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McCulloch_ViPER_FineRoots_2020.R
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McCulloch_ViPER_FineRoots_2020.R
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#Code for statistical analysis and figures of fine root biomass
#between and within Alaskan tundra and boreal forest sites
#Data were collected in 2015 as a part of the ViPER project
#libraries ####
library(tidyverse)
library(dplyr)
library(ggplot2)
library(ggpubr)
library(lme4)
#WD and datasheets####
setwd('/Users/lmccullo/Google Drive/Alaska2015/AK_data')
ak<- read.csv("ViPER_roots_2015_LM.csv")
akk<- read.csv("ViPER_roots_2015_LM.1.csv")
tt<- read.csv("agg_temp_10cm.csv")
colnames(tt)[1] <- "Site"
#join tt to ak
ak2 <- join(ak,tt, by="Site",type="left")
ak2$temp[ak2$Site==16]= NA
#Adding other variables #####
ak2$live.dens <- (ak2$FineLive/(10*ak2$w*ak2$l))*10
ak2$dead.dens <- (ak2$FineDead/(10*ak2$w*ak2$l))*10
ak2$fine.dead.live <- ak2$dead.dens/ak2$live.dens
ak2$Boreal.Tundra <- factor(ak2$Boreal.Tundra, exclude = "Tundra", labels = c("Boreal", "Tundra"))
akk$dead.dens = (akk$FineDead/(10*akk$W*akk$L))*10
akk$live.dens = (akk$FineLive/(10*akk$W*akk$L))*10
akk$Fine.Dead.Live = akk$dead.dens/akk$live.dens
#Linear models with OLD (site average)####
m1 = lm(fine.dead.live ~ OLDsite, data=ak2)
summary(m1)
plot(fine.dead.live ~ OLDsite, data=ak2)
m2 = lm(live.dens ~ OLDsite, data=ak2)
summary(m2)
plot(live.dens ~ OLDsite, data=ak2)
m3 = lm(dead.dens ~ OLDsite, data=ak2)
summary(m3)
plot(dead.dens ~ OLDsite, data=ak2)
#Linear models with TD (site average)####
m1 = lm(fine.dead.live ~ TDsite, data=ak2)
summary(m1)
plot(fine.dead.live ~ TDsite, data=ak2)
m2 = lm(live.dens ~ TDsite, data=ak2)
summary(m2)
plot(live.dens ~ OLDsite, data=ak2)
m3 = lm(dead.dens ~ TDsite, data=ak2)
summary(m3)
plot(dead.dens ~ TDsite, data=ak2)
#########################################
#Coefficient of Variation analyses ######
#########################################
cv = (sd(ak2$fine.dead.live)/mean(ak2$fine.dead.live))*100
cv.b = (sd(ak2[ak2$Boreal.Tundra == "Boreal",]$fine.dead.live)/mean(ak2[ak2$Boreal.Tundra == "Boreal",]$fine.dead.live))*100
cv.t= (sd(ak2[ak2$Boreal.Tundra == "Tundra",]$fine.dead.live)/mean(ak2[ak2$Boreal.Tundra == "Tundra",]$fine.dead.live))*100
cv.l = (sd(akk$live.dens)/mean(akk$live.dens))*100
cv.b.l = (sd(ak2[ak2$Boreal.Tundra == "Boreal",]$live.dens)/mean(ak2[ak2$Boreal.Tundra == "Boreal",]$live.dens))*100
cv.t.l= (sd(ak2[ak2$Boreal.Tundra == "Tundra",]$live.dens)/mean(ak2[ak2$Boreal.Tundra == "Tundra",]$live.dens))*100
cv = (sd(akk$dead.dens)/mean(akk$dead.dens))*100
cv.b = (sd(ak2[ak2$Boreal.Tundra == "Boreal",]$dead.dens)/mean(ak2[ak2$Boreal.Tundra == "Boreal",]$dead.dens))*100
cv.t= (sd(ak2[ak2$Boreal.Tundra == "Tundra",]$dead.dens)/mean(ak2[ak2$Boreal.Tundra == "Tundra",]$dead.dens))*100
