1st commit

WEDC_Msc.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: knitr
+LaTeX: XeLaTeX

data/gauges_coord.csv

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+stationRef,start,end,@id,label,notation,riverName,RLOIid,catchmentN,dateOpened,wiskiID,town,datumOffse,status,stageScale,downstageS,lat,long,easting,northing,gridRefere,measures,parameterN,parameter,qualifier,period,unitName
+4082,1981-11-01T09:00:00Z,2017-08-25T23:45:00Z,http://environment.data.gov.uk/flood-monitoring/id/stations/4082,Littlethorpe,4082,River Soar,2136,Soar,1971-08-01,4082,Littlethorpe,NA,http://environment.data.gov.uk/flood-monitoring/def/core/statusActive,http://environment.data.gov.uk/flood-monitoring/id/stations/4082/stageScale,NA,52.571268,-1.201273,454230,297350,NA,http://environment.data.gov.uk/flood-monitoring/id/measures/4082-level-stage-i-15_min-mASD|http://environment.data.gov.uk/flood-monitoring/id/measures/4082-flow--i-15_min-m3_s,Water Level|Flow,level|flow,|Stage,900,m3/s|mASD
+4086,1989-01-01T09:00:00Z,2017-08-25T23:45:00Z,http://environment.data.gov.uk/flood-monitoring/id/stations/4086,South Wigston,4086,River Sence (Soar),2139,Soar,1971-08-01,4086,South Wigston,NA,http://environment.data.gov.uk/flood-monitoring/def/core/statusActive,http://environment.data.gov.uk/flood-monitoring/id/stations/4086/stageScale,NA,52.573856,-1.13453,458750,297690,NA,http://environment.data.gov.uk/flood-monitoring/id/measures/4086-level-stage-i-15_min-mASD|http://environment.data.gov.uk/flood-monitoring/id/measures/4086-flow--i-15_min-m3_s,Water Level|Flow,level|flow,Stage|,900,m3/s|mASD
+4145,2000-05-05T09:00:00Z,2017-08-25T04:00:00Z,http://environment.data.gov.uk/flood-monitoring/id/stations/4145,Sharnford,4145,River Soar,2187,Soar,2000-05-05,4145,Sharnford,NA,http://environment.data.gov.uk/flood-monitoring/def/core/statusActive,http://environment.data.gov.uk/flood-monitoring/id/stations/4145/stageScale,NA,52.522794,-1.29766,447750,291890,SP47759189,http://environment.data.gov.uk/flood-monitoring/id/measures/4145-level-stage-i-15_min-mASD,Water Level,level,Stage,900,mASD
+4161,2001-12-17T12:30:00Z,2017-08-25T04:00:00Z,http://environment.data.gov.uk/flood-monitoring/id/stations/4161,Great Glen,4161,River Sence (Soar),2188,Soar,2001-12-17,4161,Great Glen,NA,http://environment.data.gov.uk/flood-monitoring/def/core/statusActive,http://environment.data.gov.uk/flood-monitoring/id/stations/4161/stageScale,NA,52.574167,-1.035067,465490,297810,SP65499781,http://environment.data.gov.uk/flood-monitoring/id/measures/4161-level-stage-i-15_min-mASD,Water Level,level,Stage,900,mASD
+4174,2002-03-25T09:00:00Z,2017-08-25T04:00:00Z,http://environment.data.gov.uk/flood-monitoring/id/stations/4174,Freemans Weir,4174,River Soar,2158,Soar,2002-03-25,4174,Aylestone,NA,http://environment.data.gov.uk/flood-monitoring/def/core/statusActive,http://environment.data.gov.uk/flood-monitoring/id/stations/4174/stageScale,NA,52.619792,-1.146475,457880,302790,NA,http://environment.data.gov.uk/flood-monitoring/id/measures/4174-level-stage-i-15_min-mASD,Water Level,level,Stage,900,mASD
+4195,2002-11-25T12:45:00Z,2017-08-25T23:45:00Z,http://environment.data.gov.uk/flood-monitoring/id/stations/4195,Whetstone,4195,Whetstone Brook,2160,Soar,2002-11-25,4195,Whetstone,NA,http://environment.data.gov.uk/flood-monitoring/def/core/statusActive,http://environment.data.gov.uk/flood-monitoring/id/stations/4195/stageScale,NA,52.553447,-1.171951,456240,295390,NA,http://environment.data.gov.uk/flood-monitoring/id/measures/4195-level-stage-i-15_min-mASD,Water Level,level,Stage,900,mASD

