R/figures/seed_black_white.R
In davan690/beech-publication-wr: Small mammal dynamics in NZ beech forests
# By grid plot
# Base plot code
# May2019 fully sorted
# # Can I turn this into a function I can use to select either one of 3 different estimates of abundance into
# # seed, density, rats?
# meanS <- dat.msr.1 %>%
# filter(spp == "seed") %>%
# mutate(true.date = as.Date(true.date),
# mean.s = est.dat)
#
# #comes from summary Rscript.
# # source(./R/figures/summar...)
# meanS.1 <- mean1 %>%
# filter(spp == "seed") %>%
# mutate(true.date = as.Date(true.date))
# Cleaning up total dataset
# plot.dat.all1 # already done!
# summaries
seed.mean <- plot.dat.all1 %>%
group_by(Control, Valley, Date) %>%
summarise(
mean.s = mean(cum.seed),
sd.s = sd(cum.seed),
se.s = sd(cum.seed) / sqrt(length(cum.seed)) * 1.96,
lcl.s = mean(cum.seed) - (sd(cum.seed) / sqrt(length(cum.seed)) *
1.96),
ucl.s = mean(cum.seed) + (sd(cum.seed) / sqrt(length(cum.seed)) *
1.96)
) %>%
ungroup()
seed.mean <- seed.mean %>%
mutate(
gp.treat = factor(paste(Valley, Control)),
cum.seed = mean.s,
Rats = factor("Full")
)
# levels(seed.mean$gp.treat)
# note that plot uses both meanS and meanS.1
# seed.aver.plot <-
ggplot(data = plot.dat.all1,
aes(
y = cum.seed,
x = Date,
shape = Valley,
fill = Control,
col = Rats)) +
# extra goodies
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_point(aes(fill = Control), stroke = 1.15, size = 3) +
# geom_line(data = seed.mean, aes(y = mean.s,
# x = Date, group = gp.treat), size = 0.9) +
#
# # +
# # geom_errorbar(data = meanS.1, mapping = aes(ymin = lcl.s, ymax = ucl.s), width = 0, alpha = 0.5, lwd = 0.75) +
#
geom_line(data = seed.mean,
aes(y = mean.s,
x = Date),
size = 1,
col = "grey50") +
geom_point(data = seed.mean, aes(y = mean.s,
x = Date), size = 5) +
scale_color_manual(name = "Stoat Control",
values = c("white", "black")) +
scale_shape_manual(name = "Ecosystem",
values = c(24, 21)) +
# manually define the fill colours
#
scale_fill_manual(
name = "Stoat Control",
values = c("cornflowerblue", "darkorange", "white", "black")
) +
# defining size with 2 marginally different values
scale_size_manual(name = "Rat Control", values = c(5, 4)) +
# geom_abline(intercept = 5, slope = 0, size = 1) +
# theme
# theme_new() +
# labels
# scale_y_discrete(labels = c("1","2","3","4"," ","1","2","3","4")) +
# scale_x_date() +
# defining size with 2 marginally different values
# scale_size_manual(name = "Rat Control", values = c(4, 3)) +
# Remove fill legend and replace the fill legend using the newly created size
guides(
col = "none",
shape = guide_legend(override.aes = list(shape = c(24, 21))),
fill = guide_legend(override.aes = list(col = c(
"cornflowerblue", "darkorange"
)))
)
# study design plot
# may 2019
#anthony
source("./R/davidson_2019_theme.r")
# source("./R/figures/study-design-data.R")
p.design <- plot.dat.all1 %>%
