exec/Figure3_Root_by_depth_wholeprofile_revision.R
In bmcnellis/SDEF.analysis: Data Analysis for 2016 San Dimas Experimental Forest Project
library(ggplot2)
library(gridExtra)
library(cowplot)
library(scales)
setwd("D:/R_Workspace/SDEF/SDEF.analysis/data")
load("Alldates_depthbin_rootbiomass.Rdata")
load("RootBiomass_totals.Rdata")
alldates$se_length <- ((alldates$sd_length)/sqrt(alldates$n_length))
alldates$se_diameter <- ((alldates$sd_diameter)/sqrt(alldates$n_diameter))
alldates$surfacearea <- ((pi*((alldates$mean_diameter)^2)*alldates$mean_length))
### add in native v invasive
ad <- subset(alldates, alldates$site == "adenostoma")
ad$veg_type <- rep("Native", times = 19)
g <- subset(alldates, alldates$site == "grass")
g$veg_type <- rep("Invasive", times = 20)
alldates <- rbind(ad, g)
rm(ad, g)
###
ad <- subset(Totals, Totals$veg_type == "Adenostoma")
ad$veg_type <- rep("Native", times = 5)
g <- subset(Totals, Totals$veg_type == "Grass")
g$veg_type <- rep("Invasive", times = 5)
Totals <- rbind(ad, g)
rm(ad, g)
### Subset by depth
zt10 <- subset(alldates, alldates$depth_bin == 1)
tent20 <- subset(alldates, alldates$depth_bin == 2)
twent30 <- subset(alldates, alldates$depth_bin == 3)
thirt40 <- subset(alldates, alldates$depth_bin == 4)
### add in zero value for Adenostoma in december
zt10[10, ] <- rbind(zt10[1, ])
zt10[10, 2] <- "Dec"
zt10[10, c(4:20,22:24)] <- 0
zt10[10, 21] <- as.Date("12/01/2015", format = "%m/%d/%Y")
##########BW FIGURE########
# make graph each panel is a separate dept, x axis date, y axis time
#0-10
ad10 <- subset(zt10, zt10$site == "adenostoma")
g10 <- subset(zt10, zt10$site == "grass")
p1 <- ggplot(data = ad10, aes(y = mean_biodensity_dm, x = Date)) +
scale_x_date(labels = date_format("%b-%y"), date_breaks = "2 month")+
geom_point(data = ad10, aes(colour = "Native", size = 1), show.legend = F)+
geom_errorbar(data = ad10, aes(x = Date, ymin=minse, ymax=maxse, width = 10, colour = "Native") ) +
ylab(expression(paste("Root biomass per soil volume (g ", dm^-3, ")"))) +
xlab("") +
ggtitle("0-10 cm") +
scale_y_continuous(limits = c(0, .75), breaks = c(0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6,0.7)) +
geom_point(data = g10,position = position_nudge(x = 10),shape = 17, aes(colour = "Invasive", size = 1), show.legend = F)+
geom_errorbar(data = g10, position = position_nudge(x = 10), aes(x = Date, ymin=minse, ymax=maxse, width = 15, colour = "Invasive") ) +
scale_colour_manual("", breaks = c("Native", "Invasive"), values=c("grey50", "black"), guide = F) +
theme_bw()+
theme(plot.title = element_text(hjust = 0.5),
text = element_text(size=18))
p1
# 10 -20
ad20 <- subset(tent20, tent20$site == "adenostoma")
g20 <- subset(tent20, tent20$site == "grass")
p2 <- ggplot(data = ad20, aes(y = mean_biodensity_dm, x = Date)) +
scale_x_date(labels = date_format("%b-%y"), date_breaks = "2 month")+
geom_point(data = ad20, aes(colour = "Native", size = 1), show.legend = F)+
geom_errorbar(data = ad20, aes(x = Date, ymin=minse, ymax=maxse, width = 10, colour = "Native") ) +
xlab("") +
ggtitle("10-20 cm") +
scale_y_continuous(limits = c(0, .75))+
geom_point(data = g20,position = position_nudge(x = 10), shape = 17, aes(colour = "Invasive", size = 1), show.legend = F)+
geom_errorbar(data = g20, position = position_nudge(x = 10), aes(x = Date, ymin=minse, ymax=maxse, width = 15, colour = "Invasive") ) +
scale_colour_manual("", breaks = c("Native", "Invasive"), values=c("grey50", "black"), guide = F) +
theme_bw() +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
plot.title = element_text(hjust = 0.5),
text = element_text(size=18))
p2
### 20-30
ad30 <- subset(twent30, twent30$site == "adenostoma")
g30 <- subset(twent30, twent30$site == "grass")
p3 <- ggplot(data = ad30, aes(y = mean_biodensity_dm, x = Date)) +
scale_x_date(labels = date_format("%b-%y"), date_breaks = "2 month")+
geom_point(data = ad30, aes(colour = "Native", size = 1), show.legend = F)+
geom_errorbar(data = ad30, aes(x = Date, ymin=minse, ymax=maxse, width = 10, colour = "Native") ) +
xlab("") +
ggtitle("20-30 cm") +
scale_y_continuous(limits = c(0, .75))+
geom_point(data = g30,position = position_nudge(x = 10), shape = 17, aes(colour = "Invasive", size = 1), show.legend = F)+
geom_errorbar(data = g30, position = position_nudge(x = 10), aes(x = Date, ymin=minse, ymax=maxse, width = 15, colour = "Invasive") ) +
scale_colour_manual("", breaks = c("Native", "Invasive"), values=c("grey50", "black"), guide = F) +
theme_bw() +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
plot.title = element_text(hjust = 0.5),
text = element_text(size=18))
p3
# 30-40
ad40 <- subset(thirt40, thirt40$site == "adenostoma")
g40 <- subset(thirt40, thirt40$site == "grass")
p4 <- ggplot(data = ad40, aes(y = mean_biodensity_dm, x = Date)) +
scale_x_date(labels = date_format("%b-%y"), date_breaks = "2 month")+
geom_point(data = ad40, aes(colour = "Native", size = 1), show.legend = F)+
geom_errorbar(data = ad40, aes(x = Date, ymin=minse, ymax=maxse, width = 10, colour = "Native") ) +
xlab("") +
ggtitle("30-40 cm") +
scale_y_continuous(limits = c(0, .75))+
geom_point(data = g40,position = position_nudge(x = 10), aes(colour = "Invasive", size = 1), shape = 17, show.legend = F)+
geom_errorbar(data = g40, position = position_nudge(x = 10), aes(x = Date, ymin=minse, ymax=maxse, width = 15, colour = "Invasive") ) +
scale_colour_manual("", breaks = c("Native", "Invasive"), values=c("black", "grey50"), guide = F) +
theme_bw() +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
plot.title = element_text(hjust = 0.5),
text = element_text(size=18))
p4
## Total
adtot <- subset(Totals, Totals$veg_type == "Native")
gtot <- subset(Totals, Totals$veg_type == "Invasive")