scripts/Wedc_class.R

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+#In this demo we are going to create an R project, load libraries,
+#read the data, clean data and compute the annual maximum water 
+#level and examine if there is any trend. 
+#We will also visualize the data in various stages of the analysis.
+
+# Load the necessary libraries 
+
+library(tidyverse)
+library(GGally)
+library(tibbletime)
+library(lubridate)
+library(leaflet)
+
+# Data path
+data_path <- "data/water_level.csv"
+#data_path <- "https://www.dropbox.com/s/0109edsvr4fuawd/all_stages.csv?dl=1"
+# Read the data 
+stage <- read_csv(data_path, skip = 21,progress = T) #skip = 21
+
+# Change variable names 
+stage <- rename(stage, st.4082 = s_15_4082.csv,
+         st.4086 = s_15_4086.csv,
+         st.4145 = s_4145.csv,
+         st.4161 = s_4161.csv, 
+         st.4174 = s_4174.csv,
+         st.4195 = s_4195.csv)
+
+
+# Compute the annual maximum water level at each gauging station
+stage <- as_tbl_time(stage, date_time)
+ann_max <- stage %>% time_summarise(period = "yearly",
+                          amax.4082 = max(st.4082, na.rm = T),
+                          amax.4086 = max(st.4086, na.rm = T),
+                          amax.4145 = max(st.4145, na.rm = T),
+                          amax.4161 = max(st.4161, na.rm = T),
+                          amax.4174 = max(st.4174, na.rm = T),
+                          amax.4195 = max(st.4195, na.rm = T))
+ann_max$year <- year(ann_max$date_time)
+# Plot the data and and fit linear regression line
+
+plot1 <- ann_max %>% gather("station", "stage", 2:7) %>% 
+  ggplot(., aes(year, stage))+
+  theme_bw()+
+  geom_point()+
+  geom_smooth(method = "lm", se=T, span=0.50,color = "blue")+ # loess (Locally Weighted Scatterplot Smoothing)
+  facet_grid(station ~ ., scales = "free_y") #facet_wrap(~station)
+
+plot1
+plot1+geom_line()
+
+fit <- lm(formula = amax.4174 ~ year, data = ann_max)
+# Plot in the same graphic   
+  clrs <-  colorRamps::primary.colors(5)
+  ann_max %>% gather("station", "stage", 2:6) %>% 
+    ggplot(.,aes(x = date_time, y = stage, colour = station))+
+    theme_bw()+
+    geom_line()+
+    scale_color_manual(values = clrs)
+
+
+# Summary graphic 
+ggpairs(ann_max, columns = 2:6)
+
+# Correlation matrix 
+ggcorr(ann_max[, -c(1,8)],label = TRUE,
+       label_alpha = TRUE)
+
+# Mapping the stations
+
+locations <- read_csv("data/gauges_coord.csv")
+
+leaflet(data = locations) %>% addTiles() %>%
+  addMarkers(~long, ~lat, popup = ~as.character(riverName), label = ~as.character(riverName))
+
+

