R/raw-uniform-plots.R
In davan690/beech-publication-wr: Small mammal dynamics in NZ beech forests
##final script for figure 2-4 Davidsonetal2019
#Anthony Davidson
#oct2019
# libraries needed
source("./R/r-packages-needed.R", echo = FALSE)
source("./R/theme_raw_fig3s.r", echo = FALSE)
source("./R/davidson_2019_theme.r", echo = FALSE)
source("./R/Davidson_2019_Data_wrangling.R")
# fig.3.plot.seed.sum.final
# jitter everything the same is harrrrrd
location.move <- position_dodge(width = 30)
# plot
plot.final.f3.1 <- ggplot(p.design2,
aes(
y = cum.seed,
col = Rats,
shape = Valley,
fill = Control,
x = Date
),
size = 7) +
geom_rect(aes(xmin=ymd('2000-01-01'),xmax = ymd('2000-12-31'),ymin = -Inf,ymax = Inf), colour = "grey90", fill = "grey90") +
geom_rect(aes(xmin=ymd('2002-01-01'),xmax = ymd('2002-12-31'),ymin = -Inf,ymax = Inf), colour = "grey90", fill = "grey90") +
geom_rect(aes(xmin=ymd('2004-01-01'),xmax = ymd('2004-12-31'),ymin = -Inf,ymax = Inf), colour = "grey90", fill = "grey90") +
geom_errorbar(aes(ymin = lcl.slog, ymax = ucl.slog, width = 0), lwd = 0.4, col = "black", position = location.move, alpha = 0.7) +
geom_line(col = "grey50") +
geom_point(aes(y = cum.seed,
x = Date
),alpha = 0.7, size = 3, stroke = 1.25, position = location.move) +
xlab(expression(paste("Time", "(", italic(t), ")"))) +
ylab(expression(paste("Available seed "," ", "(", italic(Seed[jt]), ")"))) +
scale_color_manual(name = "Stoat Control",
values = c("black", "white", "white")) +
scale_shape_manual(name = "Ecosystem",
values = c(24, 21)) +
scale_size_manual(name = "Rat Control", values = c(2.5, 3, 2.5)) +
# manually define the fill colours
scale_fill_manual(name = "Stoat Control",
values = c("white", "black", "white")) +
# Remove fill legend and replace the fill legend using the newly created size
guides(
col = "none",
size = guide_legend(override.aes = list(
shape = c(15,0),alpha = 1
)),
shape = guide_legend(override.aes = list(
shape = c(24, 21), size = 4
)),
fill = guide_legend(override.aes = list(
col = c("white", "black"),shape = c("square"),
size = 4
))
) +
theme_tufte() +
theme_bw() +
theme(strip.background = element_blank(),
strip.text.y = element_blank(),
plot.title = element_text(hjust = 0, size=24, family = "Times", color="black", margin = margin(t = 10, b = 10)),
plot.subtitle=element_text(size=16, face="italic", color="black"),
legend.position = "none",
legend.key = element_blank(),
legend.background = element_rect(fill="white", size=1),
legend.key.size=unit(1,"cm"),
legend.text = element_text(colour = "black", size =16, family = "Times"),
legend.title = element_text(colour = "black", size =16, family = "Times"),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.spacing = unit(2, "lines"),
panel.border = element_blank(),
axis.title.y = element_text(colour = "black",size =20, family = "Times", angle = 90),
axis.title.x = element_text(colour = "black", size =20, family = "Times"),
axis.text.y=element_text(colour = "black",size = 20, family = "Times"),
axis.text.x = element_text(colour = "black", size =20, family = "Times"),
axis.ticks.x = element_line(size = 1),
axis.ticks.y = element_line(size = 1),
axis.line.x = element_line(size = 1),
axis.line.y = element_line(size = 1),
strip.text = element_text(face="bold",colour = "black",size =14, family = "Times"))
plot.final.f3.1
## ----new-mice------------------------------------------------------------
# plot raw seed
fig.3.N <-
ggplot(p.design2,
aes(
y = N,
col = Rats,
shape = Valley,
fill = Control,