mutate(grid = as.numeric(factor(grid)))
# glimpse(plot.dat.all1)
# adding NA grid to plot
bd.row <- p.design[1, ]
bd.row$grid <- "blank"
bd.row$grid <- "blank"
bd.row$grid <- "blank"
bd.row$grid <- "blank"
bd.row$Date <- NA
# bind row to plot data
p.design145 <- rbind(p.design, bd.row)
# glimpse(p.design145$grid)
# labels
rat.labs <- c("No", "Reduced")
#re-factoring
p.design1 <- p.design145 %>%
mutate(grid = factor(grid, levels = c(
"1", "2", "3", "4", "blank", "5", "6", "7", "8"
)),
Rats = factor(Rats, labels = rat.labs))
#checking
# tail(p.design1)
# tail(filter(p.design1, grid == "blank"))
# levels(p.design1$grid)
# labels() <- c("1","2","3","4"," ","5","6","7","8")
# p.design1$grid <- factor(p.design1$grid, labels = c("1","2","3","4"," ","1","2","3","4"))
#plot raw seed
fig.3.plot.seed <- ggplot(p.design1,
aes(
y = cum.seed,
col = Rats,
shape = Valley,
fill = Control,
x = Date
),
size = 4) +
# geom_line(col = "grey50") +
geom_point(aes(size = Rats,
group = grid), stroke = 1.25) +
scale_color_manual(name = "Stoat Control",
values = c("white", "black")) +
scale_shape_manual(name = "Ecosystem",
values = c(24, 21)) +
# manually define the fill colours
scale_fill_manual(name = "Stoat Control",
values = c("cornflowerblue", "darkorange")) +
# geom_abline(intercept = 5, slope = 0, size = 1) +
# theme
theme_new() +
scale_size_manual(name = "Rat Control", values = c(4, 3)) +
# labels
# scale_y_discrete(labels = c("1","2","3","4"," ","1","2","3","4")) +
# scale_x_date() +
# defining size with 2 marginally different values
# Remove fill legend and replace the fill legend using the newly created size
guides(
col = "none",
size = guide_legend(override.aes = list(shape = c(16, 1))),
shape = guide_legend(override.aes = list(
shape = c(24, 21), size = 4
)),
fill = guide_legend(override.aes = list(
col = c("cornflowerblue", "darkorange"),
size = 4
))
) +
# col = "none",
# # size = guide_legend(override.aes = list(shape = c(16, 1))),
# shape = guide_legend(override.aes = list(
# shape = c(24, 21), size = 4
# ))
# # fill = guide_legend(override.aes = list(
# # col = c("cornflowerblue", "darkorange"), size = 4
# # ))
# ) +
# geom_hline(yintercept = 0,
# lty = 5,
# alpha = 0.7) +
#
xlab(expression(paste("Time", "(", italic(t), ")"))) +
ylab(expression(paste("Available seed ", "(", italic(Seed[jt]), ")")))
fig.3.plot.seed
# sorting summary dataset for the last time -------------------------------
#summarising seed
table(is.na(p.design1$grid))
#remove NA for making space in last plot
p.design1 <- p.design1[1:144, ]
#no grid na anymore
table(is.na(p.design1$grid))
#making datasest
p.design2 <- p.design1 %>%
group_by(Control, Valley, Date) %>%
summarise(cum.seed = mean(cum.seed),
Rats = factor("Full", levels = c("Full", "Reduced"))) %>%
ungroup() %>%
mutate(grid = factor(paste(Control, Valley)))