#########################################
#Nested T-test analyses #################
#########################################
#dead density
data.nest.lme <- lme(dead.dens ~ Boreal.Tundra, random = ~1 | Site, akk, method = "REML")
summary(data.nest.lme)
#live density
data.nest.lme <- lme(live.dens ~ Boreal.Tundra, random = ~1 | Site, akk, method = "REML")
summary(data.nest.lme)
#dead to live ratio
data.nest.lme <- lme(Fine.Dead.Live ~ Boreal.Tundra, random = ~1 | Site, akk, method = "REML")
summary(data.nest.lme)
#live C:N
data.nest.lme <- lme(livec.n ~ Boreal.Tundra, random = ~1 | Site, akk, method = "REML")
summary(data.nest.lme)
#dead C:N
data.nest.lme <- lme(deadc.n ~ Boreal.Tundra, random = ~1 | Site, akk, method = "REML")
summary(data.nest.lme)
#dead n %
data.nest.lme <- lme(dead.n.per ~ Boreal.Tundra, random = ~1 | Site, akk, method = "REML")
summary(data.nest.lme)
#live n %
data.nest.lme <- lme(live.n.per ~ Boreal.Tundra, random = ~1 | Site, akk, method = "REML")
summary(data.nest.lme)
#dead c %
data.nest.lme <- lme(dead.c.per ~ Boreal.Tundra, random = ~1 | Site, akk, method = "REML")
summary(data.nest.lme1)
#live c %
data.nest.lme <- lme(live.c.per ~ Boreal.Tundra, random = ~1 | Site, akk, method = "REML")
summary(data.nest.lme)
#dead p
data.nest.lme <- lme(dead.p ~ Boreal.Tundra, random = ~1 | Site, akk, method = "REML")
summary(data.nest.lme)
#live p
data.nest.lme <- lme(live.p ~ Boreal.Tundra, random = ~1 | Site, akk, method = "REML")
summary(data.nest.lme)
########################################
#Linear models for root nutrients#######
########################################
m1 = lm(live.p ~ dead.p, data = akk)
summary (m1)
m2 = lm(live.n.per ~ dead.n.per, data = akk)
summary (m2)
m3 = lm(live.n.per ~ s.cov, data = akk)
summary(m3)
m4 = lm(live.c.per ~ s.cov, data = akk)
summary(m4)
#########################################
#Multivariate linear models analyses ####
#########################################
#Dead:live FRB
m1 <- lm(ak2$fine.dead.live~ak2$soilc.n+ak2$m.cov+ak2$temp+ak2$org.moisture+ak2$Boreal.Tundra+ak2$t-old)
summary(m1)
#Live FRB
m1 <- lm(ak2$live.dens~ak2$soilc.n+ak2$m.cov+ak2$temp+ak2$org.moisture+ak2$Boreal.Tundra+ak2$t-old)
summary(m1)
#Dead FRB
m1 <- lm(ak2$dead.dens~ak2$soilc.n+ak2$m.cov+ak2$temp+ak2$org.moisture+ak2$Boreal.Tundra+ak2$t-old)
summary(m1)
##############################################
##Above to belowground biomass comparisons####
##############################################
ak.t = ak2 %>%
filter(Boreal.Tundra == "Tundra")
ak.t$blw.abv.ld <- ((ak.t$live.dens)+(ak.t$dead.dens)+
((ak.t$CoarseLive/(ak.t$l*ak.t$w*10)*10))+
((ak.t$CoarseDead/(ak.t$l*ak.t$w*10)*10)))/(ak.t$US.bio/1000)
ak.t$blw.abv.l = ((ak.t$live.dens)+
((ak.t$CoarseLive/(ak.t$l*ak.t$w*10)*10)))/(ak.t$US.bio/1000)
