Nothing
#' Compare RSI, IBR, and Cliff's delta
#'
#' \code{compare} calculates RSI assigned values, IBR translated scores, and
#' Cliff's delta in the hypothetical case study.
#'
#' @param sam a data frame, the first output of \code{\link{simul}}.
#' @param sam_mean a data frame, the third output of \code{\link{simul}}.
#'
#' @references Blaise, C., Gagné, F., Pellerin, J., Hansen, P.-D., & Trottier,
#' S. (2002). Molluscan shellfish biomarker study of the Quebec, Canada,
#' Saguenay Fjord with the soft-shell clam, Mya arenaria. Environmental
#' Toxicology, 17(3), 170–186. \doi{10.1002/tox.10048}. \cr \cr Beliaeff, B.,
#' & Burgeot, T. (2002). Integrated biomarker response: A useful tool for
#' ecological risk assessment. Environmental Toxicology and Chemistry, 21(6),
#' 1316–1322. \doi{10.1002/etc.5620210629}.
#'
#' @return \code{compare} returns a list of length 5: \item{\code{blaise}}{RSI
#' assigned values and final RSI.} \item{\code{beliaeff}}{IBR translated
#' scores and final IBR.} \item{\code{pham}}{Cliff's delta and the average of
#' absolute Cliff’s delta.} \item{\code{fig1}}{ggplot object of comparisions
#' among RSI assigned values, IBR translated scores, and Cliff's delta.}
#' \item{\code{fig2}}{ggplot object of comparision among RSI, IBR, and the
#' average of absolute Cliff’s delta.}
#'
#' @examples
#' \donttest{
#' set.seed(1)
#' setting <- setpop()
#' temp <- simul(setting$pop_mean)
#' compare(temp$sam, temp$sam_mean)
#' } #might take more than 5s in some machines
#'
#' @export
compare <- function(sam, sam_mean){
Index <- Biomarker <- Value <- Bmk1 <- Bmk5 <- Site <- avg <- NULL #no visible binding for global variable
fivecolor <- c("#E69F00", "#56B4E9" , "#009E73" , "#D55E00" , "#CC79A7")
blaise <- blaise2002(sam, sam_mean)
beliaeff <- beliaeff2002(sam_mean)
pham_full <- mbr(sam)
p1 <- blaise %>% select(-Index) %>% gather(Biomarker, Value, Bmk1:Bmk5) %>%
ggplot(aes(x = Site,
y = Value,
group = 1)) +
geom_line(size = 1.5, color = rep(
fivecolor,
each = 5
)) + geom_point(size = 5, shape = 21, color = "white", fill = rep(
fivecolor,
each = 5
)) +
facet_wrap(~ Biomarker, nrow = 1) +
ylab("RSI assigned value")+
xlab(NULL)+
theme_minimal_grid(font_size = 14, rel_small = 1) +
theme(
axis.text.x=element_blank()
)
p2 <- beliaeff %>% select(-Index) %>% gather(Biomarker, Value, Bmk1:Bmk5) %>%
ggplot(aes(x = Site,
y = Value,
group = 1)) +
geom_line(size = 1.5, color = rep(
fivecolor,
each = 5
)) + geom_point(size = 5, shape = 21, color = "white", fill = rep(
fivecolor,
each = 5
)) +
facet_wrap(~ Biomarker, nrow = 1) +
ylab("IBR translated score")+
xlab(NULL)+
theme_minimal_grid(font_size = 14, rel_small = 1) +
theme(strip.text.x = element_blank(),
axis.text.x=element_blank()
)
pham <- pham_full$idx %>% add_row(
Site = "S0",
Bmk1 = 0,
Bmk2 = 0,
Bmk3 = 0,
Bmk4 = 0,
Bmk5 =0,
avg = 0,
.before = 1
)
p3 <- pham %>% select(-avg) %>% gather(Biomarker, Value, Bmk1:Bmk5) %>%
ggplot(aes(x = Site,
y = Value,
group = 1)) +
geom_hline(yintercept = 0, linetype="dashed", size = 1)+
geom_line(size = 1.5, color = rep(
fivecolor,
each = 5
)) + geom_point(size = 5, shape = 21, color = "white", fill = rep(
fivecolor,
each = 5
)) +
facet_wrap(~ Biomarker, nrow = 1) +
ylab("Cliff's delta")+
theme_minimal_grid(font_size = 14, rel_small = 1) +
theme(strip.text.x = element_blank())
fig1 <- plot_grid(p1, p2, p3, ncol = 1, align ="hv", labels="auto")
p4 <- blaise %>%
ggplot(aes(x = Site,
y = Index,
group = 1)) +
geom_line(size = 1.5, color = "#0072B2") + geom_point(size = 5, shape = 22, color = "white", fill = "#0072B2") +
labs(x = NULL, y = NULL, title = "RSI") +
theme_cowplot(font_size = 14, rel_small = 1) +
theme(plot.title = element_text(hjust = 0.5))
p5 <- beliaeff %>%
ggplot(aes(x = Site,
y = Index,
group = 1)) +
geom_line(size = 1.5, color = "#0072B2") + geom_point(size = 5, shape = 23, color = "white", fill = "#0072B2") +
labs(y = NULL, title = "IBR") +
theme_cowplot(font_size = 14, rel_small = 1) +
theme(plot.title = element_text(hjust = 0.5))
p6 <- pham %>%
ggplot(aes(x = Site,
y = avg,
group = 1)) +
geom_line(size = 1.5, color = "#0072B2") + geom_point(size = 5, shape = 24, color = "white", fill = "#0072B2") +
labs(x = NULL, y = NULL, title = "Average |Cliff's delta|") +
theme_cowplot(font_size = 14, rel_small = 1) +
theme(plot.title = element_text(hjust = 0.5))
fig2 <- plot_grid(p4, p5, p6, nrow = 1, align ="hv")
list(
blaise = blaise,
beliaeff = beliaeff,
pham = pham,
fig1 = fig1,
fig2 = fig2
)
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.