p5 <- ggplot(data = adtot, aes(y = biomass, x = Date)) +
scale_x_date(labels = date_format("%b-%y"), date_breaks = "2 month")+
geom_point(data = adtot, aes(colour = "Native", size = 1), show.legend = F)+
geom_errorbar(data = adtot, aes(x = Date, ymin=minse, ymax=maxse, width = 10, colour = "Native") ) +
xlab("") +
ggtitle("0-40 cm") +
scale_y_continuous(limits = c(0, .75))+
geom_point(data = gtot,position = position_nudge(x = 10), shape = 17, aes(colour = "Invasive", size = 1), show.legend = F)+
geom_errorbar(data = gtot, position = position_nudge(x = 10), aes(x = Date, ymin=minse, ymax=maxse, width = 15, colour = "Invasive") ) +
scale_colour_manual("", breaks = c("Native", "Invasive"), values=c("black", "grey50"), guide =F) +
theme_bw() +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
plot.title = element_text(hjust = 0.5),
text = element_text(size=18),
legend.position = "bottom")
p5
grid.arrange(p1, p2, p3, p4, p5, ncol=5)
#######COLOR###########
##########Make the same figure in COLOR
ad10 <- subset(zt10, zt10$site == "adenostoma")
g10 <- subset(zt10, zt10$site == "grass")
p1 <- ggplot(data = ad10, aes(y = mean_biodensity_dm, x = Date)) +
scale_x_date(labels = date_format("%b-%y"), date_breaks = "2 month")+
geom_point(data = ad10, aes(colour = "Native", size = 1), show.legend = F)+
geom_errorbar(data = ad10, aes(x = Date, ymin=minse, ymax=maxse, width = 10, colour = "Native") ) +
ylab(expression(paste("Root biomass per soil volume (g ", dm^-3, ")"))) +
xlab("") +
ggtitle("0-10 cm") +
scale_y_continuous(limits = c(0, .75), breaks = c(0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6,0.7)) +
geom_point(data = g10,position = position_nudge(x = 10), aes(colour = "Invasive", size = 1), shape = 17, show.legend = F)+
geom_errorbar(data = g10, position = position_nudge(x = 10), aes(x = Date, ymin=minse, ymax=maxse, width = 15, colour = "Invasive") ) +
scale_colour_manual("", breaks = c("Native", "Invasive"), values=c("#E58601", "#E2D200"), guide = F) +
theme_bw()+
theme(plot.title = element_text(hjust = 0.5),
text = element_text(size=18))
p1
# 10 -20
ad20 <- subset(tent20, tent20$site == "adenostoma")
g20 <- subset(tent20, tent20$site == "grass")
p2 <- ggplot(data = ad20, aes(y = mean_biodensity_dm, x = Date)) +
scale_x_date(labels = date_format("%b-%y"), date_breaks = "2 month")+
geom_point(data = ad20, aes(colour = "Native", size = 1), show.legend = F)+
geom_errorbar(data = ad20, aes(x = Date, ymin=minse, ymax=maxse, width = 10, colour = "Native") ) +
xlab("") +
ggtitle("10-20 cm") +
scale_y_continuous(limits = c(0, .75))+
geom_point(data = g20,position = position_nudge(x = 10), aes(colour = "Invasive", size = 1), shape = 17, show.legend = F)+
geom_errorbar(data = g20, position = position_nudge(x = 10), aes(x = Date, ymin=minse, ymax=maxse, width = 15, colour = "Invasive") ) +
scale_colour_manual("", breaks = c("Native", "Invasive"), values=c("#E58601", "#E2D200"), guide = F) +
theme_bw() +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
plot.title = element_text(hjust = 0.5),
text = element_text(size=18))
p2
### 20-30
ad30 <- subset(twent30, twent30$site == "adenostoma")
g30 <- subset(twent30, twent30$site == "grass")
p3 <- ggplot(data = ad30, aes(y = mean_biodensity_dm, x = Date)) +
scale_x_date(labels = date_format("%b-%y"), date_breaks = "2 month")+
geom_point(data = ad30, aes(colour = "Native", size = 1), show.legend = F)+
geom_errorbar(data = ad30, aes(x = Date, ymin=minse, ymax=maxse, width = 10, colour = "Native") ) +
xlab("") +
ggtitle("20-30 cm") +
scale_y_continuous(limits = c(0, .75))+
geom_point(data = g30,position = position_nudge(x = 10), aes(colour = "Invasive", size = 1),shape = 17, show.legend = F)+
geom_errorbar(data = g30, position = position_nudge(x = 10), aes(x = Date, ymin=minse, ymax=maxse, width = 15, colour = "Invasive") ) +
scale_colour_manual("", breaks = c("Native", "Invasive"), values=c("#E58601", "#E2D200"), guide = F) +
theme_bw() +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
plot.title = element_text(hjust = 0.5),
text = element_text(size=18))
p3
# 30-40
ad40 <- subset(thirt40, thirt40$site == "adenostoma")
g40 <- subset(thirt40, thirt40$site == "grass")
p4 <- ggplot(data = ad40, aes(y = mean_biodensity_dm, x = Date)) +
scale_x_date(labels = date_format("%b-%y"), date_breaks = "2 month")+
geom_point(data = ad40, aes(colour = "Native", size = 1), show.legend = F)+
geom_errorbar(data = ad40, aes(x = Date, ymin=minse, ymax=maxse, width = 10, colour = "Native") ) +
xlab("") +
ggtitle("30-40 cm") +
scale_y_continuous(limits = c(0, .75))+
geom_point(data = g40,position = position_nudge(x = 10), aes(colour = "Invasive", size = 1),shape = 17, show.legend = F)+
geom_errorbar(data = g40, position = position_nudge(x = 10), aes(x = Date, ymin=minse, ymax=maxse, width = 15, colour = "Invasive") ) +
scale_colour_manual("", breaks = c("Native", "Invasive"), values=c("#E58601", "#E2D200"), guide = F) +
theme_bw() +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
plot.title = element_text(hjust = 0.5),
text = element_text(size=18))
p4
## Total
adtot <- subset(Totals, Totals$veg_type == "Native")
gtot <- subset(Totals, Totals$veg_type == "Invasive")
p5 <- ggplot(data = adtot, aes(y = biomass, x = Date)) +
scale_x_date(labels = date_format("%b-%y"), date_breaks = "2 month")+
geom_point(data = adtot, aes(colour = "Native", size = 1), show.legend = F)+
geom_errorbar(data = adtot, aes(x = Date, ymin=minse, ymax=maxse, width = 10, colour = "Native") ) +
xlab("") +
ggtitle("Total") +
scale_y_continuous(limits = c(0, .75))+
geom_point(data = gtot,position = position_nudge(x = 10), aes(colour = "Invasive", size = 1),shape = 17, show.legend = F)+