##############################################
################# FIGURES ####################
##############################################
#Figure 2 ####
#Live and dead FRB - Boreal versus tundra
a <- ggplot(ak2, aes(x=Boreal.Tundra, y=live.dens,fill = Boreal.Tundra))+
geom_boxplot()+
scale_y_continuous(expand= c(0,0),limits = c(0,0.75))+
scale_x_discrete(labels = c('Boreal', "Tundra"))+
scale_fill_manual(values=c("gray40","gray75"),
labels=c("Boreal", "Tundra"))+
xlab ("")+
ylab (bquote("Live FRB (kg "*"m"
^-2* " of soil)"))+
theme_pubr()+
theme(axis.title=element_text(size=15),
axis.text=element_text(size=15),
legend.position= "none")
b <- ggplot(ak2, aes(x=Boreal.Tundra, y=dead.dens, fill = Boreal.Tundra))+
geom_boxplot()+
scale_y_continuous(expand= c(0,0),limits = c(0,0.75))+
scale_x_discrete(labels = c('Boreal', "Tundra"))+
scale_fill_manual(values=c("gray40","gray75"),
labels=c("Boreal", "Tundra"))+
xlab ("") +
ylab (bquote("Dead FRB (kg "*"m"
^-2* " of soil)"))+
theme_pubr()+
theme(axis.title=element_text(size=15),
axis.text=element_text(size=15),
legend.position= "none")
ggarrange(a, b,
labels = c("a", "b"),
ncol = 2, nrow = 1,
heights = c(1,1),
align = "v")
ggsave("Figure2.tiff", width=8, height=5, units = ("in"))
#Figure 3####
#Coefficient of Variation ###
CV.ld<- akk %>%
group_by(Boreal.Tundra, Site) %>%
summarise(
n=n(),
mean=mean(Fine.Dead.Live),
sd=sd(Fine.Dead.Live),
cv.l = (sd(Fine.Dead.Live)/mean(Fine.Dead.Live))*100
) %>%
mutate( se=sd/sqrt(n)) %>%
mutate( ic=se * qt((1-0.05)/2 + .5, n-1)) %>%
mutate( mean2 = mean(cv.l)) %>%
mutate( sd2 = sd(cv.l))
CV.live<- akk %>%
group_by(Boreal.Tundra, Site) %>%
summarise(
n=n(),
mean=mean(live.dens),
sd=sd(live.dens),
cv.l = (sd(live.dens)/mean(live.dens))*100
) %>%
mutate( se=sd/sqrt(n)) %>%
mutate( ic=se * qt((1-0.05)/2 + .5, n-1)) %>%
mutate( mean2 = mean(cv.l)) %>%
mutate( sd2 = sd(cv.l))
CV.dead<- akk %>%
group_by(Boreal.Tundra, Site) %>%
summarise(
n=n(),
mean=mean(dead.dens),
sd=sd(dead.dens),
cv.l = (sd(dead.dens)/mean(dead.dens))*100
) %>%
mutate( se=sd/sqrt(n)) %>%
mutate( ic=se * qt((1-0.05)/2 + .5, n-1)) %>%
mutate( mean2 = mean(cv.l)) %>%
mutate( sd2 = sd(cv.l))
dead = ggplot(CV.dead, aes(x=Boreal.Tundra, y=cv.l, fill = Boreal.Tundra))+
geom_boxplot()+
xlab ("") +
ylab (bquote("Dead FRB coefficient of varaition (%) "))+
scale_y_continuous(expand= c(0,0),limits = c(0,150))+
scale_x_discrete(labels = c('Boreal', "Tundra"))+
scale_fill_manual(values=c("gray40","gray75"),
labels=c("Boreal", "Tundra"))+
theme_pubr()+
theme(axis.title=element_text(size=15),
axis.text=element_text(size=15),
legend.position= "none")+
geom_dotplot(binaxis='y', stackdir='center', dotsize=3, binwidth = 1, fill = "black")
live = ggplot(CV.live, aes(x=Boreal.Tundra, y=cv.l, fill = Boreal.Tundra))+
geom_boxplot()+