# grouping of grid correct?
levels(p.design2$grid)
p.design2$Rats
# glimpse(p.design2)
#plot summary seed
# Add NA so legend works
row.input.leg <- p.design2[1, ]
row.input.leg$Control <- NA
row.input.leg$Valley <- NA
row.input.leg$Date <- NA
row.input.leg$cum.seed <- NA
row.input.leg$Rats <- "Reduced"
row.input.leg$grid <- NA
p.design3 <- rbind(p.design2, row.input.leg)
# glimpse(p.design3)
levels(p.design3$Rats)
col = c("cornflowerblue", "darkorange")
#plot raw seed
fig.3.plot.seed.sum <- ggplot(p.design2,
aes(
y = cum.seed,
col = Rats,
shape = Valley,
fill = Control,
x = Date
),
size = 4) +
geom_line(col = "grey50") +
geom_point(aes(size = Rats,
group = grid), stroke = 1.25) +
scale_color_manual(name = "Stoat Control",
values = c("white", "black")) +
scale_shape_manual(name = "Ecosystem",
values = c(24, 21)) +
scale_size_manual(name = "Rat Control", values = c(4, 3)) +
# manually define the fill colours
scale_fill_manual(name = "Stoat Control",
values = c("cornflowerblue", "darkorange")) +
# geom_abline(intercept = 5, slope = 0, size = 1) +
# theme
theme_new() +
# labels
# scale_y_discrete(labels = c("1","2","3","4"," ","1","2","3","4")) +
# scale_x_date() +
# defining size with 2 marginally different values
# Remove fill legend and replace the fill legend using the newly created size
guides(
col = "none",
size = "none",
shape = guide_legend(override.aes = list(
shape = c(24, 21), size = 4
)),
fill = guide_legend(override.aes = list(
col = c("cornflowerblue", "darkorange"),shape = c("square"),
size = 4
))
) +
# col = "none",
# # size = guide_legend(override.aes = list(shape = c(16, 1))),
# shape = guide_legend(override.aes = list(
# shape = c(24, 21), size = 4
# ))
# # fill = guide_legend(override.aes = list(
# # col = c("cornflowerblue", "darkorange"), size = 4
# # ))
# ) +
# geom_hline(yintercept = 0,
# lty = 5,
# alpha = 0.7) +
#
xlab(expression(paste("Time", "(", italic(t), ")"))) +
ylab(expression(paste("Available seed ", "(", italic(Seed[jt]), ")")))
fig.3.plot.seed.sum
# Combine them ------------------------------------------------------------
#plot raw seed
fig.3.seed <- ggplot(p.design1,
aes(
y = cum.seed,
col = Rats,
shape = Valley,
fill = Control,
x = Date
)) +
# geom_line(col = "grey50") +
geom_point(aes(size = Rats,
group = grid),
stroke = 1.25,
alpha = 0.5) +
scale_color_manual(name = "Stoat Control",
values = c("white", "black", "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("cornflowerblue", "darkorange", "cornflowerblue")
) +
geom_line(
data = p.design2,
aes(y = cum.seed,
x = Date),
size = 0.95,
col = "grey50"
) +
geom_point(
data = p.design2,
aes(
y = cum.seed,
col = Rats,
shape = Valley,
fill = Control,
x = Date
),
size = 7
) +
# 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("cornflowerblue", "darkorange"),shape = c("square"),
size = 4
))
) +
xlab(expression(paste("Timing of sample", "(", italic(t), ")"))) +
ylab(expression(paste("Available seed ", "(", italic(Seed[jt]), ")")))
fig.3.seed
## ----conf-intervals-above-zero-------------------------------------------
#making datasest
p.design2 <- p.design1 %>%
group_by(Control, Valley, Date) %>%
summarise(N = mean(ifelse(cum.seed > 0, ifelse(cum.seed > 0, log(cum.seed), 0), 0)),
Rats = factor("Full", levels = c("Full", "Reduced")),
sd.s = sd(ifelse(cum.seed > 0, log(cum.seed), 0), na.rm = TRUE),
se.s = sd(ifelse(cum.seed > 0, log(cum.seed), 0)) / sqrt(length(cum.seed)) * 1.96,
lcl.s = mean(ifelse(cum.seed > 0, log(cum.seed), 0)) - (sd(ifelse(cum.seed > 0, log(cum.seed), 0)) / sqrt(length(cum.seed)) *
1.96),
lcl.slog = exp(lcl.s),
ucl.s = mean(ifelse(cum.seed > 0, log(cum.seed), 0)) + (sd(ifelse(cum.seed > 0, log(cum.seed), 0)) / sqrt(length(cum.seed)) *
1.96),
ucl.slog = exp(ucl.s)) %>%
ungroup() %>%
mutate(cum.seed = exp(N),
grid = factor(paste(Control, Valley)))
fig.3.plot.seed.sum.final <- ggplot(p.design2,
aes(
y = cum.seed,
col = Rats,
shape = Valley,
fill = Control,
x = Date
),
size = 4) +
geom_errorbar(data = p.design2, aes(ymin = lcl.slog, ymax = ucl.slog, width = 0), lwd = 1.1, col = "black") +