x = Date
)) +
geom_rect(aes(xmin=ymd('2000-01-01'),xmax = ymd('2000-12-31'),ymin = -Inf,ymax = Inf), colour = "grey90", fill = "grey90") +
geom_rect(aes(xmin=ymd('2002-01-01'),xmax = ymd('2002-12-31'),ymin = -Inf,ymax = Inf), colour = "grey90", fill = "grey90") +
geom_rect(aes(xmin=ymd('2004-01-01'),xmax = ymd('2004-12-31'),ymin = -Inf,ymax = Inf), colour = "grey90", fill = "grey90") +
geom_errorbar(aes(ymin = lcl.slog, ymax = ucl.slog, width = 0), lwd = 0.7, col = "black", position = location.move, alpha = 0.7) +
geom_line(col = "grey50") +
geom_point(aes(y = N,
x = Date
),size = 5, stroke = 1.25, position = location.move) +
xlab(expression(paste("Time", "(", italic(t), ")"))) +
ylab(expression(paste("Mouse abundance ", " (", italic(N[jt]), ")"))) +
scale_color_manual(name = "Stoat Control",
values = c("black", "white", "white")) +
scale_shape_manual(name = "Ecosystem",
values = c(24, 21)) +
scale_size_manual(name = "Rat Control", values = c(2.5, 3, 2.5)) +
# manually define the fill colours
scale_fill_manual(name = "Stoat Control",
values = c("white", "black", "white")) +
# Remove fill legend and replace the fill legend using the newly created size
guides(
col = "none",
size = guide_legend(override.aes = list(
shape = c(15,0),alpha = 1
)),
shape = guide_legend(override.aes = list(
shape = c(24, 21), size = 4
)),
fill = guide_legend(override.aes = list(
col = c("white", "black"),shape = c("square"),
size = 4
))
) +
theme_tufte() +
theme_bw() +
theme(strip.background = element_blank(),
strip.text.y = element_blank(),
plot.title = element_text(hjust = 0, size=24, family = "Times", color="black", margin = margin(t = 10, b = 10)),
plot.subtitle=element_text(size=16, face="italic", color="black"),
legend.position = "none",
legend.key = element_blank(),
legend.background = element_rect(fill="white", size=1),
legend.key.size=unit(1,"cm"),
legend.text = element_text(colour = "black", size =16, family = "Times"),
legend.title = element_text(colour = "black", size =16, family = "Times"),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.spacing = unit(2, "lines"),
panel.border = element_blank(),
axis.title.y = element_text(colour = "black",size =20, family = "Times", angle = 90),
axis.title.x = element_text(colour = "black", size =20, family = "Times"),
axis.text.y=element_text(colour = "black",size = 20, family = "Times"),
axis.text.x = element_text(colour = "black", size =20, family = "Times"),
axis.ticks.x = element_line(size = 1),
axis.ticks.y = element_line(size = 1),
axis.line.x = element_line(size = 1),
axis.line.y = element_line(size = 1),
strip.text = element_text(face="bold",colour = "black",size =14, family = "Times"))
fig.3.N
## ----new-rats
rat.plot <- ggplot(p.design2, aes(y = N,col = Rats,shape = Valley,fill = Control,x = Date)) +geom_rect(aes(xmin=ymd('2000-01-01'),xmax = ymd('2000-12-31'),ymin = -Inf,ymax = Inf), colour = "grey90", fill = "grey90") +
geom_rect(aes(xmin=ymd('2002-01-01'),xmax = ymd('2002-12-31'),ymin = -Inf,ymax = Inf), colour = "grey90", fill = "grey90") +
geom_rect(aes(xmin=ymd('2004-01-01'),xmax = ymd('2004-12-31'),ymin = -Inf,ymax = Inf), colour = "grey90", fill = "grey90") +
geom_errorbar(aes(ymin = lcl.slog, ymax = ucl.slog, width = 0), lwd = 0.7, col = "black", position = location.move) +
geom_line(data = rat.mean,
aes(y = mean.rat,
x = Date),
size = 0.95,
col = "grey50", position = location.move) +
geom_point(data = rat.mean,aes( y = mean.rat, col = Rats,
shape = Valley,
fill = Control,
x = Date