xlab ("") +
ylab (bquote("Live FRB coefficient of varaition (%) "))+
scale_x_discrete(labels = c('Boreal', "Tundra"))+
scale_y_continuous(expand= c(0,0),limits = c(0,150))+
scale_fill_manual(values=c("gray40","gray75"),
labels=c("Boreal", "Tundra"))+
theme_pubr()+
theme(axis.title=element_text(size=15),
axis.text=element_text(size=15),
legend.position= "none")+
geom_dotplot(binaxis='y', stackdir='center', dotsize=3, binwidth = 1, fill = "black")
ggarrange(live, dead,
labels = c("a", "b"),
ncol = 2, nrow = 1,
heights = c(1,1),
align = "v",
common.legend = TRUE,
legend = "none")
ggsave("Figure3.tiff", width=8, height=5, units = ("in"))
#Figure 4####
#Multivariate figure
a <- ggplot (data=ak2, aes(x=soilc.n, y=fine.dead.live)) +
geom_point(aes(shape = Boreal.Tundra), size = 4)+
scale_shape_manual(values = c("Boreal"= "triangle", "Tundra" = "circle"))+
geom_smooth(method="lm", se = FALSE, color = "black")+
xlab ("Soil C:N")+
ylab ("Dead:Live FRB")+
theme_pubr() +
theme(axis.title=element_text(size=25),
axis.text = element_text(size=25),
legend.position= "none")
b <- ggplot (data=ak2, aes(x=org.moisture, y=fine.dead.live)) +
geom_point(aes(shape = Boreal.Tundra), size = 4)+
scale_shape_manual(values = c("Boreal"= "triangle", "Tundra" = "circle"))+
geom_smooth(method="lm", se = FALSE, color = "black")+
xlab (bquote("Organic soil moisture ("*"cm"
^3* " water" *" cm"^-3* " soil)"))+
ylab ("")+
theme_pubr()+
theme(axis.title=element_text(size=25),
axis.text = element_text(size=25),
legend.position= "none")
c <- ggplot (data=ak2, aes(x=temp, y=fine.dead.live)) +
geom_point(aes(shape = Boreal.Tundra), size = 4)+
scale_shape_manual(values = c("Boreal"= "triangle", "Tundra" = "circle"))+
geom_smooth(method="lm", se = FALSE, color = "black")+
xlab (expression("Soil temperature ("*degree*"C)"))+
ylab ("")+
theme_pubr()+
theme(axis.title=element_text(size=25),
axis.text = element_text(size=25),
legend.position= "none")
d <- ggplot (data=ak2, aes(x=m.cov, y=fine.dead.live)) +
geom_point(aes(shape = Boreal.Tundra), size = 4)+
scale_shape_manual(values = c("Boreal"= "triangle", "Tundra" = "circle"))+
geom_smooth(method="lm", se = FALSE, color = "black")+
xlab ("Moss cover (%)")+
ylab ("")+
theme_pubr()+
theme(axis.title=element_text(size=25),
axis.text = element_text(size=25),
legend.position= "none")
al <- ggplot (data=ak2, aes(x=soilc.n, y=live.dens)) +
geom_point(aes(shape = Boreal.Tundra), size = 4)+
scale_shape_manual(values = c("Boreal"= "triangle", "Tundra" = "circle"))+
geom_smooth(method="lm", se = FALSE, color = "black")+
xlab ("")+
ylab (bquote("Live FRB (kg "*"m"
^-2* "of soil)"))+
theme_pubr()+
theme(axis.title=element_text(size=25),
axis.text = element_text(size=25),
legend.position= "none")
bl <- ggplot (data=ak2, aes(x=org.moisture, y=live.dens)) +
geom_point(aes(shape = Boreal.Tundra), size = 4)+
