdate, flow = flow, qcode = qcode.seq)
# my.data can be replaced with a data set

# Tabulate quality codes

with(my.data, table(qcode))

#   1   2  15  50 151 255 
# 704 340  37   9   4   2 

# Percentage of data with each code
with(my.data, round(100*prop.table(table(qcode)), 2 ))
#     1     2    15    50   151   255 
# 64.23 31.02  3.38  0.82  0.36  0.18 

# Tree map of quality codes
qcode.table.df <- with(my.data, as.data.frame(table(qcode)))
treemap(qcode.table.df, index="qcode", vSize="Freq", title="", algorithm="pivotSize", palette=rev(brewer.pal(8, "RdYlGn")))


#  Tile plot showing the occurance of quality codes
# set up x-axes labels
month.start <- yday( seq(as.Date('2000-01-01'),as.Date('2000-12-31'), by = 'months' ))


pl<- ggplot(my.data,aes(yday(xdate), year(xdate)))
pl + geom_tile(aes(fill = factor(qcode))) + 
  scale_fill_manual(values = rev(brewer.pal(8, "RdYlGn")), name='Quality Code' ) +
  theme_bw() +
  theme(axis.title.x = element_text(colour="grey20", size=20, vjust=-2)) +
  theme(axis.text.x = element_text(colour="grey20",size=12)) +
  theme(axis.title.y = element_text(colour="grey20",size=20, vjust=0)) +
  theme(axis.text.y = element_text(colour="grey20",size=12)) +
  theme(legend.title = element_text(colour="grey20",size=12)) +
  theme(plot.margin = unit(c(2.5, 2.5, 2.5, 2.5), "cm")) +
  ylab("Year") +
  scale_x_continuous(name="Month", breaks=month.start, labels=month.abb)


# Time series showing the occurance of quality codes

pl <- ggplot(my.data, aes(x=xdate, y=flow, color=factor(qcode) ))
pl + geom_point() +
  scale_color_manual(values = rev(brewer.pal(8, "RdYlGn")), name = "Quality code") +
  theme_bw() +
  theme(axis.title.x = element_text(colour="grey20", size=20, vjust=-2)) +
  theme(axis.text.x = element_text(colour="grey20",size=10)) +
  theme(axis.title.y = element_text(colour="grey20",size=20, vjust=0)) +
  theme(axis.text.y = element_text(colour="grey20",size=15)) +
  theme(legend.title = element_text(colour="grey20",size=12)) +
  theme(legend.text = element_text(colour="grey20",size=12)) +
  theme(plot.margin = unit(c(2.5, 2.5, 2.5, 2.5), "cm")) +
  labs(x = "Date") +
  labs(y = "Flow")

# Box plot by quality code

pl <- ggplot(my.data, aes(x=factor(qcode), y=flow))
pl + geom_boxplot(aes(fill=factor(qcode)), outlier.size=0) +
  geom_jitter(alpha=0.3) +
  scale_fill_manual(values=rev(brewer.pal(8, "RdYlGn")), name="Quality code") +
  
  labs(x = "Quality code") +
  labs(y = "Flow") +
  
  theme_bw() +
  theme(axis.title.x = element_text(colour="grey20", size=20, vjust=-2)) +
  theme(axis.text.x = element_text(colour="grey20",size=12)) +
  theme(axis.title.y = element_text(colour="grey20",size=20, vjust=0)) +
  theme(axis.text.y = element_text(colour="grey20",size=12)) +
  theme(legend.title = element_text(colour="grey20",size=12)) +
  theme(plot.margin = unit(c(2.5, 2.5, 2.5, 2.5), "cm")) 

For details see blog at https://tonyladson.wordpress.com/2015/02/17/quality-codes-in-hydrologic-data/