Loading in packages

# loading packages
library(ggplot2)
library(dplyr)

## 
## Attaching package: 'dplyr'

## The following objects are masked from 'package:stats':
## 
##     filter, lag

## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union

library(lubridate)

## 
## Attaching package: 'lubridate'

## The following objects are masked from 'package:base':
## 
##     date, intersect, setdiff, union

library(tidyr)
library(gridExtra)

## 
## Attaching package: 'gridExtra'

## The following object is masked from 'package:dplyr':
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##     combine

Ground Temperatures

# importing ground temp data for 6-19 through 9-20
grndtmp619_920=read.csv("/Users/qwe2qh/UVA/Utqiagvik/Season_GRNDTMP_6_19_22_9_20_22_2022_09_21_16_19_26_UTC_1.csv")
  
# data cleaning for dataset
names(grndtmp619_920) <- sub("....C..RX3000_BRW1", "", names(grndtmp619_920))
names(grndtmp619_920) <- sub("....C..RX3000_BRW4", "", names(grndtmp619_920))
names(grndtmp619_920) <- sub("....C..RX3000_BRW5", "", names(grndtmp619_920))
names(grndtmp619_920) <- sub("....C..RX3000_BRW6", "", names(grndtmp619_920))
names(grndtmp619_920) <- sub("..RXW.GP6.", "", names(grndtmp619_920))
grndtmp619_920$Date <-as.POSIXct(grndtmp619_920$Date,format="%m/%d/%y %H:%M",tz="UTC")

# Putting all lines onto same graph: THNA Ground Temperature at 10 cm
a <- ggplot(data = grndtmp619_920, mapping = aes(x=Date)) +
  geom_line(mapping = aes(y=Temperature21198259.21206939.8, color = "THNA BASE")) +
  geom_line(mapping = aes(y=Temperature21198259.21393047.8, color = "THNA SC")) +
  geom_line(mapping = aes(y=Temperature21198259.21398593.8, color = "THNA SA")) +
  geom_line(mapping = aes(y=Temperature21198259.21398601.8, color = "THNA SB")) +
  labs (title= "THNA Ground Temperature (10 cm)", y="Temperature (C)",color="Site") +
  scale_x_datetime(date_breaks = "1 weeks") +
  theme(axis.text.x=element_text(angle = 45, hjust = 1), axis.line = element_line(colour = "black", size =0.5, linetype = "solid")) +
  scale_y_continuous(breaks=c(-5,-2.5,0,2.5,5,7.5,10,12.5,15), limits=c(-6, 14)) +
  scale_color_manual(values = c("THNA BASE"="blue", "THNA SC"="green", "THNA SA"="red", "THNA SB"="purple"))

# THNA Ground Temperature at 40 cm
b <- ggplot(data = grndtmp619_920, mapping = aes(x=Date)) +
  geom_line(mapping = aes(y=Temperature21198259.21206939.11, color = "THNA BASE")) +
  geom_line(mapping = aes(y=Temperature21198259.21398593.11, color = "THNA SA")) +
  geom_line(mapping = aes(y=Temperature21198259.21398601.11, color = "THNA SB")) +
  geom_line(mapping = aes(y=Temperature21198259.21393047.11, color = "THNA SC")) +
  labs (title= "THNA Ground Temperature (40 cm)", y="Temperature (C)",color="Site") +
    scale_x_datetime(date_breaks = "1 weeks") + 
    theme(axis.text.x=element_text(angle = 45, hjust = 1), axis.line = element_line(colour = "black", size =0.5, linetype = "solid")) +
    scale_y_continuous(breaks=c(-5,-2.5,0,2.5,5,7.5,10,12.5,15), limits=c(-6, 14)) +
    scale_color_manual(values = c("THNA BASE"="blue","THNA SA"="red", "THNA SB"="purple", "THNA SC"="green"))
  
# THNA SA appears to be very high. I checked the serial number and that should be the 40 cm serial for THNA SA. 
#I have re downloaded and compared the .csv row for 21198259.21398593.11 and the data has a maximum value of 9, so this is a true sensor read error here or is real and very high?