scale_shape_manual(values = c("Boreal"= "triangle", "Tundra" = "circle"))+
geom_smooth(method="lm", se = FALSE, color = "black")+
xlab ("")+
ylab ("")+
theme_pubr()+
theme(axis.title=element_text(size=25),
axis.text = element_text(size=25),
legend.position= "none")
cl <- ggplot (data=ak2, aes(x=temp, y=live.dens)) +
geom_point(aes(shape = Boreal.Tundra), size = 4)+
scale_shape_manual(values = c("Boreal"= "triangle", "Tundra" = "circle"))+
geom_smooth(method="lm", se = FALSE, color = "black")+
xlab ("")+
ylab ("")+
theme_pubr()+
theme(axis.title=element_text(size=25),
axis.text = element_text(size=25),
legend.position= "none")
dl <- ggplot (data=ak2, aes(x=m.cov, y=live.dens)) +
geom_point(aes(shape = Boreal.Tundra), size = 4)+
scale_shape_manual(values = c("Boreal"= "triangle", "Tundra" = "circle"))+
geom_smooth(method="lm", se = FALSE, color = "black")+
xlab ("")+
ylab ("")+
theme_pubr()+
theme(axis.title=element_text(size=25),
axis.text = element_text(size=25),
legend.position= "none")
ad <- ggplot (data=ak2, aes(x=soilc.n, y=dead.dens)) +
geom_point(aes(shape = Boreal.Tundra), size = 4)+
scale_shape_manual(values = c("Boreal"= "triangle", "Tundra" = "circle"))+
geom_smooth(method="lm", se = FALSE, color = "black")+
xlab ("")+
ylab (bquote("Dead FRB (kg "*"m"
^-2* "of soil)"))+
theme_pubr()+
theme(axis.title=element_text(size=25),
axis.text = element_text(size=25),
legend.position= "none")
bd <- ggplot (data=ak2, aes(x=org.moisture, y=dead.dens)) +
geom_point(aes(shape = Boreal.Tundra), size = 4)+
scale_shape_manual(values = c("Boreal"= "triangle", "Tundra" = "circle"))+
geom_smooth(method="lm", se = FALSE, color = "black")+
xlab ("")+
ylab ("")+
theme_pubr()+
theme(axis.title=element_text(size=25),
axis.text = element_text(size=25),
legend.position= "none")
cd <- ggplot (data=ak2, aes(x=temp, y=dead.dens)) +
geom_point(aes(shape = Boreal.Tundra), size = 4)+
scale_shape_manual(values = c("Boreal"= "triangle", "Tundra" = "circle"))+
geom_smooth(method="lm", se = FALSE, color = "black")+
xlab ("")+
ylab ("")+
theme_pubr()+
theme(axis.title=element_text(size=25),
axis.text = element_text(size=25),
legend.position= "none")
dd <- ggplot (data=ak2, aes(x=m.cov, y=dead.dens)) +
geom_point(aes(shape = Boreal.Tundra), size = 4)+
scale_shape_manual(values = c("Boreal"= "triangle", "Tundra" = "circle"))+
geom_smooth(method="lm", se = FALSE, color = "black")+
xlab ("")+
ylab ("")+
theme_pubr()+
theme(axis.title=element_text(size=25),
axis.text = element_text(size=25),
legend.position= "none")
ggarrange(ad, bd, cd,dd,al, bl, cl, dl,a,b, c, d,
labels = c("a", "b", "c", 'd', "e", "f", "g", "h", "i", "j", "k", "l"),
ncol = 4, nrow = 3,
font.label = list(size = 20),
align = "v",
heights = c(1,1))
ggsave("AK_figure4_.pdf", width=20, height=16, units = ("in"))