geom_errorbar(data = gtot, position = position_nudge(x = 10), aes(x = Date, ymin=minse, ymax=maxse, width = 15, colour = "Invasive") ) +
scale_colour_manual("", breaks = c("Native", "Invasive"), values=c("#E58601", "#E2D200"), guide =F) +
theme_bw() +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
plot.title = element_text(hjust = 0.5),
text = element_text(size=18),
legend.position = "bottom")
p5
grid.arrange(p1, p2, p3, p4, p5, ncol=5)
#########LENGTH###########
ad10 <- subset(zt10, zt10$site == "adenostoma")
g10 <- subset(zt10, zt10$site == "grass")
p1 <- ggplot(data = ad10, aes(y = mean_length, x = Date)) +
scale_x_date(labels = date_format("%b-%y"), date_breaks = "2 month")+
geom_point(data = ad10, aes(colour = "Native", size = 1), show.legend = F)+
geom_errorbar(data = ad10, aes(x = Date, ymin=(mean_length - sd_length), ymax=(mean_length +sd_length), width = 10, colour = "Native") ) +
ylab("") +
xlab("") +
ggtitle("0-10 cm") +
scale_y_continuous(limits = c(0, 25))+
geom_point(data = g10,position = position_nudge(x = 10), aes(colour = "Invasive", size = 1),shape = 17, show.legend = F)+
geom_errorbar(data = g10, position = position_nudge(x = 10), aes(x = Date, ymin=(mean_length - se_length), ymax=(mean_length +se_length), width = 15, colour = "Invasive") ) +
scale_colour_manual("", breaks = c("Native", "Invasive"), values=c("#E58601", "#E2D200"), guide = F) +
theme_bw()+
theme(plot.title = element_text(hjust = 0.5),
text = element_text(size=18))
p1
# 10 -20
ad20 <- subset(tent20, tent20$site == "adenostoma")
g20 <- subset(tent20, tent20$site == "grass")
p2 <- ggplot(data = ad20, aes(y = mean_length, x = Date)) +
scale_x_date(labels = date_format("%b-%y"), date_breaks = "2 month")+
geom_point(data = ad20, aes(colour = "Native", size = 1), show.legend = F)+
geom_errorbar(data = ad20, aes(x = Date, ymin=(mean_length - se_length), ymax=(mean_length +se_length), width = 10, colour = "Native") ) +
ylab("") +
xlab("") +
ggtitle("10-20 cm") +
scale_y_continuous(limits = c(0, 25))+
geom_point(data = g20,position = position_nudge(x = 10), aes(colour = "Invasive", size = 1), shape = 17, show.legend = F)+
geom_errorbar(data = g20, position = position_nudge(x = 10), aes(x = Date, ymin=(mean_length - se_length), ymax=(mean_length +se_length), width = 15, colour = "Invasive") ) +
scale_colour_manual("", breaks = c("Native", "Invasive"), values=c("#E58601", "#E2D200"), guide = F) +
theme_bw()+
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
plot.title = element_text(hjust = 0.5),
text = element_text(size=18),
legend.position = "bottom")
p2
### 20-30
ad30 <- subset(twent30, twent30$site == "adenostoma")
g30 <- subset(twent30, twent30$site == "grass")
p3 <- ggplot(data = ad30, aes(y = mean_length, x = Date)) +
scale_x_date(labels = date_format("%b-%y"), date_breaks = "2 month")+
geom_point(data = ad30, aes(colour = "Native", size = 1), show.legend = F)+
geom_errorbar(data = ad30, aes(x = Date, ymin=(mean_length - se_length), ymax=(mean_length +se_length), width = 10, colour = "Native") ) +
ylab("") +
xlab("") +
ggtitle("20-30 cm") +
scale_y_continuous(limits = c(0, 25))+
geom_point(data = g30,position = position_nudge(x = 10), aes(colour = "Invasive", size = 1), shape = 17, show.legend = F)+
geom_errorbar(data = g30, position = position_nudge(x = 10), aes(x = Date, ymin=(mean_length - se_length), ymax=(mean_length +se_length), width = 15, colour = "Invasive") ) +
scale_colour_manual("", breaks = c("Native", "Invasive"), values=c("#E58601", "#E2D200"), guide = F) +
theme_bw()+
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
plot.title = element_text(hjust = 0.5),
text = element_text(size=18),
legend.position = "bottom")
p3
# 30-40
ad40 <- subset(thirt40, thirt40$site == "adenostoma")
g40 <- subset(thirt40, thirt40$site == "grass")
p4 <- ggplot(data = ad40, aes(y = mean_length, x = Date)) +
scale_x_date(labels = date_format("%b-%y"), date_breaks = "2 month")+
geom_point(data = ad40, aes(colour = "Native", size = 1), show.legend = F)+
geom_errorbar(data = ad40, aes(x = Date, ymin=(mean_length - se_length), ymax=(mean_length +se_length), width = 10, colour = "Native") ) +
ylab("") +
xlab("") +
ggtitle("30-40 cm") +
scale_y_continuous(limits = c(0, 25))+
geom_point(data = g40,position = position_nudge(x = 10), aes(colour = "Invasive", size = 1),shape = 17, show.legend = F)+
geom_errorbar(data = g40, position = position_nudge(x = 10), aes(x = Date, ymin=(mean_length - se_length), ymax=(mean_length +se_length), width = 15, colour = "Invasive") ) +
scale_colour_manual("", breaks = c("Native", "Invasive"), values=c("#E58601", "#E2D200"), guide = F) +
theme_bw()+
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
plot.title = element_text(hjust = 0.5),
text = element_text(size=18),
legend.position = "bottom")
p4
adtot <- subset(Totals, Totals$veg_type == "Native")
gtot <- subset(Totals, Totals$veg_type == "Invasive")
p5 <- ggplot(data = adtot, aes(y = length, x = Date)) +
scale_x_date(labels = date_format("%b-%y"), date_breaks = "2 month")+
geom_point(data = adtot, aes(colour = "Native", size = 1), show.legend = F)+
geom_errorbar(data = adtot, aes(x = Date, ymin=(length - se_length), ymax= (length + se_length), width = 10, colour = "Native") ) +
xlab("") +
ggtitle("0-40 cm") +
scale_y_continuous(limits = c(0, 25))+
geom_point(data = gtot,position = position_nudge(x = 10), aes(colour = "Invasive", size = 1), shape = 17,show.legend = F)+
geom_errorbar(data = gtot, position = position_nudge(x = 10), aes(x = Date, ymin=(length - se_length), ymax= (length + se_length), width = 15, colour = "Invasive") ) +
scale_colour_manual("", breaks = c("Native", "Invasive"), values=c("#E58601", "#E2D200"), guide =F) +