scripts/gauges_coord.csv

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+stationRef,start,end,@id,label,notation,riverName,RLOIid,catchmentN,dateOpened,wiskiID,town,datumOffse,status,stageScale,downstageS,lat,long,easting,northing,gridRefere,measures,parameterN,parameter,qualifier,period,unitName
+4082,1981-11-01T09:00:00Z,2017-08-25T23:45:00Z,http://environment.data.gov.uk/flood-monitoring/id/stations/4082,Littlethorpe,4082,River Soar,2136,Soar,1971-08-01,4082,Littlethorpe,NA,http://environment.data.gov.uk/flood-monitoring/def/core/statusActive,http://environment.data.gov.uk/flood-monitoring/id/stations/4082/stageScale,NA,52.571268,-1.201273,454230,297350,NA,http://environment.data.gov.uk/flood-monitoring/id/measures/4082-level-stage-i-15_min-mASD|http://environment.data.gov.uk/flood-monitoring/id/measures/4082-flow--i-15_min-m3_s,Water Level|Flow,level|flow,|Stage,900,m3/s|mASD
+4086,1989-01-01T09:00:00Z,2017-08-25T23:45:00Z,http://environment.data.gov.uk/flood-monitoring/id/stations/4086,South Wigston,4086,River Sence (Soar),2139,Soar,1971-08-01,4086,South Wigston,NA,http://environment.data.gov.uk/flood-monitoring/def/core/statusActive,http://environment.data.gov.uk/flood-monitoring/id/stations/4086/stageScale,NA,52.573856,-1.13453,458750,297690,NA,http://environment.data.gov.uk/flood-monitoring/id/measures/4086-level-stage-i-15_min-mASD|http://environment.data.gov.uk/flood-monitoring/id/measures/4086-flow--i-15_min-m3_s,Water Level|Flow,level|flow,Stage|,900,m3/s|mASD
+4145,2000-05-05T09:00:00Z,2017-08-25T04:00:00Z,http://environment.data.gov.uk/flood-monitoring/id/stations/4145,Sharnford,4145,River Soar,2187,Soar,2000-05-05,4145,Sharnford,NA,http://environment.data.gov.uk/flood-monitoring/def/core/statusActive,http://environment.data.gov.uk/flood-monitoring/id/stations/4145/stageScale,NA,52.522794,-1.29766,447750,291890,SP47759189,http://environment.data.gov.uk/flood-monitoring/id/measures/4145-level-stage-i-15_min-mASD,Water Level,level,Stage,900,mASD
+4161,2001-12-17T12:30:00Z,2017-08-25T04:00:00Z,http://environment.data.gov.uk/flood-monitoring/id/stations/4161,Great Glen,4161,River Sence (Soar),2188,Soar,2001-12-17,4161,Great Glen,NA,http://environment.data.gov.uk/flood-monitoring/def/core/statusActive,http://environment.data.gov.uk/flood-monitoring/id/stations/4161/stageScale,NA,52.574167,-1.035067,465490,297810,SP65499781,http://environment.data.gov.uk/flood-monitoring/id/measures/4161-level-stage-i-15_min-mASD,Water Level,level,Stage,900,mASD
+4174,2002-03-25T09:00:00Z,2017-08-25T04:00:00Z,http://environment.data.gov.uk/flood-monitoring/id/stations/4174,Freemans Weir,4174,River Soar,2158,Soar,2002-03-25,4174,Aylestone,NA,http://environment.data.gov.uk/flood-monitoring/def/core/statusActive,http://environment.data.gov.uk/flood-monitoring/id/stations/4174/stageScale,NA,52.619792,-1.146475,457880,302790,NA,http://environment.data.gov.uk/flood-monitoring/id/measures/4174-level-stage-i-15_min-mASD,Water Level,level,Stage,900,mASD
+4195,2002-11-25T12:45:00Z,2017-08-25T23:45:00Z,http://environment.data.gov.uk/flood-monitoring/id/stations/4195,Whetstone,4195,Whetstone Brook,2160,Soar,2002-11-25,4195,Whetstone,NA,http://environment.data.gov.uk/flood-monitoring/def/core/statusActive,http://environment.data.gov.uk/flood-monitoring/id/stations/4195/stageScale,NA,52.553447,-1.171951,456240,295390,NA,http://environment.data.gov.uk/flood-monitoring/id/measures/4195-level-stage-i-15_min-mASD,Water Level,level,Stage,900,mASD