),size = 6 , position = location.move) +
xlab(expression(paste("Time", "(", italic(t), ")"))) +
ylab(expression(atop(paste("Minimum "," ", " number"," "),
paste(" ", "of"," ",
"rats"," ","(",italic(R[jt]),")"))) ) +
scale_color_manual(name = "Stoat Control",
values = c("black", "white", "white")) +
scale_shape_manual(name = "Ecosystem",
values = c(24, 21)) +
scale_size_manual(name = "Rat Control", values = c(2.5, 3, 2.5)) +
# manually define the fill colours
scale_fill_manual(name = "Stoat Control",
values = c("white", "black", "white")) +
# Remove fill legend and replace the fill legend using the newly created size
guides(
col = "none",
size = guide_legend(override.aes = list(
shape = c(15,0),alpha = 1
)),
shape = guide_legend(override.aes = list(
shape = c(24, 21), size = 4
)),
fill = guide_legend(override.aes = list(
col = c("white", "black"),shape = c("square"),
size = 4
))
) +
xlab(expression(paste("Time", "(", italic(t), ")"))) +
ylab(expression(atop(paste("Minimum "," ", " number"," "),
paste(" ", "of"," ",
"rats"," ","(",italic(R[jt]),")"))) ) +
# scale_y_continuous(expand = c(0,0.01),breaks = seq(-4,4,1)) +
theme_tufte() +
theme_bw() +
theme(strip.background = element_blank(),
strip.text.y = element_blank(),
plot.title = element_text(hjust = 0, size=24, family = "Times", color="black", margin = margin(t = 10, b = 10)),
plot.subtitle=element_text(size=16, face="italic", color="black"),
legend.position = "none",
legend.key = element_blank(),
legend.background = element_rect(fill="white", size=1),
legend.key.size=unit(1,"cm"),
legend.text = element_text(colour = "black", size =16, family = "Times"),
legend.title = element_text(colour = "black", size =16, family = "Times"),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.spacing = unit(2, "lines"),
panel.border = element_blank(),
axis.title.y = element_text(colour = "black",size =20, family = "Times", angle = 90),
axis.title.x = element_text(colour = "black", size =20, family = "Times"),
axis.text.y=element_text(colour = "black",size = 20, family = "Times"),
axis.text.x = element_text(colour = "black", size =20, family = "Times"),
axis.ticks.x = element_line(size = 1),
axis.ticks.y = element_line(size = 1),
axis.line.x = element_line(size = 1),
axis.line.y = element_line(size = 1),
strip.text = element_text(face="bold",colour = "black",size =14, family = "Times"))
rat.plot
## ----message=FALSE, warning=FALSE----------------------------------------
# save csv file
write.csv(p.design2, "C://Code/data/seed-summary-data-june2019.csv")
# export plot for example vignette
#desktop
#png("C://Code/beech-publication-wr/figs/plot.final.f3.1.png")
#laptop
# png("C://Code/beech-publication-wr/test.seedp.png")
#
plot.final.f3.1
# dev.off()
write.csv(p.design2, "C://Code/data/mouse_summary_data.csv")
# export plot for example vignette
#desktop
# png("C://Code/beech-publication-wr/figs/mice.plot.png")
#laptop
# png("C://GIT/beech-publication-wr/figs/mice_plot.png")
#laptop
# png("C://Code/simple-anova-beech/figs/mouse_plot.png")
fig.3.N
# dev.off()
# export data
write_csv(plot.dat.all1, "C://Code/data/plot_all_data1.csv")
# write_csv(out.final, "./data/final-outputs.csv")
write_csv(abund.dat5, "C://Code/data/abundance5.csv")
# export plot for example vignette
# png("C://GIT/beech-publication-wr/figs/rat_plot.png")
fig.3.rat
# dev.off()
# png("C://Code/simple-anova-beech/figs/rat_plot.png")
rat.plot
# dev.off()
davan690/beech-publication-wr documentation built on March 29, 2020, 11:09 a.m.
