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workflows/environment_Rscript.R

+#Load libraries
+
+library(dplyr)
+library(ggplot2)
+library(tidyverse)
+library(lubridate)
+library(ggpubr)
+
+#set working directory
+
+setwd("~/Documents/QuinoaDiveristy/FIELDTRIAL_publicationdata/FieldTrial_R/WeatherData")
+
+#import Night data
+
+Envdata_Night<- read.csv(file = "EnvironmentAll_night_values.csv", head = TRUE, sep = ' ')
+
+
+#Calculate mean temp per night
+
+EnvdataNight_meantemp <- Envdata_Night %>% dplyr::group_by(das) %>% summarise(mean(AT_DEGC, na.rm = TRUE))
+
+#import Day data
+
+Envdata_Day<- read.csv(file = "EnvironmentAll_Day_values.csv", head = TRUE, sep = ' ')
+
+#Calculate parameters
+#Daily Max temp
+
+EnvdataDay_maxtemp <- Envdata_Day %>% dplyr::group_by(das) %>% summarise(max(AT_DEGC, na.rm = TRUE))
+
+#Daily max VDP
+
+EnvdataDay_maxVPD <- Envdata_Day %>% dplyr::group_by(das) %>% summarise(max(VPD_kPa, na.rm = TRUE))
+
+#Daily sum Radiation
+
+EnvdataDay_sumRAD <- Envdata_Day %>% dplyr::group_by(das) %>% summarise(sum(RAD_maxWM2, na.rm = TRUE))
+
+#Rename columns
+
+#Daily max temp
+colnames(EnvdataDay_maxtemp)
+
+names (EnvdataDay_maxtemp)[names(EnvdataDay_maxtemp) == "max(AT_DEGC, na.rm = TRUE)"] <- "Daily_MaxTemp"
+
+#Average night temp
+
+colnames(EnvdataNight_meantemp)
+
+names (EnvdataNight_meantemp)[names(EnvdataNight_meantemp) == "mean(AT_DEGC, na.rm = TRUE)"] <- "Nightly_MeanTemp"
+
+#Daily max VPD
+
+colnames(EnvdataDay_maxVPD)
+
+names (EnvdataDay_maxVPD)[names(EnvdataDay_maxVPD) == "max(VPD_kPa, na.rm = TRUE)"] <- "Daily_MaxVPD"
+
+#Daily sum RAD
+
+colnames(EnvdataDay_sumRAD)
+
+names (EnvdataDay_sumRAD)[names(EnvdataDay_sumRAD) == "sum(RAD_maxWM2, na.rm = TRUE)"] <- "Daily_sumRAD"
+
+
+#Day and Night Temperatures
+
+Temps_all <- cbind(EnvdataDay_maxtemp$das, EnvdataDay_maxtemp$Daily_MaxTemp, 
+                   EnvdataNight_meantemp$Nightly_MeanTemp)
+tempheadings <- c("das", "Daily_MaxTemp", "Nightly_MeanTemp")
+
+colnames(Temps_all) <- tempheadings
+
+Temps_DayNight <- as.data.frame(Temps_all)
+
+#Import SWC data
+
+SWCData<- read.csv(file = "~/Documents/QuinoaDiveristy/FIELDTRIAL_publicationdata/FieldTrial_R/WeatherData/SoilVWC_averages.csv", head = TRUE, sep = ' ')
+
+SWCData_WWmeanSWC <- SWCData %>% dplyr::group_by(das) %>% summarise(mean(soilVWC_WW))
+
+SWCData_WDmeanSWC <- SWCData %>% dplyr::group_by(das) %>% summarise(mean(soilVWC_WD))
+
+
+#Soil Water Content data
+
+SWCData_meanVWC<- cbind(SWCData_WWmeanSWC$das, SWCData_WWmeanSWC$`mean(soilVWC_WW)`, SWCData_WDmeanSWC$`mean(soilVWC_WD)`)
+
+headings <-c("das", "SWC_WW", "SWC_WD") 
+
+colnames(SWCData_meanVWC) <- headings
+
+SWCData_VWC <- as.data.frame(SWCData_meanVWC)
+
+class(SWCData_VWC[,3])
+
+levels(SWCData_VWC)
+
+#reorder levels
+
+
+
+#line graphs
+
+#MaxTempLG <-EnvdataDay_maxtemp %>%
+  #ggplot(aes (x=das, y=Daily_MaxTemp)) +
+  # geom_line()+
+  #theme(panel.grid = element_blank())+
+  #labs(y= expression( Temperature~(degree*C)),
+  #     title= "Daily Maximum Temperature")