theme_bw() +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
plot.title = element_text(hjust = 0.5),
text = element_text(size=18),
legend.position = "bottom")
p5
grid.arrange(p1, p2, p3, p4, p5, ncol=5)
#########LENGTH_BW###########
ad10 <- subset(zt10, zt10$site == "adenostoma")
g10 <- subset(zt10, zt10$site == "grass")
p1 <- ggplot(data = ad10, aes(y = mean_length, x = Date)) +
scale_x_date(labels = date_format("%b-%y"), date_breaks = "2 month")+
geom_point(data = ad10, aes(colour = "Native", size = 1), show.legend = F)+
geom_errorbar(data = ad10, aes(x = Date, ymin=(mean_length - sd_length), ymax=(mean_length +sd_length), width = 10, colour = "Native") ) +
ylab("") +
xlab("") +
ggtitle("0-10 cm") +
scale_y_continuous(limits = c(0, 25))+
geom_point(data = g10,position = position_nudge(x = 10), aes(colour = "Invasive", size = 1),shape = 17, show.legend = F)+
geom_errorbar(data = g10, position = position_nudge(x = 10), aes(x = Date, ymin=(mean_length - se_length), ymax=(mean_length +se_length), width = 15, colour = "Invasive") ) +
scale_colour_manual("", breaks = c("Native", "Invasive"), values=c("black","grey50"), guide = F) +
theme_bw()+
theme(plot.title = element_text(hjust = 0.5),
text = element_text(size=18))
p1
# 10 -20
ad20 <- subset(tent20, tent20$site == "adenostoma")
g20 <- subset(tent20, tent20$site == "grass")
p2 <- ggplot(data = ad20, aes(y = mean_length, x = Date)) +
scale_x_date(labels = date_format("%b-%y"), date_breaks = "2 month")+
geom_point(data = ad20, aes(colour = "Native", size = 1), show.legend = F)+
geom_errorbar(data = ad20, aes(x = Date, ymin=(mean_length - se_length), ymax=(mean_length +se_length), width = 10, colour = "Native") ) +
ylab("") +
xlab("") +
ggtitle("10-20 cm") +
scale_y_continuous(limits = c(0, 25))+
geom_point(data = g20,position = position_nudge(x = 10), aes(colour = "Invasive", size = 1),shape = 17, show.legend = F)+
geom_errorbar(data = g20, position = position_nudge(x = 10), aes(x = Date, ymin=(mean_length - se_length), ymax=(mean_length +se_length), width = 15, colour = "Invasive") ) +
scale_colour_manual("", breaks = c("Native", "Invasive"), values=c("black","grey50"), guide = F) +
theme_bw()+
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
plot.title = element_text(hjust = 0.5),
text = element_text(size=18),
legend.position = "bottom")
p2
### 20-30
ad30 <- subset(twent30, twent30$site == "adenostoma")
g30 <- subset(twent30, twent30$site == "grass")
p3 <- ggplot(data = ad30, aes(y = mean_length, x = Date)) +
scale_x_date(labels = date_format("%b-%y"), date_breaks = "2 month")+
geom_point(data = ad30, aes(colour = "Native", size = 1), show.legend = F)+
geom_errorbar(data = ad30, aes(x = Date, ymin=(mean_length - se_length), ymax=(mean_length +se_length), width = 10, colour = "Native") ) +
ylab("") +
xlab("") +
ggtitle("20-30 cm") +
scale_y_continuous(limits = c(0, 25))+
geom_point(data = g30,position = position_nudge(x = 10), aes(colour = "Invasive", size = 1), shape = 17, show.legend = F)+
geom_errorbar(data = g30, position = position_nudge(x = 10), aes(x = Date, ymin=(mean_length - se_length), ymax=(mean_length +se_length), width = 15, colour = "Invasive") ) +
scale_colour_manual("", breaks = c("Native", "Invasive"), values=c("black","grey50"), guide = F) +
theme_bw()+
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
plot.title = element_text(hjust = 0.5),
text = element_text(size=18),
legend.position = "bottom")
p3
# 30-40
ad40 <- subset(thirt40, thirt40$site == "adenostoma")
g40 <- subset(thirt40, thirt40$site == "grass")
p4 <- ggplot(data = ad40, aes(y = mean_length, x = Date)) +
scale_x_date(labels = date_format("%b-%y"), date_breaks = "2 month")+
geom_point(data = ad40, aes(colour = "Native", size = 1), show.legend = F)+
geom_errorbar(data = ad40, aes(x = Date, ymin=(mean_length - se_length), ymax=(mean_length +se_length), width = 10, colour = "Native") ) +
ylab("") +
xlab("") +
ggtitle("30-40 cm") +
scale_y_continuous(limits = c(0, 25))+
geom_point(data = g40,position = position_nudge(x = 10), aes(colour = "Invasive", size = 1), shape = 17, show.legend = F)+
geom_errorbar(data = g40, position = position_nudge(x = 10), aes(x = Date, ymin=(mean_length - se_length), ymax=(mean_length +se_length), width = 15, colour = "Invasive") ) +
scale_colour_manual("", breaks = c("Native", "Invasive"), values=c("black","grey50"), guide = F) +
theme_bw()+
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
plot.title = element_text(hjust = 0.5),
text = element_text(size=18),
legend.position = "bottom")
p4
adtot <- subset(Totals, Totals$veg_type == "Native")
gtot <- subset(Totals, Totals$veg_type == "Invasive")
p5 <- ggplot(data = adtot, aes(y = length, x = Date)) +
scale_x_date(labels = date_format("%b-%y"), date_breaks = "2 month")+
geom_point(data = adtot, aes(colour = "Native", size = 1), show.legend = F)+
geom_errorbar(data = adtot, aes(x = Date, ymin=(length - se_length), ymax= (length + se_length), width = 10, colour = "Native") ) +
xlab("") +
ggtitle("0-40 cm") +
scale_y_continuous(limits = c(0, 25))+
geom_point(data = gtot,position = position_nudge(x = 10), shape = 17, aes(colour = "Invasive", size = 1), show.legend = F)+
geom_errorbar(data = gtot, position = position_nudge(x = 10), aes(x = Date, ymin=(length - se_length), ymax= (length + se_length), width = 15, colour = "Invasive") ) +
scale_colour_manual("", breaks = c("Native", "Invasive"), values=c("black","grey50"), guide =F) +
theme_bw() +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
plot.title = element_text(hjust = 0.5),
text = element_text(size=18),
legend.position = "bottom")
p5
grid.arrange(p1, p2, p3, p4, p5, ncol=5)
bmcnellis/SDEF.analysis documentation built on June 4, 2019, 10 a.m.