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##final script for figure 2-4 Davidsonetal2019
#Anthony Davidson
#oct2019
# libraries needed
source("./R/r-packages-needed.R", echo = FALSE)
source("./R/theme_raw_fig3s.r", echo = FALSE)
source("./R/davidson_2019_theme.r", echo = FALSE)
source("./R/Davidson_2019_Data_wrangling.R")
# fig.3.plot.seed.sum.final
# jitter everything the same is harrrrrd
location.move <- position_dodge(width = 30)
# plot
plot.final.f3.1 <- ggplot(p.design2,
aes(
y = cum.seed,
col = Rats,
shape = Valley,
fill = Control,
x = Date
),
size = 7) +
geom_rect(aes(xmin=ymd('2000-01-01'),xmax = ymd('2000-12-31'),ymin = -Inf,ymax = Inf), colour = "grey90", fill = "grey90") +
geom_rect(aes(xmin=ymd('2002-01-01'),xmax = ymd('2002-12-31'),ymin = -Inf,ymax = Inf), colour = "grey90", fill = "grey90") +
geom_rect(aes(xmin=ymd('2004-01-01'),xmax = ymd('2004-12-31'),ymin = -Inf,ymax = Inf), colour = "grey90", fill = "grey90") +
geom_errorbar(aes(ymin = lcl.slog, ymax = ucl.slog, width = 0), lwd = 0.4, col = "black", position = location.move, alpha = 0.7) +
geom_line(col = "grey50") +
geom_point(aes(y = cum.seed,
x = Date
),alpha = 0.7, size = 3, stroke = 1.25, position = location.move) +
xlab(expression(paste("Time", "(", italic(t), ")"))) +
ylab(expression(paste("Available seed "," ", "(", italic(Seed[jt]), ")"))) +
scale_color_manual(name = "Stoat Control",
values = c("black", "white", "white")) +
scale_shape_manual(name = "Ecosystem",
values = c(24, 21)) +
scale_size_manual(name = "Rat Control", values = c(2.5, 3, 2.5)) +
# manually define the fill colours
scale_fill_manual(name = "Stoat Control",
values = c("white", "black", "white")) +
# Remove fill legend and replace the fill legend using the newly created size
guides(
col = "none",
size = guide_legend(override.aes = list(
shape = c(15,0),alpha = 1
)),
shape = guide_legend(override.aes = list(
shape = c(24, 21), size = 4
)),
fill = guide_legend(override.aes = list(
col = c("white", "black"),shape = c("square"),
size = 4
))
) +
theme_tufte() +
theme_bw() +
theme(strip.background = element_blank(),
strip.text.y = element_blank(),
plot.title = element_text(hjust = 0, size=24, family = "Times", color="black", margin = margin(t = 10, b = 10)),
plot.subtitle=element_text(size=16, face="italic", color="black"),
legend.position = "none",
legend.key = element_blank(),
legend.background = element_rect(fill="white", size=1),
legend.key.size=unit(1,"cm"),
legend.text = element_text(colour = "black", size =16, family = "Times"),
legend.title = element_text(colour = "black", size =16, family = "Times"),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.spacing = unit(2, "lines"),
panel.border = element_blank(),
axis.title.y = element_text(colour = "black",size =20, family = "Times", angle = 90),
axis.title.x = element_text(colour = "black", size =20, family = "Times"),
axis.text.y=element_text(colour = "black",size = 20, family = "Times"),
axis.text.x = element_text(colour = "black", size =20, family = "Times"),
axis.ticks.x = element_line(size = 1),
axis.ticks.y = element_line(size = 1),
axis.line.x = element_line(size = 1),
axis.line.y = element_line(size = 1),
strip.text = element_text(face="bold",colour = "black",size =14, family = "Times"))
plot.final.f3.1
## ----new-mice------------------------------------------------------------
# plot raw seed
fig.3.N <-
ggplot(p.design2,
aes(
y = N,
col = Rats,
shape = Valley,
fill = Control,
x = Date
)) +