geom_line(col = "grey50") +
geom_point(aes(size = Rats,
group = grid), stroke = 1.25) +
scale_color_manual(name = "Stoat Control",
values = c("white", "black")) +
scale_shape_manual(name = "Ecosystem",
values = c(24, 21)) +
scale_size_manual(name = "Rat Control", values = c(4, 3)) +
scale_fill_manual(name = "Stoat Control",
values = c("cornflowerblue", "darkorange")) +
theme_new() +
guides(
col = "none",
size = "none",
shape = guide_legend(override.aes = list(
shape = c(24, 21), size = 4
)),
fill = guide_legend(override.aes = list(
col = c("cornflowerblue", "darkorange"),shape = c("square"),
size = 4
))
) +
xlab(expression(paste("Time", "(", italic(t), ")"))) +
ylab(expression(paste("Available seed ", "(", italic(Seed[jt]), ")")))
fig.3.plot.seed.sum.final
## ----combining-plots-old-------------------------------------------------
#plot raw seed
fig.3.seed <- ggplot(p.design1,
aes(
y = cum.seed,
col = Rats,
shape = Valley,
fill = Control,
x = Date
)) +
geom_point(aes(size = Rats,
group = grid),
stroke = 1.25,
alpha = 0.5) +
scale_color_manual(name = "Stoat Control",
values = c("white", "black", "white")) +
scale_shape_manual(name = "Ecosystem",
values = c(24, 21)) +
scale_size_manual(name = "Rat Control", values = c(2.5, 3, 2.5)) +
scale_fill_manual(
name = "Stoat Control",
values = c("cornflowerblue", "darkorange", "cornflowerblue")
) +
geom_line(
data = p.design2,
aes(y = cum.seed,
x = Date),
size = 0.95,
col = "grey50"
) +
geom_point(
data = p.design2,
aes(
y = cum.seed,
col = Rats,
shape = Valley,
fill = Control,
x = Date
),
size = 7
) +
geom_errorbar(data = p.design2, aes(ymin = lcl.s, ymax = ucl.s, width = 0), lwd = 1.1) +
# 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("cornflowerblue", "darkorange"),shape = c("square"),
size = 4
))
) +
xlab(expression(paste("Timing of sample", "(", italic(t), ")"))) +
ylab(expression(paste("Available seed ", "(", italic(Seed[jt]), ")")))
fig.3.seed
## ------------------------------------------------------------------------
# fig.3.plot.seed.sum.final
# jitter everything the same is harrrrrd
location.move <- position_dodge(width = 20)
# plot
plot.final.f3.1 <- ggplot(p.design2,
aes(
y = cum.seed,
col = Rats,
shape = Valley,
fill = Control,
x = Date
),
size = 4) +
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 = 0.4) +
geom_line(col = "grey50") +
geom_point(aes(y = cum.seed,
x = Date
),size = 5, stroke = 1.25, position = location.move) +
scale_color_manual(name = "Stoat Control",
values = c("white", "black")) +
scale_shape_manual(name = "Ecosystem",
values = c(24, 21)) +
scale_fill_manual(name = "Stoat Control",
values = c("cornflowerblue", "darkorange")) +
guides(
col = "none",
size = "none",
shape = guide_legend(override.aes = list(
shape = c(24, 21), size = 4
)),
fill = guide_legend(override.aes = list(
col = c("cornflowerblue", "darkorange"),shape = c("square"),
size = 4
))
) +
xlab(expression(paste("Time", "(", italic(t), ")"))) +
ylab(expression(paste("Available seed ", "(", italic(Seed[jt]), ")")))+
xlab(expression(paste("Time", "(", italic(t), ")"))) +
ylab(expression(paste("Available seed "," ", "(", italic(Seed[jt]), ")"))) +
theme_bw()+
theme_new() +
theme(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 =12),
legend.title = element_text(colour = "black", size =12),
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 =12,angle = 90),
axis.title.x = element_text(colour = "black",size = 10),
axis.text.y=element_text(colour = "black",size = 10),
axis.text.x = element_text(colour = "black",size = 10),
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))
plot.final.f3.1
## ------------------------------------------------------------------------
# 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
)) +
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 = 6, position = location.move, size = 0.95) +
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
# # export plot for example vignette
# jpeg("./figs/fig-3.1-study.jpeg")
# fig.2.plot.design
# dev.off()
davan690/beech-publication-wr documentation built on March 29, 2020, 11:09 a.m.