+
+#MeanTempNightLG <-EnvdataNight_meantemp %>%
+#  ggplot(aes (x=das, y=Nightly_MeanTemp)) +
+#  geom_line()+
+#  theme(panel.grid = element_blank())+
+#  labs(y= expression( Temperature~(degree*C)),
+      # title= "Nightly Average Temperature")
+
+
+temperatures <- rep(c("solid", "dashed"),2)
+
+AllTempsLG <- Temps_DayNight %>%
+  ggplot(aes (x=das)) +
+  annotate(geom = "rect", xmin=0, xmax=60, ymin=-Inf, ymax=Inf, 
+           fill="palegreen2", alpha=0.5)+
+  annotate(geom = "rect", xmin=60, xmax=105, ymin=-Inf, ymax=Inf, 
+           fill="paleturquoise2", alpha=0.7)+
+  annotate(geom = "rect", xmin=105, xmax=155, ymin=-Inf, ymax=Inf, 
+           fill="gray80", alpha=0.5)+
+  geom_line(aes(y=Daily_MaxTemp, linetype="Daily Maximum Temperature"))+
+  geom_line(aes(y=Nightly_MeanTemp, linetype="Nightly Mean Temperature"))+
+    labs(y= expression(Temperature~(degree*C)),
+         title= "Daily Maximum and Nightly Average Temperatures",
+         x= "Days after sowing")+
+  theme(panel.grid = element_blank(),  
+        panel.background = element_rect(fill= "White"),
+        panel.border = element_blank(),
+        axis.line = element_line(),
+        legend.title = element_blank(),
+        legend.position = c(0.5,1.10),
+        legend.direction ="horizontal",
+        legend.background= element_rect(fill=NA),
+        legend.key=element_blank()) +
+  scale_linetype_manual(values = temperatures) +
+  scale_x_continuous(expand = c(0,0))+
+  scale_fill_discrete(name=NULL)
+  
+AllTempsLG
+  
+MaxVPDLG <-EnvdataDay_maxVPD %>%
+  ggplot(aes (x=das, y=Daily_MaxVPD)) +
+  annotate(geom = "rect", xmin=0, xmax=60, ymin=-Inf, ymax=Inf, 
+           fill="palegreen2", alpha=0.5)+
+  annotate(geom = "rect", xmin=60, xmax=105, ymin=-Inf, ymax=Inf, 
+           fill="paleturquoise2", alpha=0.7)+
+  annotate(geom = "rect", xmin=105, xmax=155, ymin=-Inf, ymax=Inf, 
+           fill="gray80", alpha=0.5)+
+  theme(panel.grid = element_blank())+
+  geom_line()+
+  labs(y= expression( VPD~(kPa) ),
+       title= "Daily Maximum Vapor-Pressure Deficit", x= "Days after sowing")+
+  theme(panel.grid = element_blank(), 
+        panel.background = element_rect(fill= "White"),
+        panel.border = element_blank(),
+        axis.line = element_line(),
+        legend.title = element_blank()) +
+  scale_x_continuous(expand = c(0,0))+
+  scale_fill_discrete(name=NULL)
+
+MaxVPDLG
+
+SumRADLG <-EnvdataDay_sumRAD %>%
+  ggplot(aes (x=das, y=Daily_sumRAD)) +
+  annotate(geom = "rect", xmin=0, xmax=60, ymin=-Inf, ymax=Inf, 
+           fill="palegreen2", alpha=0.5)+
+  annotate(geom = "rect", xmin=60, xmax=105, ymin=-Inf, ymax=Inf, 
+           fill="paleturquoise2", alpha=0.7)+
+  annotate(geom = "rect", xmin=105, xmax=155, ymin=-Inf, ymax=Inf, 
+           fill="gray80", alpha=0.5)+
+  geom_line()+
+  theme(panel.grid = element_blank())+
+labs(y= expression(Radiation~(W/m^2)),
+     title= "Daily Total Radiation", x= "Days after sowing")+
+  theme(panel.grid = element_blank(), 