# THNA Ground Temperature at 90 cm
c <- ggplot(data = grndtmp619_920, mapping = aes(x=Date)) +
  geom_line(mapping = aes(y=Temperature21198259.21206939.17, color = "THNA BASE")) +
  geom_line(mapping = aes(y=Temperature21198259.21393047.17, color = "THNA SC")) +
  geom_line(mapping = aes(y=Temperature21198259.21398593.17, color = "THNA SA")) +
  geom_line(mapping = aes(y=Temperature21198259.21398601.17, color = "THNA SB")) +
  labs (title= "THNA Ground Temperature (90 cm)", y="Temperature (C)",color="Site") +
  scale_x_datetime(date_breaks = "1 weeks") + 
  theme(axis.text.x=element_text(angle = 45, hjust = 1), axis.line = element_line(colour = "black", size =0.5, linetype = "solid")) +
  scale_y_continuous(breaks=c(-5,-2.5,0,2.5,5,7.5,10,12.5,15), limits=c(-6, 14)) +
  scale_color_manual(values = c("THNA BASE"="blue", "THNA SC"="green", "THNA SA"="red", "THNA SB"="purple"))

plots <- list(a,b,c)

layout <- rbind(c(1,2),c(3,4))

grid.arrange(grobs=plots,layout_matrix=layout)

# SSMH Ground Temperatures

# SSMH Ground Temperature at 10 cm
d <- ggplot(data = grndtmp619_920, mapping = aes(x=Date)) +
  geom_line(mapping = aes(y=Temperature21401801.21393049.8, color = "SSMH BASE")) +
  geom_line(mapping = aes(y=Temperature21401801.21398599.8, color = "SSMH SA")) +
  geom_line(mapping = aes(y=Temperature21401801.21393044.8, color = "SSMH SB")) +
  labs (title= "SSMH Ground Temperature (10 cm)", y="Temperature (C)",color="Site") +
  scale_x_datetime(date_breaks = "1 weeks") + 
  theme(axis.text.x=element_text(angle = 45, hjust = 1), axis.line = element_line(colour = "black", size =0.5, linetype = "solid"))+
  scale_y_continuous(breaks=c(-5,-2.5,0,2.5,5,7.5,10,12.5,15), limits=c(-6, 14)) +
  scale_color_manual(values = c("SSMH BASE"="blue", "SSMH SB"="green", "SSMH SA"="red"))

# SSMH Ground Temperature at 40 cm
e <- ggplot(data = grndtmp619_920, mapping = aes(x=Date)) +
  geom_line(mapping = aes(y=Temperature21401801.21393049.11, color = "SSMH BASE")) +
  geom_line(mapping = aes(y=Temperature21401801.21398599.11, color = "SSMH SA")) +
  geom_line(mapping = aes(y=Temperature21401801.21393044.11, color = "SSMH SB")) +
  labs (title= "SSMH Ground Temperature (40 cm)", y="Temperature (C)",color="Site") +
  scale_x_datetime(date_breaks = "1 weeks") + 
  theme(axis.text.x=element_text(angle = 45, hjust = 1), axis.line = element_line(colour = "black", size =0.5, linetype = "solid")) +
  scale_y_continuous(breaks=c(-5,-2.5,0,2.5,5,7.5,10,12.5,15), limits=c(-6, 14)) +
  scale_color_manual(values = c("SSMH BASE"="blue", "SSMH SB"="green", "SSMH SA"="red"))

# 40 cm values seem high again but this time it is all of the station sites

# SSMH Ground Temperature at 90 cm
f <- ggplot(data = grndtmp619_920, mapping = aes(x=Date)) +
  geom_line(mapping = aes(y=Temperature21401801.21393049.17, color = "SSMH BASE")) +
  geom_line(mapping = aes(y=Temperature21401801.21398599.17, color = "SSMH SA")) +
  geom_line(mapping = aes(y=Temperature21401801.21393044.17, color = "SSMH SB")) +
  labs (title= "SSMH Ground Temperature (90 cm)", y="Temperature (C)",color="Site") +
  scale_x_datetime(date_breaks = "1 weeks") + 
  theme(axis.text.x=element_text(angle = 45, hjust = 1), axis.line = element_line(colour = "black", size =0.5, linetype = "solid")) +
  scale_y_continuous(breaks=c(-5,-2.5,0,2.5,5,7.5,10,12.5,15), limits=c(-6, 14)) +
  scale_color_manual(values = c("SSMH BASE"="blue", "SSMH SB"="green", "SSMH SA"="red"))

plots <- list(d,e,f)

layout <- rbind(c(1,2),c(3,4))

grid.arrange(grobs=plots,layout_matrix=layout)