R Package Documentation
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library(ggplot2)
library(gridExtra)
library(cowplot)
library(scales)
setwd("D:/R_Workspace/SDEF/SDEF.analysis/data")
load("Alldates_depthbin_rootbiomass.Rdata")
load("RootBiomass_totals.Rdata")
alldates$se_length <- ((alldates$sd_length)/sqrt(alldates$n_length))
alldates$se_diameter <- ((alldates$sd_diameter)/sqrt(alldates$n_diameter))
alldates$surfacearea <- ((pi*((alldates$mean_diameter)^2)*alldates$mean_length))
### add in native v invasive
ad <- subset(alldates, alldates$site == "adenostoma")
ad$veg_type <- rep("Native", times = 19)
g <- subset(alldates, alldates$site == "grass")
g$veg_type <- rep("Invasive", times = 20)
alldates <- rbind(ad, g)
rm(ad, g)
###
ad <- subset(Totals, Totals$veg_type == "Adenostoma")
ad$veg_type <- rep("Native", times = 5)
g <- subset(Totals, Totals$veg_type == "Grass")
g$veg_type <- rep("Invasive", times = 5)
Totals <- rbind(ad, g)
rm(ad, g)
### Subset by depth
zt10 <- subset(alldates, alldates$depth_bin == 1)
tent20 <- subset(alldates, alldates$depth_bin == 2)
twent30 <- subset(alldates, alldates$depth_bin == 3)
thirt40 <- subset(alldates, alldates$depth_bin == 4)
### add in zero value for Adenostoma in december
zt10[10, ] <- rbind(zt10[1, ])
zt10[10, 2] <- "Dec"
zt10[10, c(4:20,22:24)] <- 0
zt10[10, 21] <- as.Date("12/01/2015", format = "%m/%d/%Y")
##########BW FIGURE########
# make graph each panel is a separate dept, x axis date, y axis time
#0-10
ad10 <- subset(zt10, zt10$site == "adenostoma")
g10 <- subset(zt10, zt10$site == "grass")
p1 <- ggplot(data = ad10, aes(y = mean_biodensity_dm, x = Date)) +
scale_x_date(labels = date_format("%b-%y"), date_breaks = "2 month")+
geom_point(data = ad10, aes(colour = "Native", size = 1), show.legend = F)+
geom_errorbar(data = ad10, aes(x = Date, ymin=minse, ymax=maxse, width = 10, colour = "Native") ) +
ylab(expression(paste("Root biomass per soil volume (g ", dm^-3, ")"))) +
xlab("") +
ggtitle("0-10 cm") +
scale_y_continuous(limits = c(0, .75), breaks = c(0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6,0.7)) +
geom_point(data = g10,position = position_nudge(x = 10),shape = 17, aes(colour = "Invasive", size = 1), show.legend = F)+
geom_errorbar(data = g10, position = position_nudge(x = 10), aes(x = Date, ymin=minse, ymax=maxse, width = 15, colour = "Invasive") ) +
scale_colour_manual("", breaks = c("Native", "Invasive"), values=c("grey50", "black"), guide = F) +
theme_bw()+
theme(plot.title = element_text(hjust = 0.5),
text = element_text(size=18))
p1
# 10 -20
ad20 <- subset(tent20, tent20$site == "adenostoma")
g20 <- subset(tent20, tent20$site == "grass")
p2 <- ggplot(data = ad20, aes(y = mean_biodensity_dm, x = Date)) +
scale_x_date(labels = date_format("%b-%y"), date_breaks = "2 month")+
geom_point(data = ad20, aes(colour = "Native", size = 1), show.legend = F)+
geom_errorbar(data = ad20, aes(x = Date, ymin=minse, ymax=maxse, width = 10, colour = "Native") ) +
xlab("") +
ggtitle("10-20 cm") +
scale_y_continuous(limits = c(0, .75))+
geom_point(data = g20,position = position_nudge(x = 10), shape = 17, aes(colour = "Invasive", size = 1), show.legend = F)+
geom_errorbar(data = g20, position = position_nudge(x = 10), aes(x = Date, ymin=minse, ymax=maxse, width = 15, colour = "Invasive") ) +
scale_colour_manual("", breaks = c("Native", "Invasive"), values=c("grey50", "black"), guide = F) +
theme_bw() +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
plot.title = element_text(hjust = 0.5),
text = element_text(size=18))
p2
### 20-30
ad30 <- subset(twent30, twent30$site == "adenostoma")
g30 <- subset(twent30, twent30$site == "grass")
p3 <- ggplot(data = ad30, aes(y = mean_biodensity_dm, x = Date)) +
scale_x_date(labels = date_format("%b-%y"), date_breaks = "2 month")+
geom_point(data = ad30, aes(colour = "Native", size = 1), show.legend = F)+
geom_errorbar(data = ad30, aes(x = Date, ymin=minse, ymax=maxse, width = 10, colour = "Native") ) +
xlab("") +
ggtitle("20-30 cm") +
scale_y_continuous(limits = c(0, .75))+
geom_point(data = g30,position = position_nudge(x = 10), shape = 17, aes(colour = "Invasive", size = 1), show.legend = F)+
geom_errorbar(data = g30, position = position_nudge(x = 10), aes(x = Date, ymin=minse, ymax=maxse, width = 15, colour = "Invasive") ) +
scale_colour_manual("", breaks = c("Native", "Invasive"), values=c("grey50", "black"), guide = F) +
theme_bw() +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
plot.title = element_text(hjust = 0.5),
text = element_text(size=18))
p3
# 30-40
ad40 <- subset(thirt40, thirt40$site == "adenostoma")
g40 <- subset(thirt40, thirt40$site == "grass")
p4 <- ggplot(data = ad40, aes(y = mean_biodensity_dm, x = Date)) +
scale_x_date(labels = date_format("%b-%y"), date_breaks = "2 month")+
geom_point(data = ad40, aes(colour = "Native", size = 1), show.legend = F)+
geom_errorbar(data = ad40, aes(x = Date, ymin=minse, ymax=maxse, width = 10, colour = "Native") ) +
xlab("") +
ggtitle("30-40 cm") +
scale_y_continuous(limits = c(0, .75))+
geom_point(data = g40,position = position_nudge(x = 10), aes(colour = "Invasive", size = 1), shape = 17, show.legend = F)+
geom_errorbar(data = g40, position = position_nudge(x = 10), aes(x = Date, ymin=minse, ymax=maxse, width = 15, colour = "Invasive") ) +
scale_colour_manual("", breaks = c("Native", "Invasive"), values=c("black", "grey50"), guide = F) +
theme_bw() +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
plot.title = element_text(hjust = 0.5),
text = element_text(size=18))
p4
## Total
adtot <- subset(Totals, Totals$veg_type == "Native")
gtot <- subset(Totals, Totals$veg_type == "Invasive")
p5 <- ggplot(data = adtot, aes(y = biomass, x = Date)) +