geom_rect(aes(xmin=ymd('2000-01-01'),xmax = ymd('2000-12-31'),ymin = -Inf,ymax = Inf), colour = "grey90", fill = "grey90") +
geom_rect(aes(xmin=ymd('2002-01-01'),xmax = ymd('2002-12-31'),ymin = -Inf,ymax = Inf), colour = "grey90", fill = "grey90") +
geom_rect(aes(xmin=ymd('2004-01-01'),xmax = ymd('2004-12-31'),ymin = -Inf,ymax = Inf), colour = "grey90", fill = "grey90") +
geom_errorbar(aes(ymin = lcl.slog, ymax = ucl.slog, width = 0), lwd = 0.7, col = "black", position = location.move, alpha = 0.7) +
geom_line(col = "grey50") +
geom_point(aes(y = N,
x = Date
),size = 5, stroke = 1.25, position = location.move) +
xlab(expression(paste("Time", "(", italic(t), ")"))) +
ylab(expression(paste("Mouse abundance ", " (", italic(N[jt]), ")"))) +
scale_color_manual(name = "Stoat Control",
values = c("black", "white", "white")) +
scale_shape_manual(name = "Ecosystem",
values = c(24, 21)) +
scale_size_manual(name = "Rat Control", values = c(2.5, 3, 2.5)) +
# manually define the fill colours
scale_fill_manual(name = "Stoat Control",
values = c("white", "black", "white")) +
# Remove fill legend and replace the fill legend using the newly created size
guides(
col = "none",
size = guide_legend(override.aes = list(
shape = c(15,0),alpha = 1
)),
shape = guide_legend(override.aes = list(
shape = c(24, 21), size = 4
)),
fill = guide_legend(override.aes = list(
col = c("white", "black"),shape = c("square"),
size = 4
))
) +
theme_tufte() +
theme_bw() +
theme(strip.background = element_blank(),
strip.text.y = element_blank(),
plot.title = element_text(hjust = 0, size=24, family = "Times", color="black", margin = margin(t = 10, b = 10)),
plot.subtitle=element_text(size=16, face="italic", color="black"),
legend.position = "none",
legend.key = element_blank(),
legend.background = element_rect(fill="white", size=1),
legend.key.size=unit(1,"cm"),
legend.text = element_text(colour = "black", size =16, family = "Times"),
legend.title = element_text(colour = "black", size =16, family = "Times"),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.spacing = unit(2, "lines"),
panel.border = element_blank(),
axis.title.y = element_text(colour = "black",size =20, family = "Times", angle = 90),
axis.title.x = element_text(colour = "black", size =20, family = "Times"),
axis.text.y=element_text(colour = "black",size = 20, family = "Times"),
axis.text.x = element_text(colour = "black", size =20, family = "Times"),
axis.ticks.x = element_line(size = 1),
axis.ticks.y = element_line(size = 1),
axis.line.x = element_line(size = 1),
axis.line.y = element_line(size = 1),
strip.text = element_text(face="bold",colour = "black",size =14, family = "Times"))
fig.3.N
## ----new-rats
rat.plot <- ggplot(p.design2, aes(y = N,col = Rats,shape = Valley,fill = Control,x = Date)) +geom_rect(aes(xmin=ymd('2000-01-01'),xmax = ymd('2000-12-31'),ymin = -Inf,ymax = Inf), colour = "grey90", fill = "grey90") +
geom_rect(aes(xmin=ymd('2002-01-01'),xmax = ymd('2002-12-31'),ymin = -Inf,ymax = Inf), colour = "grey90", fill = "grey90") +
geom_rect(aes(xmin=ymd('2004-01-01'),xmax = ymd('2004-12-31'),ymin = -Inf,ymax = Inf), colour = "grey90", fill = "grey90") +
geom_errorbar(aes(ymin = lcl.slog, ymax = ucl.slog, width = 0), lwd = 0.7, col = "black", position = location.move) +
geom_line(data = rat.mean,
aes(y = mean.rat,
x = Date),
size = 0.95,
col = "grey50", position = location.move) +
geom_point(data = rat.mean,aes( y = mean.rat, col = Rats,
shape = Valley,
fill = Control,
x = Date