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# By grid plot
# Base plot code
# May2019 fully sorted
# # Can I turn this into a function I can use to select either one of 3 different estimates of abundance into
# # seed, density, rats?
# meanS <- dat.msr.1 %>%
# filter(spp == "seed") %>%
# mutate(true.date = as.Date(true.date),
# mean.s = est.dat)
#
# #comes from summary Rscript.
# # source(./R/figures/summar...)
# meanS.1 <- mean1 %>%
# filter(spp == "seed") %>%
# mutate(true.date = as.Date(true.date))
# Cleaning up total dataset
# plot.dat.all1 # already done!
# summaries
seed.mean <- plot.dat.all1 %>%
group_by(Control, Valley, Date) %>%
summarise(
mean.s = mean(cum.seed),
sd.s = sd(cum.seed),
se.s = sd(cum.seed) / sqrt(length(cum.seed)) * 1.96,
lcl.s = mean(cum.seed) - (sd(cum.seed) / sqrt(length(cum.seed)) *
1.96),
ucl.s = mean(cum.seed) + (sd(cum.seed) / sqrt(length(cum.seed)) *
1.96)
) %>%
ungroup()
seed.mean <- seed.mean %>%
mutate(
gp.treat = factor(paste(Valley, Control)),
cum.seed = mean.s,
Rats = factor("Full")
)
# levels(seed.mean$gp.treat)
# note that plot uses both meanS and meanS.1
# seed.aver.plot <-
ggplot(data = plot.dat.all1,
aes(
y = cum.seed,
x = Date,
shape = Valley,
fill = Control,
col = Rats)) +
# extra goodies
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_point(aes(fill = Control), stroke = 1.15, size = 3) +
# geom_line(data = seed.mean, aes(y = mean.s,
# x = Date, group = gp.treat), size = 0.9) +
#
# # +
# # geom_errorbar(data = meanS.1, mapping = aes(ymin = lcl.s, ymax = ucl.s), width = 0, alpha = 0.5, lwd = 0.75) +
#
geom_line(data = seed.mean,
aes(y = mean.s,
x = Date),
size = 1,
col = "grey50") +
geom_point(data = seed.mean, aes(y = mean.s,
x = Date), size = 5) +
scale_color_manual(name = "Stoat Control",
values = c("white", "black")) +
scale_shape_manual(name = "Ecosystem",
values = c(24, 21)) +
# manually define the fill colours
#
scale_fill_manual(
name = "Stoat Control",
values = c("cornflowerblue", "darkorange", "white", "black")
) +
# defining size with 2 marginally different values
scale_size_manual(name = "Rat Control", values = c(5, 4)) +
# geom_abline(intercept = 5, slope = 0, size = 1) +
# theme
# theme_new() +
# labels
# scale_y_discrete(labels = c("1","2","3","4"," ","1","2","3","4")) +
# scale_x_date() +
# defining size with 2 marginally different values
# scale_size_manual(name = "Rat Control", values = c(4, 3)) +
# Remove fill legend and replace the fill legend using the newly created size
guides(
col = "none",
shape = guide_legend(override.aes = list(shape = c(24, 21))),
fill = guide_legend(override.aes = list(col = c(
"cornflowerblue", "darkorange"
)))
)
# study design plot
# may 2019
#anthony
source("./R/davidson_2019_theme.r")
# source("./R/figures/study-design-data.R")
p.design <- plot.dat.all1 %>%
