# Figure 4. assessing the environmental drivers of H2 uptake. library(readr) library(tidyverse) library(gvlma) data<- read_csv("Buzzard-RWH-H2-insitu-Fluxes20211119.csv") soil.h2<-as.data.frame(data) ### h2 All by soil moisture #control soil.h2.ctrl<- soil.h2 %>% filter(Treatment == "Control") lm.ctrl<- lm(soil.h2.ctrl$Hydrogen.flux ~ soil.h2.ctrl$sm) summary(lm.ctrl) # significant p-value: 0.001247 Adjusted R-squared: 0.5037 slope: -26.351 soil.h2.bpc<- soil.h2 %>% filter(Treatment == "Passive") lm.bpc<- lm(soil.h2.bpc$Hydrogen.flux ~ soil.h2.bpc$sm) summary(lm.bpc) # significant p-value: 0.0007153 Adjusted R-squared: 0.5399 slope: -34.306 soil.h2.bai<- soil.h2 %>% filter(Treatment == "Active") lm.bai<- lm(soil.h2.bai$Hydrogen.flux ~ soil.h2.bai$sm) summary(lm.bai) # not significant p-value: 0.09438 Adjusted R-squared: 0.1289 slope: -10.5853 soil.h2.gwi<- soil.h2 %>% filter(Treatment == "Greywater") lm.gwi<- lm(soil.h2.gwi$Hydrogen.flux ~ soil.h2.gwi$sm) summary(lm.gwi) # significant p-value: 0.02404 Adjusted R-squared: 0.2647 slope: -29.530 # Reorder data along treatment gradient new data frame treatment_ordered.h2 <- soil.h2 %>% mutate(Treatment = fct_relevel(Treatment, "Control", "Passive", "Active", "Greywater")) ## generalized multiple mixed linear model (soil hydrogen ~ sm and treatment) library(rsq) glm <- glm(treatment_ordered.h2$Hydrogen.flux ~ treatment_ordered.h2$sm +treatment_ordered.h2$Treatment) summary(glm) # significant p-value h2 sm < 0.0001 rsq(glm) # R-squared: 0.3971 rsq(glm, adj = T) # R-squared: 0.3563 ## generalized linear model (soil hydrogen ~ sm) glm.sm <- glm(treatment_ordered.h2$Hydrogen.flux ~ treatment_ordered.h2$sm) summary(glm.sm) # significant p-value h2 sm < 0.001 rsq(glm.sm) # r-squared = 0.1944 rsq(glm.sm, adj = T) # R-squared: 0.1814 ## generalized multiple mixed linear model (soil hydrogen ~ temp and treatment) glm.t <- glm(treatment_ordered.h2$Hydrogen.flux ~ treatment_ordered.h2$temp +treatment_ordered.h2$Treatment) summary(glm.t) # significant p-value < 0.0001 rsq(glm.t) # R-squared: 0.2844 rsq(glm.t, adj = T) # r-squared = 0.2359 ## generalized linear model (soil hydrogen ~ temp) glm.temp <- glm(treatment_ordered.h2$Hydrogen.flux ~ treatment_ordered.h2$temp) summary(glm.temp) # significant p-value < 0.0001 rsq(glm.temp) # R-squared: 0.2453 rsq(glm.temp, adj = T) # r-squared = 0.2331 ######## modeled using the new h2 fluxes that are calculated using the sampling event response factor ## generalized multiple mixed linear model (soil hydrogen ~ sm and treatment) library(rsq) glm <- glm(treatment_ordered.h2$Hydrogen.Uptake ~ treatment_ordered.h2$sm +treatment_ordered.h2$Treatment) summary(glm) # significant p-value h2 sm < 0.001 rsq(glm) # R-squared: 0.3346395 rsq(glm, adj = T) # R-squared: 0.2895303 ## generalized linear model (soil hydrogen ~ sm) glm.sm <- glm(treatment_ordered.h2$Hydrogen.Uptake ~ treatment_ordered.h2$sm) summary(glm.sm) # significant p-value h2 sm < 0.01 rsq(glm.sm) # r-squared = 0.1547107 rsq(glm.sm, adj = T) # R-squared: 0.141077 ## generalized multiple mixed linear model (soil hydrogen ~ temp and treatment) glm.t <- glm(treatment_ordered.h2$Hydrogen.Uptake ~ treatment_ordered.h2$temp +treatment_ordered.h2$Treatment) summary(glm.t) # significant p-value < 0.0001 rsq(glm.t) # R-squared: 0.1885558 rsq(glm.t, adj = T) # r-squared = 0.1335426 ## generalized linear model (soil hydrogen ~ temp) glm.temp <- glm(treatment_ordered.h2$Hydrogen.Uptake ~ treatment_ordered.h2$temp) summary(glm.temp) # significant p-value < 0.01 rsq(glm.temp) # R-squared: 0.1189634 rsq(glm.temp, adj = T) # r-squared = 0.1047532 library(ggpubr) library(cowplot) library(ggplot2) library(wesanderson) coef(glm(soil.h2$Hydrogen.flux~soil.h2$sm+soil.h2$Treatment)) coef(glm(soil.h2$Hydrogen.flux~soil.h2$sm)) #with boxplots sm.hydro<-ggscatterhist( treatment_ordered.h2, x = "sm", y = "Hydrogen.flux", color = "Treatment", size = 3, shape="Season", palette = rev(wes_palette("Moonrise2")), margin.plot = "boxplot", xlab =expression("Soil Moisture"*" (m"^"3"*"m"^"-3"*")"), ggtheme = theme_bw(), legend = "right", ylab =expression("Hydrogen Fluxes (nmol H "['2']*" m "^"-2"*" s "^"-1"*")") ) sm.hydro$sp <- sm.hydro$sp + geom_abline(intercept = -0.6967, slope = -12.7466) sm.hydro #with boxplots for new response factor calculated for each sampling event sm.hydro<-ggscatterhist( treatment_ordered.h2, x = "sm", y = "Hydrogen.Uptake", color = "Treatment", size = 3, shape="Season", palette = rev(wes_palette("Moonrise2")), margin.plot = "boxplot", xlab =expression("Soil Moisture"*" (m"^"3"*"m"^"-3"*")"), ggtheme = theme_bw(), legend = "right", ylab =expression("Hydrogen Fluxes (nmol H "['2']*" m "^"-2"*" s "^"-1"*")") ) coef(glm(soil.h2$Hydrogen.Uptake~soil.h2$sm+soil.h2$Treatment)) coef(glm(soil.h2$Hydrogen.Uptake~soil.h2$sm)) sm.hydro$sp <- sm.hydro$sp + geom_abline(intercept = -1.201065, slope = -9.481161) sm.hydro ggplot2::ggsave("Fig4-H2-sm-p-single-RF20211129.tiff",width = 6, height = 4, dpi = 600, units = "in") coef(glm(soil.h2$Hydrogen.flux~soil.h2$temp+soil.h2$Treatment)) coef(glm(soil.h2$Hydrogen.flux~soil.h2$temp)) st.hydro<-ggscatterhist( treatment_ordered.h2, x = "temp", y = "Hydrogen.flux", color = "Treatment", size = 3, shape="Season", palette = rev(wes_palette("Moonrise2")), margin.plot = "boxplot", xlab="Soil Temperature °C", ggtheme = theme_bw(), legend = "right", ylab =expression("Hydrogen Fluxes (nmol H "['2']*" m "^"-2"*" s "^"-1"*")") ) st.hydro$sp <- st.hydro$sp + geom_abline(intercept = -4.28, slope = 0.108) st.hydro coef(glm(soil.h2$Hydrogen.Uptake~soil.h2$temp+soil.h2$Treatment)) coef(glm(soil.h2$Hydrogen.Uptake~soil.h2$temp)) st.hydro<-ggscatterhist( treatment_ordered.h2, x = "temp", y = "Hydrogen.Uptake", color = "Treatment", size = 3, shape="Season", palette = rev(wes_palette("Moonrise2")), margin.plot = "boxplot", xlab="Soil Temperature °C", ggtheme = theme_bw(), legend = "right", ylab =expression("New-Hydrogen Fluxes (nmol H "['2']*" m "^"-2"*" s "^"-1"*")") ) st.hydro$sp <- st.hydro$sp + geom_abline(intercept = -3.61682284, slope = 0.03237263) st.hydro ggplot2::ggsave("Fig4-H2-temp-single-RF20211129.tiff",width = 6, height = 4, dpi = 600, units = "in")