+        panel.background = element_rect(fill= "White"),
+        panel.border = element_blank(),
+        axis.line = element_line(),
+        legend.title = element_blank()) +
+  scale_x_continuous(expand = c(0,0))+
+  scale_fill_discrete(name=NULL)
+
+
+treatment <- c("solid", "dashed")
+
+SumSWCLG <-SWCData_VWC %>%
+  ggplot(aes (x=das)) +
+  annotate(geom = "rect", xmin=0, xmax=60, ymin=-Inf, ymax=Inf, 
+           fill="palegreen2", alpha=0.5)+
+  annotate(geom = "rect", xmin=60, xmax=105, ymin=-Inf, ymax=Inf, 
+           fill="paleturquoise2", alpha=0.7)+
+  annotate(geom = "rect", xmin=105, xmax=155, ymin=-Inf, ymax=Inf, 
+           fill="gray80", alpha=0.5)+
+  geom_line(aes(y=SWC_WW, linetype="Full Irrigation"))+
+  geom_line(aes(y=SWC_WD, linetype="Reduced Irrigation"))+
+  labs(y= expression(VSWC~(m^3*m^3)),
+     title= "Daily Volumetric Soil Water Content", x= "Days after sowing")+
+  theme(panel.grid = element_blank(),
+        panel.background = element_rect(fill= "White"),
+        panel.border = element_blank(),
+        axis.line = element_line(),
+        legend.title = element_blank(),
+        legend.position = c(0.5,1.10),
+        legend.direction ="horizontal",
+        legend.background= element_rect(fill=NA),
+        legend.key=element_blank())+
+  scale_linetype_manual(values = treatment, breaks=c("Full Irrigation","Reduced Irrigation"))+
+  scale_x_continuous(expand = c(0,0))
+
+SumSWCLG
+
+background <- SWCData_WDmeanSWC %>%
+ggplot(aes (x=das, y="mean(soilVWC_WD)")) +
+  annotate(geom = "rect", xmin=0, xmax=60, ymin=-Inf, ymax=Inf, 
+           fill="palegreen2", alpha=0.5)+
+  annotate(geom = "rect", xmin=60, xmax=105, ymin=-Inf, ymax=Inf, 
+           fill="paleturquoise2", alpha=0.7)+
+  annotate(geom = "rect", xmin=105, xmax=155, ymin=-Inf, ymax=Inf, 
+           fill="gray80", alpha=0.5)+
+  theme(panel.grid = element_blank(),
+        panel.background = element_rect(fill= "White"),
+        panel.border = element_blank(),
+        axis.text.y = element_blank(),
+        axis.ticks.y = element_blank())+
+  scale_x_continuous(expand = c(0,0))+
+  labs(y=" ", x=" ")+
+  geom_line()
+
+background
+
+figure <- ggarrange(AllTempsLG, MaxVPDLG, SumRADLG, SumSWCLG, background,
+                      labels = c("A", "B", "C", "D", " "),
+                      ncol = 1, nrow = 5, align = "v")
+
+figure
+
+
+colnames(SWCData_WDmeanSWC)
+
+
+
+
+#Graphs with different rectangle colors
+MaxTempLG <-EnvdataDay_maxtemp %>%
+  ggplot(aes (x=das, y=Daily_MaxTemp)) +
+  geom_line()+
+  theme(panel.grid = element_blank())+
+  labs(y= expression( Temperature~(degree*C)),
+       title= "Daily Maximum Temperature")+
+  geom_rect(aes(xmin=0, xmax=60, ymin=-Inf, ymax=Inf),
+            fill= 'gray100', alpha = 0.002)+
+  geom_rect(aes(xmin=60, xmax=105, ymin=-Inf, ymax=Inf),
+            fill= 'gray78', alpha = 0.002)+
+  geom_rect(aes(xmin=105, xmax=156, ymin=-Inf, ymax=Inf),
+            fill= 'gray61', alpha = 0.002)
+
+
+
+
+