# BUECI Ground Temperatures

# BUECI Ground Temperature at 10 cm
g <- ggplot(data = grndtmp619_920, mapping = aes(x=Date)) +
  geom_line(mapping = aes(y=Temperature21401800.21398585.8, color = "BUECI BASE")) +
  geom_line(mapping = aes(y=Temperature21401800.21398590.8, color = "BUECI SA")) +
  geom_line(mapping = aes(y=Temperature21401800.21398583.8, color = "BUECI SB")) +
  geom_line(mapping = aes(y=Temperature21401800.21393042.8, color = "BUECI SC")) +
  geom_line(mapping = aes(y=Temperature21401800.21398584.8, color = "BUECI SD")) +
  geom_line(mapping = aes(y=Temperature21401800.21398579.8, color = "BUECI SE")) +
 # geom_line(mapping = aes(y=Temperature21401800.21398578.8, color = "BUECI SF.01")) +
  #geom_line(mapping = aes(y=Temperature21401800.21398598.8, color = "BUECI SF.02")) +
  labs (title= "BUECI Ground Temperature (10 cm)", y="Temperature (C)",color="Site") +
  scale_x_datetime(date_breaks = "1 weeks") + 
  theme(axis.text.x=element_text(angle = 45, hjust = 1), axis.line = element_line(colour = "black", size =0.5, linetype = "solid"))+
  scale_y_continuous(breaks=c(-5,-2.5,0,2.5,5,7.5,10,12.5,15), limits=c(-6, 14)) +
  scale_color_manual(values = c("BUECI BASE"="blue", "BUECI SC"="purple", "BUECI SA"="red", "BUECI SB"="green", "BUECI 
                                SD"="orange","BUECI SE"="magenta1", "BUECI SF.01"="steelblue1", "BUECI SF.02"="seagreen2"))

# BUECI Ground Temperature at 40 cm
h <- ggplot(data = grndtmp619_920, mapping = aes(x=Date)) +
  geom_line(mapping = aes(y=Temperature21401800.21398585.11, color = "BUECI BASE")) +
  geom_line(mapping = aes(y=Temperature21401800.21398590.11, color = "BUECI SA")) +
  geom_line(mapping = aes(y=Temperature21401800.21398583.11, color = "BUECI SB")) +
  geom_line(mapping = aes(y=Temperature21401800.21393042.11, color = "BUECI SC")) +
  geom_line(mapping = aes(y=Temperature21401800.21398584.11, color = "BUECI SD")) +
  geom_line(mapping = aes(y=Temperature21401800.21398579.11, color = "BUECI SE")) +
 # geom_line(mapping = aes(y=Temperature21401800.21398578.11, color = "BUECI SF.01")) +
 # geom_line(mapping = aes(y=Temperature21401800.21398598.11, color = "BUECI SF.02")) +
  labs (title= "BUECI Ground Temperature (40 cm)", y="Temperature (C)",color="Site") +
  scale_x_datetime(date_breaks = "1 weeks") + 
  theme(axis.text.x=element_text(angle = 45, hjust = 1), axis.line = element_line(colour = "black", size =0.5, linetype = "solid")) +
  scale_y_continuous(breaks=c(-5,-2.5,0,2.5,5,7.5,10,12.5,15), limits=c(-6, 14)) +
  scale_color_manual(values = c("BUECI BASE"="blue", "BUECI SC"="purple", "BUECI SA"="red", "BUECI SB"="green", "BUECI SD"="orange","BUECI SE"="magenta1", "BUECI SF.01"="steelblue1", "BUECI SF.02"="seagreen2"))