),size = 6 , position = location.move) +
xlab(expression(paste("Time", "(", italic(t), ")"))) +
ylab(expression(atop(paste("Minimum "," ", " number"," "),
paste(" ", "of"," ",
"rats"," ","(",italic(R[jt]),")"))) ) +
scale_color_manual(name = "Stoat Control",
values = c("black", "white", "white")) +
scale_shape_manual(name = "Ecosystem",
values = c(24, 21)) +
scale_size_manual(name = "Rat Control", values = c(2.5, 3, 2.5)) +
# manually define the fill colours
scale_fill_manual(name = "Stoat Control",
values = c("white", "black", "white")) +
# Remove fill legend and replace the fill legend using the newly created size
guides(
col = "none",
size = guide_legend(override.aes = list(
shape = c(15,0),alpha = 1
)),
shape = guide_legend(override.aes = list(
shape = c(24, 21), size = 4
)),
fill = guide_legend(override.aes = list(
col = c("white", "black"),shape = c("square"),
size = 4
))
) +
xlab(expression(paste("Time", "(", italic(t), ")"))) +
ylab(expression(atop(paste("Minimum "," ", " number"," "),
paste(" ", "of"," ",
"rats"," ","(",italic(R[jt]),")"))) ) +
# scale_y_continuous(expand = c(0,0.01),breaks = seq(-4,4,1)) +
theme_tufte() +
theme_bw() +
theme(strip.background = element_blank(),
strip.text.y = element_blank(),
plot.title = element_text(hjust = 0, size=24, family = "Times", color="black", margin = margin(t = 10, b = 10)),
plot.subtitle=element_text(size=16, face="italic", color="black"),
legend.position = "none",
legend.key = element_blank(),
legend.background = element_rect(fill="white", size=1),
legend.key.size=unit(1,"cm"),
legend.text = element_text(colour = "black", size =16, family = "Times"),
legend.title = element_text(colour = "black", size =16, family = "Times"),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.spacing = unit(2, "lines"),
panel.border = element_blank(),
axis.title.y = element_text(colour = "black",size =20, family = "Times", angle = 90),
axis.title.x = element_text(colour = "black", size =20, family = "Times"),
axis.text.y=element_text(colour = "black",size = 20, family = "Times"),
axis.text.x = element_text(colour = "black", size =20, family = "Times"),
axis.ticks.x = element_line(size = 1),
axis.ticks.y = element_line(size = 1),
axis.line.x = element_line(size = 1),
axis.line.y = element_line(size = 1),
strip.text = element_text(face="bold",colour = "black",size =14, family = "Times"))
rat.plot
## ----message=FALSE, warning=FALSE----------------------------------------
# save csv file
write.csv(p.design2, "C://Code/data/seed-summary-data-june2019.csv")
# export plot for example vignette
#desktop
#png("C://Code/beech-publication-wr/figs/plot.final.f3.1.png")
#laptop
# png("C://Code/beech-publication-wr/test.seedp.png")
#
plot.final.f3.1
# dev.off()
write.csv(p.design2, "C://Code/data/mouse_summary_data.csv")
# export plot for example vignette
#desktop
# png("C://Code/beech-publication-wr/figs/mice.plot.png")
#laptop
# png("C://GIT/beech-publication-wr/figs/mice_plot.png")
#laptop
# png("C://Code/simple-anova-beech/figs/mouse_plot.png")
fig.3.N
# dev.off()
# export data
write_csv(plot.dat.all1, "C://Code/data/plot_all_data1.csv")
# write_csv(out.final, "./data/final-outputs.csv")
write_csv(abund.dat5, "C://Code/data/abundance5.csv")
# export plot for example vignette
# png("C://GIT/beech-publication-wr/figs/rat_plot.png")
fig.3.rat
# dev.off()
# png("C://Code/simple-anova-beech/figs/rat_plot.png")
rat.plot
# dev.off()
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