mutate(grid = as.numeric(factor(grid)))
# glimpse(plot.dat.all1)
# adding NA grid to plot
bd.row <- p.design[1, ]
bd.row$grid <- "blank"
bd.row$grid <- "blank"
bd.row$grid <- "blank"
bd.row$grid <- "blank"
bd.row$Date <- NA
# bind row to plot data
p.design145 <- rbind(p.design, bd.row)
# glimpse(p.design145$grid)
# labels
rat.labs <- c("No", "Reduced")
#re-factoring
p.design1 <- p.design145 %>%
mutate(grid = factor(grid, levels = c(
"1", "2", "3", "4", "blank", "5", "6", "7", "8"
)),
Rats = factor(Rats, labels = rat.labs))
#checking
# tail(p.design1)
# tail(filter(p.design1, grid == "blank"))
# levels(p.design1$grid)
# labels() <- c("1","2","3","4"," ","5","6","7","8")
# p.design1$grid <- factor(p.design1$grid, labels = c("1","2","3","4"," ","1","2","3","4"))
#plot raw seed
fig.3.plot.seed <- ggplot(p.design1,
aes(
y = cum.seed,
col = Rats,
shape = Valley,
fill = Control,
x = Date
),
size = 4) +
# geom_line(col = "grey50") +
geom_point(aes(size = Rats,
group = grid), stroke = 1.25) +
scale_color_manual(name = "Stoat Control",
values = c("white", "black")) +
scale_shape_manual(name = "Ecosystem",
values = c(24, 21)) +
# manually define the fill colours
scale_fill_manual(name = "Stoat Control",
values = c("cornflowerblue", "darkorange")) +
# geom_abline(intercept = 5, slope = 0, size = 1) +
# theme
theme_new() +
scale_size_manual(name = "Rat Control", values = c(4, 3)) +
# labels
# scale_y_discrete(labels = c("1","2","3","4"," ","1","2","3","4")) +
# scale_x_date() +
# defining size with 2 marginally different values
# Remove fill legend and replace the fill legend using the newly created size
guides(
col = "none",
size = guide_legend(override.aes = list(shape = c(16, 1))),
shape = guide_legend(override.aes = list(
shape = c(24, 21), size = 4
)),
fill = guide_legend(override.aes = list(
col = c("cornflowerblue", "darkorange"),
size = 4
))
) +
# col = "none",
# # size = guide_legend(override.aes = list(shape = c(16, 1))),
# shape = guide_legend(override.aes = list(
# shape = c(24, 21), size = 4
# ))
# # fill = guide_legend(override.aes = list(
# # col = c("cornflowerblue", "darkorange"), size = 4
# # ))
# ) +
# geom_hline(yintercept = 0,
# lty = 5,
# alpha = 0.7) +
#
xlab(expression(paste("Time", "(", italic(t), ")"))) +
ylab(expression(paste("Available seed ", "(", italic(Seed[jt]), ")")))
fig.3.plot.seed
# sorting summary dataset for the last time -------------------------------
#summarising seed
table(is.na(p.design1$grid))
#remove NA for making space in last plot
p.design1 <- p.design1[1:144, ]
#no grid na anymore
table(is.na(p.design1$grid))
#making datasest
p.design2 <- p.design1 %>%
group_by(Control, Valley, Date) %>%
summarise(cum.seed = mean(cum.seed),
Rats = factor("Full", levels = c("Full", "Reduced"))) %>%
ungroup() %>%
mutate(grid = factor(paste(Control, Valley)))