# BUECI Ground Temperature at 90 cm
i <- ggplot(data = grndtmp619_920, mapping = aes(x=Date)) +
  geom_line(mapping = aes(y=Temperature21401800.21398585.11, color = "BUECI BASE")) +
  geom_line(mapping = aes(y=Temperature21401800.21398590.11, color = "BUECI SA")) +
  geom_line(mapping = aes(y=Temperature21401800.21398583.11, color = "BUECI SB")) +
  geom_line(mapping = aes(y=Temperature21401800.21393042.11, color = "BUECI SC")) +
  geom_line(mapping = aes(y=Temperature21401800.21398584.11, color = "BUECI SD")) +
  geom_line(mapping = aes(y=Temperature21401800.21398579.11, color = "BUECI SE")) +
  #geom_line(mapping = aes(y=Temperature21401800.21398578.11, color = "BUECI SF.01")) +
  #geom_line(mapping = aes(y=Temperature21401800.21398598.11, color = "BUECI SF.02")) +
  labs (title= "BUECI Ground Temperature (90 cm)", y="Temperature (C)",color="Site") +
  scale_x_datetime(date_breaks = "1 weeks") + 
  theme(axis.text.x=element_text(angle = 45, hjust = 1), axis.line = element_line(colour = "black", size =0.5, linetype = "solid")) +
  scale_y_continuous(breaks=c(-5,-2.5,0,2.5,5,7.5,10,12.5,15), limits=c(-6, 14)) +
  scale_color_manual(values = c("BUECI BASE"="blue", "BUECI SC"="purple", "BUECI SA"="red", "BUECI SB"="green", "BUECI SD"="orange","BUECI SE"="magenta1", "BUECI SF.01"="steelblue1", "BUECI SF.02"="seagreen2"))

# Why are these readings so high?????

plots <- list(g,h,i)

layout <- rbind(c(1,2),c(3,4))

grid.arrange(grobs=plots,layout_matrix=layout)

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unusually high readings for ground temperature

# BEO Ground Temperatures

# BEO Ground Temperatures 10 cm
j <- ggplot(data = grndtmp619_920, mapping = aes(x=Date)) +
  geom_line(mapping = aes(y=Temperature21401803.21393048.8, color = "BEO-B06")) +
  geom_line(mapping = aes(y=Temperature21401803.21398591.8, color = "BEO-B05")) +
  labs (title= "BEO Ground Temperature (10 cm)", y="Temperature (C)",color="Site") +
  scale_x_datetime(date_breaks = "1 weeks") +
  theme(axis.text.x=element_text(angle = 45, hjust = 1), axis.line = element_line(colour = "black", size =0.5, linetype = "solid")) +
  scale_y_continuous(breaks=c(-5,-2.5,0,2.5,5,7.5,10,12.5,15), limits=c(-6, 14)) +
  scale_color_manual(values = c("BEO-B06"="blue", "BEO-B05"="red"))

# BEO Ground Temperatures 40 cm
k <- ggplot(data = grndtmp619_920, mapping = aes(x=Date)) +
  geom_line(mapping = aes(y=Temperature21401803.21393048.11, color = "BEO-B06")) +
  geom_line(mapping = aes(y=Temperature21401803.21398591.11, color = "BEO-B05")) +
  labs (title= "BEO Ground Temperature (40 cm)", y="Temperature (C)",color="Site") +
  scale_x_datetime(date_breaks = "1 weeks") + 
  theme(axis.text.x=element_text(angle = 45, hjust = 1), axis.line = element_line(colour = "black", size =0.5, linetype = "solid")) +
  scale_y_continuous(breaks=c(-5,-2.5,0,2.5,5,7.5,10,12.5,15), limits=c(-6, 14)) +
  scale_color_manual(values = c("BEO-B06"="blue", "BEO-B05"="red"))

# BEO Ground Temperatures 90 cm
l <- ggplot(data = grndtmp619_920, mapping = aes(x=Date)) +
  geom_line(mapping = aes(y=Temperature21401803.21393048.17, color = "BEO-B06")) +
  geom_line(mapping = aes(y=Temperature21401803.21398591.17, color = "BEO-B05")) +
  labs (title= "BEO Ground Temperature (90 cm)", y="Temperature (C)",color="Site") +
  scale_x_datetime(date_breaks = "1 weeks") + 
  theme(axis.text.x=element_text(angle = 45, hjust = 1), axis.line = element_line(colour = "black", size =0.5, linetype = "solid")) +
  scale_y_continuous(breaks=c(-5,-2.5,0,2.5,5,7.5,10,12.5,15), limits=c(-6, 14)) +
  scale_color_manual(values = c("BEO-B06"="blue", "BEO-B05"="red"))

plots <- list(j,k,l)

layout <- rbind(c(1,2),c(3,4))

grid.arrange(grobs=plots,layout_matrix=layout)