scale_x_date(labels = date_format("%b-%y"), date_breaks = "2 month")+
geom_point(data = adtot, aes(colour = "Native", size = 1), show.legend = F)+
geom_errorbar(data = adtot, aes(x = Date, ymin=minse, ymax=maxse, width = 10, colour = "Native") ) +
xlab("") +
ggtitle("0-40 cm") +
scale_y_continuous(limits = c(0, .75))+
geom_point(data = gtot,position = position_nudge(x = 10), shape = 17, aes(colour = "Invasive", size = 1), show.legend = F)+
geom_errorbar(data = gtot, position = position_nudge(x = 10), aes(x = Date, ymin=minse, ymax=maxse, width = 15, colour = "Invasive") ) +
scale_colour_manual("", breaks = c("Native", "Invasive"), values=c("black", "grey50"), guide =F) +
theme_bw() +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
plot.title = element_text(hjust = 0.5),
text = element_text(size=18),
legend.position = "bottom")
p5
grid.arrange(p1, p2, p3, p4, p5, ncol=5)
#######COLOR###########
##########Make the same figure in COLOR
ad10 <- subset(zt10, zt10$site == "adenostoma")
g10 <- subset(zt10, zt10$site == "grass")
p1 <- ggplot(data = ad10, aes(y = mean_biodensity_dm, x = Date)) +
scale_x_date(labels = date_format("%b-%y"), date_breaks = "2 month")+
geom_point(data = ad10, aes(colour = "Native", size = 1), show.legend = F)+
geom_errorbar(data = ad10, aes(x = Date, ymin=minse, ymax=maxse, width = 10, colour = "Native") ) +
ylab(expression(paste("Root biomass per soil volume (g ", dm^-3, ")"))) +
xlab("") +
ggtitle("0-10 cm") +
scale_y_continuous(limits = c(0, .75), breaks = c(0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6,0.7)) +
geom_point(data = g10,position = position_nudge(x = 10), aes(colour = "Invasive", size = 1), shape = 17, show.legend = F)+
geom_errorbar(data = g10, position = position_nudge(x = 10), aes(x = Date, ymin=minse, ymax=maxse, width = 15, colour = "Invasive") ) +
scale_colour_manual("", breaks = c("Native", "Invasive"), values=c("#E58601", "#E2D200"), guide = F) +
theme_bw()+
theme(plot.title = element_text(hjust = 0.5),
text = element_text(size=18))
p1
# 10 -20
ad20 <- subset(tent20, tent20$site == "adenostoma")
g20 <- subset(tent20, tent20$site == "grass")
p2 <- ggplot(data = ad20, aes(y = mean_biodensity_dm, x = Date)) +
scale_x_date(labels = date_format("%b-%y"), date_breaks = "2 month")+
geom_point(data = ad20, aes(colour = "Native", size = 1), show.legend = F)+
geom_errorbar(data = ad20, aes(x = Date, ymin=minse, ymax=maxse, width = 10, colour = "Native") ) +
xlab("") +
ggtitle("10-20 cm") +
scale_y_continuous(limits = c(0, .75))+
geom_point(data = g20,position = position_nudge(x = 10), aes(colour = "Invasive", size = 1), shape = 17, show.legend = F)+
geom_errorbar(data = g20, position = position_nudge(x = 10), aes(x = Date, ymin=minse, ymax=maxse, width = 15, colour = "Invasive") ) +
scale_colour_manual("", breaks = c("Native", "Invasive"), values=c("#E58601", "#E2D200"), guide = F) +
theme_bw() +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
plot.title = element_text(hjust = 0.5),
text = element_text(size=18))
p2
### 20-30
ad30 <- subset(twent30, twent30$site == "adenostoma")
g30 <- subset(twent30, twent30$site == "grass")
p3 <- ggplot(data = ad30, aes(y = mean_biodensity_dm, x = Date)) +
scale_x_date(labels = date_format("%b-%y"), date_breaks = "2 month")+
geom_point(data = ad30, aes(colour = "Native", size = 1), show.legend = F)+
geom_errorbar(data = ad30, aes(x = Date, ymin=minse, ymax=maxse, width = 10, colour = "Native") ) +
xlab("") +
ggtitle("20-30 cm") +
scale_y_continuous(limits = c(0, .75))+
geom_point(data = g30,position = position_nudge(x = 10), aes(colour = "Invasive", size = 1),shape = 17, show.legend = F)+
geom_errorbar(data = g30, position = position_nudge(x = 10), aes(x = Date, ymin=minse, ymax=maxse, width = 15, colour = "Invasive") ) +
scale_colour_manual("", breaks = c("Native", "Invasive"), values=c("#E58601", "#E2D200"), guide = F) +
theme_bw() +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
plot.title = element_text(hjust = 0.5),
text = element_text(size=18))
p3
# 30-40
ad40 <- subset(thirt40, thirt40$site == "adenostoma")
g40 <- subset(thirt40, thirt40$site == "grass")
p4 <- ggplot(data = ad40, aes(y = mean_biodensity_dm, x = Date)) +
scale_x_date(labels = date_format("%b-%y"), date_breaks = "2 month")+
geom_point(data = ad40, aes(colour = "Native", size = 1), show.legend = F)+
geom_errorbar(data = ad40, aes(x = Date, ymin=minse, ymax=maxse, width = 10, colour = "Native") ) +
xlab("") +
ggtitle("30-40 cm") +
scale_y_continuous(limits = c(0, .75))+
geom_point(data = g40,position = position_nudge(x = 10), aes(colour = "Invasive", size = 1),shape = 17, show.legend = F)+
geom_errorbar(data = g40, position = position_nudge(x = 10), aes(x = Date, ymin=minse, ymax=maxse, width = 15, colour = "Invasive") ) +
scale_colour_manual("", breaks = c("Native", "Invasive"), values=c("#E58601", "#E2D200"), guide = F) +
theme_bw() +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
plot.title = element_text(hjust = 0.5),
text = element_text(size=18))
p4
## Total
adtot <- subset(Totals, Totals$veg_type == "Native")
gtot <- subset(Totals, Totals$veg_type == "Invasive")
p5 <- ggplot(data = adtot, aes(y = biomass, x = Date)) +
scale_x_date(labels = date_format("%b-%y"), date_breaks = "2 month")+
geom_point(data = adtot, aes(colour = "Native", size = 1), show.legend = F)+
geom_errorbar(data = adtot, aes(x = Date, ymin=minse, ymax=maxse, width = 10, colour = "Native") ) +
xlab("") +
ggtitle("Total") +
scale_y_continuous(limits = c(0, .75))+
geom_point(data = gtot,position = position_nudge(x = 10), aes(colour = "Invasive", size = 1),shape = 17, show.legend = F)+