scripts/index.Rmd

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+---
+title: "R demo WEDC Master's students"
+author: "A.Khouakhi"
+date: "December 1, 2017"
+output:
+  html_document:
+    highlight: haddock
+    theme: readable
+  pdf_document: default
+  word_document: default
+---
+
+### 1. Load the necessary libraries
+
+```{r, eval=T, echo=T,include=T,warning= F, message=F,cache=FALSE}
+
+library(tidyverse)
+library(GGally)
+library(tibbletime)
+library(kableExtra)
+library(lubridate)
+library(leaflet)
+```
+
+### 2. Load and read the data
+
+The data contains some rows that we don't need so we will skip them using the argument `skip`
+
+```{r, eval=T, echo=T,warning= F, message=F,cache=FALSE}
+# Data path
+data_path <- "water_level.csv"
+# Read the data 
+stage <- read_csv(data_path, skip = 21, progress = T) #skip = 21
+stage 
+```
+### 3. Tidying up the data 
+
+The variable names are not consistent so we are going to rename them using the rename function from the `dplyr` package  
+
+```{r, eval=T, echo=T}
+# Change variable names 
+stage <- rename(stage, st.4082 = s_15_4082.csv,
+         st.4086 = s_15_4086.csv,
+         st.4145 = s_4145.csv,
+         st.4161 = s_4161.csv, 
+         st.4174 = s_4174.csv,
+         st.4195 = s_4195.csv)
+```
+
+### 4. Analyses 
+As example we are going to compute the annual maximum water level for each gauging station and check if there is any trend
+
+```{r, eval=T, echo=T,warning= F, message=F,cache=FALSE}
+# Compute the annual maximum water level at each gauging station
+stage <- as_tbl_time(stage, date_time)
+
+ann_max <- stage %>% 
+  mutate(year =year(date_time)) %>% 
+  group_by(year) %>% 
+  summarise_all(funs(max))
+
+
+
+
+knitr::kable(ann_max, "html") %>%
+  kable_styling(bootstrap_options = c("striped", "hover", "condensed"))
+```
+
+### 5. Modelling and visualization 
+fit a linear regression model to the data, see if there is any correlation between different stations and so on
+
+```{r, eval=T, echo=T}
+
+# Plot the data and and fit linear regression line
+plot1 <- ann_max %>% gather("station", "stage", 3:8) %>% 
+  ggplot(., aes(date_time, stage))+
+  theme_bw()+
+  geom_point()+
+  geom_smooth(method = "lm", se=T, color="blue")+
+  facet_grid(station ~ ., scales = "free_y") 
+plot1
+# Add lines
+plot1 + geom_line()
+
+
+# Plot in small graphics
+plot1 + facet_wrap(~station)
+
+# Summary graphic 
+ggpairs(ann_max, columns = 3:8)
+
+# Correlation matrix 
+ggcorr(ann_max[, -1],label = TRUE,
+       label_alpha = TRUE)
+
+```
+
+### 6. Other visualization 
+
+
+```{r, eval=T, echo=T}
+
+# Plot in the same graphic   
+  clrs <-  colorRamps::primary.colors(6)
+  ann_max %>% gather("station", "stage", 3:8) %>% 
+    ggplot(.,aes(x = date_time, y = stage, colour = station))+
+    theme_bw()+
+    geom_line()+
+    geom_point()+
+    scale_color_manual(values = clrs)
+    
+
+```
+
+### 7. Mapping gauge locations
+Mapping station locations using interactive leaflet map 
+
+```{r, eval=T, echo=T,warning= F, message=F,cache=FALSE}
+
+# Read gauges coordinates 
+locations <- read_csv("gauges_coord.csv")
+
+leaflet(data = locations) %>% addTiles() %>%
+  addMarkers(~long, ~lat, popup = ~as.character(riverName),
+             label = ~as.character(riverName))
+    
+```
+
+