## Warning: Removed 3550 row(s) containing missing values (geom_path).
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Soil Moisture (VWC)

# THNA Ground Moisture
# importing water content data for 6-19 through 9-20
mst619_920=read.csv("/Users/qwe2qh/UVA/Utqiagvik/Season_VWC_6_19_22_9_20_22_2022_09_21_16_11_28_UTC_1.csv")

# data cleaning for dataset
names(mst619_920) <- sub("...m.3.m.3..RX3000_BRW1", "", names(mst619_920))
names(mst619_920) <- sub("...m.3.m.3..RX3000_BRW4", "", names(mst619_920))
names(mst619_920) <- sub("...m.3.m.3..RX3000_BRW5", "", names(mst619_920))
names(mst619_920) <- sub("...m.3.m.3..RX3000_BRW6", "", names(mst619_920))
names(mst619_920) <- sub("..RXW.GP6.", "", names(mst619_920))
mst619_920$Date <-as.POSIXct(mst619_920$Date,format="%m/%d/%y %H:%M",tz="UTC")

# THNA Ground Moisture (15:30 cm)
m <- ggplot(data = mst619_920, mapping = aes(x=Date)) +
  geom_line(mapping = aes(y=Water.Content21198259.21206939.2, color = "THNA BASE")) +
  geom_line(mapping = aes(y=Water.Content21198259.21398593.2, color = "THNA SA")) +
  geom_line(mapping = aes(y=Water.Content21198259.21398601.2, color = "THNA SB")) +
  geom_line(mapping = aes(y=Water.Content21198259.21393047.2, color = "THNA SC")) +
  labs (title= "THNA Ground Moisture (15-30 cm)", y="Volumetric Water Content",color="Site") +
  scale_x_datetime(date_breaks = "1 weeks") + 
  theme(axis.text.x=element_text(angle = 45, hjust = 1), axis.line = element_line(colour = "black", size =0.5, linetype = "solid")) + 
  scale_y_continuous(breaks=seq(0.0, 0.6, 0.1), limits=c(0, 0.6)) +
  scale_color_manual(values = c("THNA BASE"="blue", "THNA SC"="green", "THNA SA"="red", "THNA SB"="purple"))

# THNA Ground Moisture (30:45 cm)
n <- ggplot(data = mst619_920, mapping = aes(x=Date)) +
  geom_line(mapping = aes(y=Water.Content21198259.21206939.3, color = "THNA BASE")) +
  geom_line(mapping = aes(y=Water.Content21198259.21398593.3, color = "THNA SA")) +
  geom_line(mapping = aes(y=Water.Content21198259.21398601.3, color = "THNA SB")) +
  geom_line(mapping = aes(y=Water.Content21198259.21393047.3, color = "THNA SC")) +
  labs (title= "THNA Ground Moisture (30-45 cm)", y="Volumetric Water Content",color="Site") +
  scale_x_datetime(date_breaks = "1 weeks") + 
  theme(axis.text.x=element_text(angle = 45, hjust = 1), axis.line = element_line(colour = "black", size =0.5, linetype = "solid")) + 
  scale_y_continuous(breaks=seq(0.0, 0.6, 0.1), limits=c(0, 0.6)) +
  scale_color_manual(values = c("THNA BASE"="blue", "THNA SC"="green", "THNA SA"="red", "THNA SB"="purple"))

