#' Plots results from biophysical indicator functions by site
#'
#' @description Plots results from the functions used to calculate biophysical indicators like: richness(), density(), ttrophic(), fish_biomass(), and fish_size().
#'
#' @param data dataframe generated by any of the following functions: richness(), density(), trophic(), fish_biomass(), and fish_size().
#'
#' @param reserve A quoted string that indicates which site should be used as a reserve.
#'
#' @param control A quoted string that indicates which site should be used as a control zone for the indicated reserve.
#'
#' @param error.bars A logical value indicating if error bars (1 SD) should be plotted.
#'
#' @param x.lab A string to be used as x-axis label
#'
#' @export
#'
#' @author Villasenor-Derbez, J.C.
mpa_plot3 <-
function (data,
reserve = NULL,
control = NULL,
error.bars = F,
y.lab = "Indicador") {
library(ggplot2)
library(dplyr)
library(tidyr)
if (is.null(reserve) | is.null(control)) {
stop("You must specify reserve and control sites")
}
colnames(data) <- c(
"Ano",
"Zonificacion",
"Sitio",
"Transecto",
"Indicador",
"Temperatura",
"Visibilidad",
"Profundidad"
)
data <- data %>% filter(Sitio == reserve | Sitio == control)
p <-
ggplot(data, aes(
x = Ano,
y = Indicador,
color = Zonificacion,
pch = Sitio,
fill = Zonificacion
)) +
geom_jitter(width = 0.1, size = 1) +
stat_summary(geom = "point", fun.y = mean, color = "black", size = 2, alpha = 0.5) +
stat_summary(geom = "line", fun.y = mean, color = "black", alpha = 0.5) +
stat_summary(fun.data = mean_se, geom = "ribbon", alpha = 0.5) +
scale_color_brewer(palette = "Set1") +
scale_fill_brewer(palette = "Set1") +
theme_bw() +
labs(x = "Ano", y = y.lab)
if (error.bars) {
p <- p + geom_errorbar(aes(ymin = Indicator - SD, ymax = Indicator +
SD), width = 0.2)
}
p
}
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