geom_errorbar(data = gtot, position = position_nudge(x = 10), aes(x = Date, ymin=minse, ymax=maxse, width = 15, colour = "Invasive") ) +
scale_colour_manual("", breaks = c("Native", "Invasive"), values=c("#E58601", "#E2D200"), guide =F) +
theme_bw() +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
plot.title = element_text(hjust = 0.5),
text = element_text(size=18),
legend.position = "bottom")
p5
grid.arrange(p1, p2, p3, p4, p5, ncol=5)
#########LENGTH###########
ad10 <- subset(zt10, zt10$site == "adenostoma")
g10 <- subset(zt10, zt10$site == "grass")
p1 <- ggplot(data = ad10, aes(y = mean_length, x = Date)) +
scale_x_date(labels = date_format("%b-%y"), date_breaks = "2 month")+
geom_point(data = ad10, aes(colour = "Native", size = 1), show.legend = F)+
geom_errorbar(data = ad10, aes(x = Date, ymin=(mean_length - sd_length), ymax=(mean_length +sd_length), width = 10, colour = "Native") ) +
ylab("") +
xlab("") +
ggtitle("0-10 cm") +
scale_y_continuous(limits = c(0, 25))+
geom_point(data = g10,position = position_nudge(x = 10), aes(colour = "Invasive", size = 1),shape = 17, show.legend = F)+
geom_errorbar(data = g10, position = position_nudge(x = 10), aes(x = Date, ymin=(mean_length - se_length), ymax=(mean_length +se_length), width = 15, colour = "Invasive") ) +
scale_colour_manual("", breaks = c("Native", "Invasive"), values=c("#E58601", "#E2D200"), guide = F) +
theme_bw()+
theme(plot.title = element_text(hjust = 0.5),
text = element_text(size=18))
p1
# 10 -20
ad20 <- subset(tent20, tent20$site == "adenostoma")
g20 <- subset(tent20, tent20$site == "grass")
p2 <- ggplot(data = ad20, aes(y = mean_length, x = Date)) +
scale_x_date(labels = date_format("%b-%y"), date_breaks = "2 month")+
geom_point(data = ad20, aes(colour = "Native", size = 1), show.legend = F)+
geom_errorbar(data = ad20, aes(x = Date, ymin=(mean_length - se_length), ymax=(mean_length +se_length), width = 10, colour = "Native") ) +
ylab("") +
xlab("") +
ggtitle("10-20 cm") +
scale_y_continuous(limits = c(0, 25))+
geom_point(data = g20,position = position_nudge(x = 10), aes(colour = "Invasive", size = 1), shape = 17, show.legend = F)+
geom_errorbar(data = g20, position = position_nudge(x = 10), aes(x = Date, ymin=(mean_length - se_length), ymax=(mean_length +se_length), width = 15, colour = "Invasive") ) +
scale_colour_manual("", breaks = c("Native", "Invasive"), values=c("#E58601", "#E2D200"), guide = F) +
theme_bw()+
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
plot.title = element_text(hjust = 0.5),
text = element_text(size=18),
legend.position = "bottom")
p2
### 20-30
ad30 <- subset(twent30, twent30$site == "adenostoma")
g30 <- subset(twent30, twent30$site == "grass")
p3 <- ggplot(data = ad30, aes(y = mean_length, x = Date)) +
scale_x_date(labels = date_format("%b-%y"), date_breaks = "2 month")+
geom_point(data = ad30, aes(colour = "Native", size = 1), show.legend = F)+
geom_errorbar(data = ad30, aes(x = Date, ymin=(mean_length - se_length), ymax=(mean_length +se_length), width = 10, colour = "Native") ) +
ylab("") +
xlab("") +
ggtitle("20-30 cm") +
scale_y_continuous(limits = c(0, 25))+
geom_point(data = g30,position = position_nudge(x = 10), aes(colour = "Invasive", size = 1), shape = 17, show.legend = F)+
geom_errorbar(data = g30, position = position_nudge(x = 10), aes(x = Date, ymin=(mean_length - se_length), ymax=(mean_length +se_length), width = 15, colour = "Invasive") ) +
scale_colour_manual("", breaks = c("Native", "Invasive"), values=c("#E58601", "#E2D200"), guide = F) +
theme_bw()+
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
plot.title = element_text(hjust = 0.5),
text = element_text(size=18),
legend.position = "bottom")
p3
# 30-40
ad40 <- subset(thirt40, thirt40$site == "adenostoma")
g40 <- subset(thirt40, thirt40$site == "grass")
p4 <- ggplot(data = ad40, aes(y = mean_length, x = Date)) +
scale_x_date(labels = date_format("%b-%y"), date_breaks = "2 month")+
geom_point(data = ad40, aes(colour = "Native", size = 1), show.legend = F)+
geom_errorbar(data = ad40, aes(x = Date, ymin=(mean_length - se_length), ymax=(mean_length +se_length), width = 10, colour = "Native") ) +
ylab("") +
xlab("") +
ggtitle("30-40 cm") +
scale_y_continuous(limits = c(0, 25))+
geom_point(data = g40,position = position_nudge(x = 10), aes(colour = "Invasive", size = 1),shape = 17, show.legend = F)+
geom_errorbar(data = g40, position = position_nudge(x = 10), aes(x = Date, ymin=(mean_length - se_length), ymax=(mean_length +se_length), width = 15, colour = "Invasive") ) +
scale_colour_manual("", breaks = c("Native", "Invasive"), values=c("#E58601", "#E2D200"), guide = F) +
theme_bw()+
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
plot.title = element_text(hjust = 0.5),
text = element_text(size=18),
legend.position = "bottom")
p4
adtot <- subset(Totals, Totals$veg_type == "Native")
gtot <- subset(Totals, Totals$veg_type == "Invasive")
p5 <- ggplot(data = adtot, aes(y = length, x = Date)) +
scale_x_date(labels = date_format("%b-%y"), date_breaks = "2 month")+
geom_point(data = adtot, aes(colour = "Native", size = 1), show.legend = F)+
geom_errorbar(data = adtot, aes(x = Date, ymin=(length - se_length), ymax= (length + se_length), width = 10, colour = "Native") ) +
xlab("") +
ggtitle("0-40 cm") +
scale_y_continuous(limits = c(0, 25))+
geom_point(data = gtot,position = position_nudge(x = 10), aes(colour = "Invasive", size = 1), shape = 17,show.legend = F)+
geom_errorbar(data = gtot, position = position_nudge(x = 10), aes(x = Date, ymin=(length - se_length), ymax= (length + se_length), width = 15, colour = "Invasive") ) +
scale_colour_manual("", breaks = c("Native", "Invasive"), values=c("#E58601", "#E2D200"), guide =F) +