# THNA Ground Moisture (75:90 cm)
o <- ggplot(data = mst619_920, mapping = aes(x=Date)) +
  geom_line(mapping = aes(y=Water.Content21198259.21206939.6, color = "THNA BASE")) +
  geom_line(mapping = aes(y=Water.Content21198259.21398593.6, color = "THNA SA")) +
  geom_line(mapping = aes(y=Water.Content21198259.21398601.6, color = "THNA SB")) +
  geom_line(mapping = aes(y=Water.Content21198259.21393047.6, color = "THNA SC")) +
  labs (title= "THNA Ground Moisture (75-90 cm)", y="Volumetric Water Content",color="Site") +
  scale_x_datetime(date_breaks = "1 weeks") + 
  theme(axis.text.x=element_text(angle = 45, hjust = 1), axis.line = element_line(colour = "black", size =0.5, linetype = "solid")) + 
  scale_y_continuous(breaks=seq(0.0, 0.6, 0.1), limits=c(0, 0.6)) +
  scale_color_manual(values = c("THNA BASE"="blue", "THNA SC"="green", "THNA SA"="red", "THNA SB"="purple"))

plots <- list(m,n,o)

layout <- rbind(c(1,2),c(3,4))

grid.arrange(grobs=plots,layout_matrix=layout)

# SSMH Ground Moisture

# SSMH Ground Moisture (15:30 cm)
p <- ggplot(data = mst619_920, mapping = aes(x=Date)) +
  geom_line(mapping = aes(y=Water.Content21401801.21393044.2, color = "SSMH SB")) +
  geom_line(mapping = aes(y=Water.Content21401801.21393049.2, color = "SSMH BASE")) +
  geom_line(mapping = aes(y=Water.Content21401801.21398599.2, color = "SSMH SA")) +
  labs (title= "SSMH Ground Moisture (15-30 cm)", y="Volumetric Water Content",color="Site") +
  scale_x_datetime(date_breaks = "1 weeks") + 
  theme(axis.text.x=element_text(angle = 45, hjust = 1), axis.line = element_line(colour = "black", size =0.5, linetype = "solid")) + 
  scale_y_continuous(breaks=seq(0.0, 0.6, 0.1), limits=c(0, 0.6)) +
  scale_color_manual(values = c("SSMH BASE"="blue", "SSMH SA"="green", "SSMH SB"="red"))

# SSMH Ground Moisture (30:45 cm)
q <- ggplot(data = mst619_920, mapping = aes(x=Date)) +
  geom_line(mapping = aes(y=Water.Content21401801.21393044.3, color = "SSMH SB")) +
  geom_line(mapping = aes(y=Water.Content21401801.21393049.3, color = "SSMH BASE")) +
  geom_line(mapping = aes(y=Water.Content21401801.21398599.3, color = "SSMH SA")) +
  labs (title= "SSMH Ground Moisture (30-45 cm)", y="Volumetric Water Content",color="Site") +
  scale_x_datetime(date_breaks = "1 weeks") + 
  theme(axis.text.x=element_text(angle = 45, hjust = 1), axis.line = element_line(colour = "black", size =0.5, linetype = "solid")) + 
  scale_y_continuous(breaks=seq(0.0, 0.6, 0.1), limits=c(0, 0.6)) +
  scale_color_manual(values = c("SSMH BASE"="blue", "SSMH SA"="green", "SSMH SB"="red"))

# SSMH Ground Moisture (75:90 cm)
r <- ggplot(data = mst619_920, mapping = aes(x=Date)) +
  geom_line(mapping = aes(y=Water.Content21401801.21393044.6, color = "SSMH SB")) +
  geom_line(mapping = aes(y=Water.Content21401801.21393049.6, color = "SSMH BASE")) +
  geom_line(mapping = aes(y=Water.Content21401801.21398599.6, color = "SSMH SA")) +
  labs (title= "SSMH Ground Moisture (75-90 cm)", y="Volumetric Water Content",color="Site") +
  scale_x_datetime(date_breaks = "1 weeks") + 
  theme(axis.text.x=element_text(angle = 45, hjust = 1), axis.line = element_line(colour = "black", size =0.5, linetype = "solid")) + 
  scale_y_continuous(breaks=seq(0.0, 0.6, 0.1), limits=c(0, 0.6)) +
  scale_color_manual(values = c("SSMH BASE"="blue", "SSMH SA"="green", "SSMH SB"="red"))

plots <- list(p,q,r)

layout <- rbind(c(1,2),c(3,4))

grid.arrange(grobs=plots,layout_matrix=layout)