# grouping of grid correct?
levels(p.design2$grid)
p.design2$Rats
# glimpse(p.design2)
#plot summary seed
# Add NA so legend works
row.input.leg <- p.design2[1, ]
row.input.leg$Control <- NA
row.input.leg$Valley <- NA
row.input.leg$Date <- NA
row.input.leg$cum.seed <- NA
row.input.leg$Rats <- "Reduced"
row.input.leg$grid <- NA
p.design3 <- rbind(p.design2, row.input.leg)
# glimpse(p.design3)
levels(p.design3$Rats)
col = c("cornflowerblue", "darkorange")
#plot raw seed
fig.3.plot.seed.sum <- ggplot(p.design2,
aes(
y = cum.seed,
col = Rats,
shape = Valley,
fill = Control,
x = Date
),
size = 4) +
geom_line(col = "grey50") +
geom_point(aes(size = Rats,
group = grid), stroke = 1.25) +
scale_color_manual(name = "Stoat Control",
values = c("white", "black")) +
scale_shape_manual(name = "Ecosystem",
values = c(24, 21)) +
scale_size_manual(name = "Rat Control", values = c(4, 3)) +
# manually define the fill colours
scale_fill_manual(name = "Stoat Control",
values = c("cornflowerblue", "darkorange")) +
# geom_abline(intercept = 5, slope = 0, size = 1) +
# theme
theme_new() +
# labels
# scale_y_discrete(labels = c("1","2","3","4"," ","1","2","3","4")) +
# scale_x_date() +
# defining size with 2 marginally different values
# Remove fill legend and replace the fill legend using the newly created size
guides(
col = "none",
size = "none",
shape = guide_legend(override.aes = list(
shape = c(24, 21), size = 4
)),
fill = guide_legend(override.aes = list(
col = c("cornflowerblue", "darkorange"),shape = c("square"),
size = 4
))
) +
# col = "none",
# # size = guide_legend(override.aes = list(shape = c(16, 1))),
# shape = guide_legend(override.aes = list(
# shape = c(24, 21), size = 4
# ))
# # fill = guide_legend(override.aes = list(
# # col = c("cornflowerblue", "darkorange"), size = 4
# # ))
# ) +
# geom_hline(yintercept = 0,
# lty = 5,
# alpha = 0.7) +
#
xlab(expression(paste("Time", "(", italic(t), ")"))) +
ylab(expression(paste("Available seed ", "(", italic(Seed[jt]), ")")))
fig.3.plot.seed.sum
# Combine them ------------------------------------------------------------
#plot raw seed
fig.3.seed <- ggplot(p.design1,
aes(
y = cum.seed,
col = Rats,
shape = Valley,
fill = Control,
x = Date
)) +
# geom_line(col = "grey50") +
geom_point(aes(size = Rats,
group = grid),
stroke = 1.25,
alpha = 0.5) +
scale_color_manual(name = "Stoat Control",
values = c("white", "black", "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("cornflowerblue", "darkorange", "cornflowerblue")
) +
geom_line(
data = p.design2,
aes(y = cum.seed,
x = Date),
size = 0.95,
col = "grey50"
) +
geom_point(
data = p.design2,
aes(
y = cum.seed,
col = Rats,
shape = Valley,
fill = Control,
x = Date
),
size = 7
) +
# 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("cornflowerblue", "darkorange"),shape = c("square"),
size = 4
))
) +
xlab(expression(paste("Timing of sample", "(", italic(t), ")"))) +
ylab(expression(paste("Available seed ", "(", italic(Seed[jt]), ")")))
fig.3.seed
## ----conf-intervals-above-zero-------------------------------------------
#making datasest
p.design2 <- p.design1 %>%
group_by(Control, Valley, Date) %>%
summarise(N = mean(ifelse(cum.seed > 0, ifelse(cum.seed > 0, log(cum.seed), 0), 0)),
Rats = factor("Full", levels = c("Full", "Reduced")),
sd.s = sd(ifelse(cum.seed > 0, log(cum.seed), 0), na.rm = TRUE),
se.s = sd(ifelse(cum.seed > 0, log(cum.seed), 0)) / sqrt(length(cum.seed)) * 1.96,
lcl.s = mean(ifelse(cum.seed > 0, log(cum.seed), 0)) - (sd(ifelse(cum.seed > 0, log(cum.seed), 0)) / sqrt(length(cum.seed)) *
1.96),
lcl.slog = exp(lcl.s),
ucl.s = mean(ifelse(cum.seed > 0, log(cum.seed), 0)) + (sd(ifelse(cum.seed > 0, log(cum.seed), 0)) / sqrt(length(cum.seed)) *
1.96),
ucl.slog = exp(ucl.s)) %>%
ungroup() %>%
mutate(cum.seed = exp(N),
grid = factor(paste(Control, Valley)))
fig.3.plot.seed.sum.final <- ggplot(p.design2,
aes(
y = cum.seed,
col = Rats,
shape = Valley,
fill = Control,
x = Date
),
size = 4) +
geom_errorbar(data = p.design2, aes(ymin = lcl.slog, ymax = ucl.slog, width = 0), lwd = 1.1, col = "black") +
