Sprays
Treatments analysis
Number of treatments and proportion of the total dose used in fungicide trials.
Load packages
list.of.packages <-
c(
"tidyverse",
"devtools",
"egg",
"hrbrthemes",
"sjPlot",
"effects",
"lsmeans",
"multcomp",
"multcompView",
"ggpubr",
"tableHTML",
"conflicted"
)
new.packages <-
list.of.packages[!(list.of.packages %in% installed.packages()[, "Package"])]
#Download packages that are not already present in the library
if (length(new.packages))
install.packages(new.packages)
packages_load <-
lapply(list.of.packages, require, character.only = TRUE)
#Print warning if there is a problem with installing/loading some of packages
if (any(as.numeric(packages_load) == 0)) {
warning(paste("Package/s: ", paste(list.of.packages[packages_load != TRUE], sep = ", "), "not loaded!"))
} else {
print("All packages were successfully loaded.")
}
rm(list.of.packages, new.packages, packages_load)
#Resolve conflicts
if(c("stats", "dplyr")%in% installed.packages()){
conflict_prefer("filter", "dplyr")
conflict_prefer("select", "dplyr")
}
#if instal is not working try
#install.packages("ROCR", repos = c(CRAN="https://cran.r-project.org/"))Data import
tab <-
read_csv(here::here("data", "treat", "Treatments.csv"))
years <-
tab %>%
group_by(Year) %>%
summarise(counts =n())
year_names <- unique(tab$Year)
tab[, "Year"] <- NULL
html_tab <-
tableHTML::tableHTML(
tab,
rownames = FALSE,
row_groups = list(c(years$counts), c(year_names)),
widths = c(50, 60, 70, rep(50, 6))
) %>%
# add_css_header(css = list('background-color', 'lightgray'), headers = c(1:ncol(tab)+1)) %>%
add_css_row(css = list('background-color', 'lightgray'),
rows = c(2:9, 22:29)) %>%
add_theme('scientific')
tableHTML_to_image(
html_tab,
file = here::here("results", "treat", "Programme theme.png"),
type = "png"
)
dosedf <- readRDS(file = here::here("data", "treat", "full_trt.rds") )
dosedf$treatment <-
ifelse(
dosedf$treatment == "Untreated Control",
"1.Untreated Control",
ifelse(
dosedf$treatment == "Full dose (100)",
"2.Full dose (100)",
ifelse(
dosedf$treatment == "Half dose (50)",
"3.Half dose (50)",
ifelse(
dosedf$treatment == "Irish Rules (IRp)",
"4.Irish Rules (IRp)",
ifelse(
dosedf$treatment == "Blight Man. (BMp)",
"5.Blight Man. (BMp)",
ifelse(
dosedf$treatment == "Modified I. R. (MIRp)",
"6.Modified I. R. (MIRp)",
NA
)
)
)
)
)
)
dosedf$treatment <-
factor(dosedf$treatment,
levels = c("1.Untreated Control", "2.Full dose (100)","3.Half dose (50)","4.Irish Rules (IRp)","5.Blight Man. (BMp)" ,"6.Modified I. R. (MIRp)"))The charts
# dosedf <- rename(dosedf, dose = Dose)
#Get number of treatments per year and the dose reduction
Summary <- function(x) {
data.frame(
n = length(x),
treatments = sum(as.numeric(x != 0)),
dose = round(sum(x) / length(x), 1)
)
}
p1 <-
dosedf %>%
group_by(year, treatment) %>%
do(Summary(.$dose)) %>%
ggplot(aes(
x = year,
y = dose,
fill = treatment,
group = treatment
)) +
geom_hline(yintercept = 50, colour = "gray")+
geom_hline(yintercept = 100, colour = "gray")+
geom_bar(
color = "black",
stat = "identity",
position = position_dodge(),
width = 0.9,
size = 0.5
) +
geom_text(
aes(label = treatments, color = treatment),
vjust = -0.3,
position = position_dodge(0.9),
size = 2.9
) +
geom_text(
aes(label = dose),
vjust = 1.3,
color = "white",
position = position_dodge(0.9),
size = 2.4
) +
scale_fill_brewer("Programme:", palette = "Dark2") +
scale_color_brewer("Programme:", palette = "Dark2") +
scale_y_continuous(limits = c(0, 110), breaks = seq(0, 100, 10)) +
theme_article() +
facet_grid(~ year, scales = "free") +
labs(x = "Year",
y = "Proportion of the total dose (%)\n") +
theme(
axis.title = element_text(size = 11),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
axis.text = element_text(size = 9),
legend.position = "top",
axis.text.x = element_blank(),
axis.ticks.x = element_blank()
)+
theme(text = element_text(size=12))
p1
dose_summary <-
dosedf %>%
group_by(year, treatment) %>%
do(Summary(.$dose))
p2 <-
dose_summary %>%
group_by(treatment) %>%
filter(year != 2016) %>%
summarise(mean_trt = round(mean(treatments),1),
mean = round(mean(dose),1),
sd = sd(dose)) %>%
ggplot(., aes(
x = treatment,
y = mean,
fill = treatment,
group = treatment
)) +
geom_hline(yintercept = 50, colour = "gray") +
geom_hline(yintercept = 100, colour = "gray") +
geom_bar(
color = "black",
stat = "identity",
position = position_dodge(),
width = 1,
size = 0.5
) +
geom_errorbar(aes(ymin = mean - sd,
ymax = mean + sd),
width = 0.2,
color = "gray") +
scale_fill_brewer("Programme:", palette = "Dark2") +
scale_color_brewer("Programme:", palette = "Dark2") +
theme_article() +
scale_y_continuous(limits = c(0, 110), breaks = seq(0, 100, 20)) +
theme(
axis.title = element_text(size = 11),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
axis.text = element_text(size = 11),
legend.position = "none",
axis.text.x = element_blank(),
axis.ticks.x = element_blank(),
legend.text=element_text(size=10)
)
p2 <-
p2 +
labs(x = "Overall", y= "")+
theme(axis.text = element_blank(),
axis.ticks.y = element_blank())+
theme(legend.position = "none")+
geom_text(
aes(label = mean_trt, color = treatment),
vjust = -0.3,
hjust = 0.4,
position = position_dodge(0.9),
size = 3
) +
geom_text(
aes(label = mean),
vjust = 1.4,
hjust = 0.5,
color = "white",
position = position_dodge(0.9),
size = 2.5
) +
# coord_equal(2 / 1)+
theme(text = element_text(size=12))
p <- egg::ggarrange(p1, p2, ncol = 2, widths = c(4,1))
ggsave( here::here("results", "treat", "Treatments.png"),
plot = p,
width = 7.5,
height = 4)session_info()## - Session info ----------------------------------------------------------
## setting value
## version R version 3.6.3 (2020-02-29)
## os Windows 10 x64
## system x86_64, mingw32
## ui RTerm
## language (EN)
## collate English_United States.1252
## ctype English_United States.1252
## tz Europe/London
## date 2020-05-11
##
## - Packages --------------------------------------------------------------
## package * version date lib source
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##
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## [2] C:/Program Files/R/R-3.6.3/library