Nothing
## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
load("ethnobotanydata.rda")
library(dplyr)
library(ethnobotanyR)
library(ggalluvial)
library(ggplot2)
library(ggridges)
library(magrittr)
# in case of rendering issues render with
# rmarkdown::render('vignettes/ethnobotanyr_vignette.Rmd', output_file='ethnobotanyr_vignette.html', output_dir='vignettes')
## -----------------------------------------------------------------------------
citation("ethnobotanyR")
## ---- echo= FALSE-------------------------------------------------------------
knitr::kable(head(ethnobotanydata), digits = 2, caption = "First six rows of the example ethnobotany data included with ethnobotanyR")
## ----ethno_boot_uses----------------------------------------------------------
sp_a_data <- ethnobotanydata %>% filter(sp_name == "sp_a")
sp_a_use <- ethno_boot(sp_a_data$Use_3, statistic = mean, n1 = 1000)
sp_b_data <- ethnobotanydata %>% filter(sp_name == "sp_b")
sp_b_use <- ethno_boot(sp_b_data$Use_3, statistic = mean, n1 = 1000)
## ----ethno_boot_URs-----------------------------------------------------------
quantile(sp_a_use, c(0.05, 0.95))
quantile(sp_b_use, c(0.05, 0.95))
## ----fig.width=7, fig.height=7------------------------------------------------
boot_data <- data.frame(sp_a_use, sp_b_use)
ethno_boot_melt <- reshape2::melt(boot_data)
## ----plot_boot_ridges, fig.width=7, fig.height=4------------------------------
ggplot2::ggplot(ethno_boot_melt, aes(x = value,
y = variable, fill = variable)) +
ggridges::geom_density_ridges() +
ggridges::theme_ridges() +
theme(legend.position = "none") +
labs(y= "", x = "Example Bayesian bootstraps of the probability of use for two species")
## ----ethno_sp_a---------------------------------------------------------------
ethno_sp_a <- dplyr::filter(ethnobotanydata, sp_name == "sp_a")
## ----answers------------------------------------------------------------------
answers <- 2
## ----ethno_compet_sp_a--------------------------------------------------------
ethno_compet_sp_a <- dplyr::recode(ethno_sp_a$informant,
inform_a = 0.9,inform_b = 0.5,inform_c = 0.5,
inform_d = 0.9, inform_e = 0.9, inform_f = 0.5,
inform_g = 0.7,inform_h = 0.5,inform_i = 0.9,
inform_j= 0.9, inform_eight = 0.9,inform_five = 0.6,
inform_four = 0.5,inform_nine = 0.9,
inform_one = 0.5, inform_seven = 0.5,
inform_six= 0.9, inform_ten = 0.9,
inform_three = 0.9, inform_two = 0.5)
## ----ethno_sp_a_bayes---------------------------------------------------------
ethno_sp_a_bayes <- ethnobotanyR::ethno_bayes_consensus(ethno_sp_a,
answers = 2,
#here we keep the default normal distribution with `prior = -1`
prior_for_answers = ethno_compet_sp_a)
## ----heatmap------------------------------------------------------------------
heatmap(ethno_sp_a_bayes)
## ----ethno_sp_a_rich----------------------------------------------------------
set.seed(123) #make random number reproducible
ethno_sp_a_rich <- data.frame(replicate(3,sample(0:10,20,rep=TRUE)))
names(ethno_sp_a_rich) <-
gsub(x = names(ethno_sp_a_rich),
pattern = "X", replacement = "Use_")
ethno_sp_a_rich$informant <- sample(c('User_1', 'User_2'),
20, replace=TRUE)
ethno_sp_a_rich$sp_name <- sample(c('sp_a'),
20, replace=TRUE)
## -----------------------------------------------------------------------------
ethno_compet_sp_a_rich <-
dplyr::recode(ethno_sp_a_rich$informant,
User_1 = 0.9, User_2 = 0.5)
## ----fig.width=7, fig.height=7------------------------------------------------
ethno_sp_a_bayes <- ethnobotanyR::ethno_bayes_consensus(ethno_sp_a_rich,
answers = 10,
prior_for_answers = ethno_compet_sp_a_rich,
prior=-1) #keep a normal prior in this example with -1
## ----fig.width=7, fig.height=7------------------------------------------------
ethno_sp_a_bayes_melt <- ethno_sp_a_bayes %>%
as.data.frame() %>%
reshape2::melt()
## ----fig.width=7, fig.height=4------------------------------------------------
ggplot2::ggplot(ethno_sp_a_bayes_melt, aes(x = value,
y = variable, fill = variable)) +
ggridges::geom_density_ridges() +
ggridges::theme_ridges() +
theme(legend.position = "none")+
labs(y= "", x = "Example ethno_bayes_consensus of use categories for sp_a")
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