geom_line(col = "grey50") +
geom_point(aes(size = Rats,
group = grid), stroke = 1.25) +
scale_color_manual(name = "Stoat Control",
values = c("white", "black")) +
scale_shape_manual(name = "Ecosystem",
values = c(24, 21)) +
scale_size_manual(name = "Rat Control", values = c(4, 3)) +
scale_fill_manual(name = "Stoat Control",
values = c("cornflowerblue", "darkorange")) +
theme_new() +
guides(
col = "none",
size = "none",
shape = guide_legend(override.aes = list(
shape = c(24, 21), size = 4
)),
fill = guide_legend(override.aes = list(
col = c("cornflowerblue", "darkorange"),shape = c("square"),
size = 4
))
) +
xlab(expression(paste("Time", "(", italic(t), ")"))) +
ylab(expression(paste("Available seed ", "(", italic(Seed[jt]), ")")))
fig.3.plot.seed.sum.final
## ----combining-plots-old-------------------------------------------------
#plot raw seed
fig.3.seed <- ggplot(p.design1,
aes(
y = cum.seed,
col = Rats,
shape = Valley,
fill = Control,
x = Date
)) +
geom_point(aes(size = Rats,
group = grid),
stroke = 1.25,
alpha = 0.5) +
scale_color_manual(name = "Stoat Control",
values = c("white", "black", "white")) +
scale_shape_manual(name = "Ecosystem",
values = c(24, 21)) +
scale_size_manual(name = "Rat Control", values = c(2.5, 3, 2.5)) +
scale_fill_manual(
name = "Stoat Control",
values = c("cornflowerblue", "darkorange", "cornflowerblue")
) +
geom_line(
data = p.design2,
aes(y = cum.seed,
x = Date),
size = 0.95,
col = "grey50"
) +
geom_point(
data = p.design2,
aes(
y = cum.seed,
col = Rats,
shape = Valley,
fill = Control,
x = Date
),
size = 7
) +
geom_errorbar(data = p.design2, aes(ymin = lcl.s, ymax = ucl.s, width = 0), lwd = 1.1) +
# 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("cornflowerblue", "darkorange"),shape = c("square"),
size = 4
))
) +
xlab(expression(paste("Timing of sample", "(", italic(t), ")"))) +
ylab(expression(paste("Available seed ", "(", italic(Seed[jt]), ")")))
fig.3.seed
## ------------------------------------------------------------------------
# fig.3.plot.seed.sum.final
# jitter everything the same is harrrrrd
location.move <- position_dodge(width = 20)
# plot
plot.final.f3.1 <- ggplot(p.design2,
aes(
y = cum.seed,
col = Rats,
shape = Valley,
fill = Control,
x = Date
),
size = 4) +
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 = 0.4) +
geom_line(col = "grey50") +
geom_point(aes(y = cum.seed,
x = Date
),size = 5, stroke = 1.25, position = location.move) +
scale_color_manual(name = "Stoat Control",
values = c("white", "black")) +
scale_shape_manual(name = "Ecosystem",
values = c(24, 21)) +
scale_fill_manual(name = "Stoat Control",
values = c("cornflowerblue", "darkorange")) +
guides(
col = "none",
size = "none",
shape = guide_legend(override.aes = list(
shape = c(24, 21), size = 4
)),
fill = guide_legend(override.aes = list(
col = c("cornflowerblue", "darkorange"),shape = c("square"),
size = 4
))
) +
xlab(expression(paste("Time", "(", italic(t), ")"))) +
ylab(expression(paste("Available seed ", "(", italic(Seed[jt]), ")")))+
xlab(expression(paste("Time", "(", italic(t), ")"))) +
ylab(expression(paste("Available seed "," ", "(", italic(Seed[jt]), ")"))) +
theme_bw()+
theme_new() +
theme(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 =12),
legend.title = element_text(colour = "black", size =12),
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 =12,angle = 90),
axis.title.x = element_text(colour = "black",size = 10),
axis.text.y=element_text(colour = "black",size = 10),
axis.text.x = element_text(colour = "black",size = 10),
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))
plot.final.f3.1
## ------------------------------------------------------------------------
# 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
)) +
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 = 6, position = location.move, size = 0.95) +
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
# # export plot for example vignette
# jpeg("./figs/fig-3.1-study.jpeg")
# fig.2.plot.design
# dev.off()
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