theme_bw() +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
plot.title = element_text(hjust = 0.5),
text = element_text(size=18),
legend.position = "bottom")
p5
grid.arrange(p1, p2, p3, p4, p5, ncol=5)
#########LENGTH_BW###########
ad10 <- subset(zt10, zt10$site == "adenostoma")
g10 <- subset(zt10, zt10$site == "grass")
p1 <- ggplot(data = ad10, aes(y = mean_length, x = Date)) +
scale_x_date(labels = date_format("%b-%y"), date_breaks = "2 month")+
geom_point(data = ad10, aes(colour = "Native", size = 1), show.legend = F)+
geom_errorbar(data = ad10, aes(x = Date, ymin=(mean_length - sd_length), ymax=(mean_length +sd_length), width = 10, colour = "Native") ) +
ylab("") +
xlab("") +
ggtitle("0-10 cm") +
scale_y_continuous(limits = c(0, 25))+
geom_point(data = g10,position = position_nudge(x = 10), aes(colour = "Invasive", size = 1),shape = 17, show.legend = F)+
geom_errorbar(data = g10, position = position_nudge(x = 10), aes(x = Date, ymin=(mean_length - se_length), ymax=(mean_length +se_length), width = 15, colour = "Invasive") ) +
scale_colour_manual("", breaks = c("Native", "Invasive"), values=c("black","grey50"), guide = F) +
theme_bw()+
theme(plot.title = element_text(hjust = 0.5),
text = element_text(size=18))
p1
# 10 -20
ad20 <- subset(tent20, tent20$site == "adenostoma")
g20 <- subset(tent20, tent20$site == "grass")
p2 <- ggplot(data = ad20, aes(y = mean_length, x = Date)) +
scale_x_date(labels = date_format("%b-%y"), date_breaks = "2 month")+
geom_point(data = ad20, aes(colour = "Native", size = 1), show.legend = F)+
geom_errorbar(data = ad20, aes(x = Date, ymin=(mean_length - se_length), ymax=(mean_length +se_length), width = 10, colour = "Native") ) +
ylab("") +
xlab("") +
ggtitle("10-20 cm") +
scale_y_continuous(limits = c(0, 25))+
geom_point(data = g20,position = position_nudge(x = 10), aes(colour = "Invasive", size = 1),shape = 17, show.legend = F)+
geom_errorbar(data = g20, position = position_nudge(x = 10), aes(x = Date, ymin=(mean_length - se_length), ymax=(mean_length +se_length), width = 15, colour = "Invasive") ) +
scale_colour_manual("", breaks = c("Native", "Invasive"), values=c("black","grey50"), guide = F) +
theme_bw()+
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
plot.title = element_text(hjust = 0.5),
text = element_text(size=18),
legend.position = "bottom")
p2
### 20-30
ad30 <- subset(twent30, twent30$site == "adenostoma")
g30 <- subset(twent30, twent30$site == "grass")
p3 <- ggplot(data = ad30, aes(y = mean_length, x = Date)) +
scale_x_date(labels = date_format("%b-%y"), date_breaks = "2 month")+
geom_point(data = ad30, aes(colour = "Native", size = 1), show.legend = F)+
geom_errorbar(data = ad30, aes(x = Date, ymin=(mean_length - se_length), ymax=(mean_length +se_length), width = 10, colour = "Native") ) +
ylab("") +
xlab("") +
ggtitle("20-30 cm") +
scale_y_continuous(limits = c(0, 25))+
geom_point(data = g30,position = position_nudge(x = 10), aes(colour = "Invasive", size = 1), shape = 17, show.legend = F)+
geom_errorbar(data = g30, position = position_nudge(x = 10), aes(x = Date, ymin=(mean_length - se_length), ymax=(mean_length +se_length), width = 15, colour = "Invasive") ) +
scale_colour_manual("", breaks = c("Native", "Invasive"), values=c("black","grey50"), guide = F) +
theme_bw()+
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
plot.title = element_text(hjust = 0.5),
text = element_text(size=18),
legend.position = "bottom")
p3
# 30-40
ad40 <- subset(thirt40, thirt40$site == "adenostoma")
g40 <- subset(thirt40, thirt40$site == "grass")
p4 <- ggplot(data = ad40, aes(y = mean_length, x = Date)) +
scale_x_date(labels = date_format("%b-%y"), date_breaks = "2 month")+
geom_point(data = ad40, aes(colour = "Native", size = 1), show.legend = F)+
geom_errorbar(data = ad40, aes(x = Date, ymin=(mean_length - se_length), ymax=(mean_length +se_length), width = 10, colour = "Native") ) +
ylab("") +
xlab("") +
ggtitle("30-40 cm") +
scale_y_continuous(limits = c(0, 25))+
geom_point(data = g40,position = position_nudge(x = 10), aes(colour = "Invasive", size = 1), shape = 17, show.legend = F)+
geom_errorbar(data = g40, position = position_nudge(x = 10), aes(x = Date, ymin=(mean_length - se_length), ymax=(mean_length +se_length), width = 15, colour = "Invasive") ) +
scale_colour_manual("", breaks = c("Native", "Invasive"), values=c("black","grey50"), guide = F) +
theme_bw()+
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
plot.title = element_text(hjust = 0.5),
text = element_text(size=18),
legend.position = "bottom")
p4
adtot <- subset(Totals, Totals$veg_type == "Native")
gtot <- subset(Totals, Totals$veg_type == "Invasive")
p5 <- ggplot(data = adtot, aes(y = length, x = Date)) +
scale_x_date(labels = date_format("%b-%y"), date_breaks = "2 month")+
geom_point(data = adtot, aes(colour = "Native", size = 1), show.legend = F)+
geom_errorbar(data = adtot, aes(x = Date, ymin=(length - se_length), ymax= (length + se_length), width = 10, colour = "Native") ) +
xlab("") +
ggtitle("0-40 cm") +
scale_y_continuous(limits = c(0, 25))+
geom_point(data = gtot,position = position_nudge(x = 10), shape = 17, aes(colour = "Invasive", size = 1), show.legend = F)+
geom_errorbar(data = gtot, position = position_nudge(x = 10), aes(x = Date, ymin=(length - se_length), ymax= (length + se_length), width = 15, colour = "Invasive") ) +
scale_colour_manual("", breaks = c("Native", "Invasive"), values=c("black","grey50"), guide =F) +
theme_bw() +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
plot.title = element_text(hjust = 0.5),
text = element_text(size=18),
legend.position = "bottom")
p5
grid.arrange(p1, p2, p3, p4, p5, ncol=5)
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