In clarkbar88/TDA: Trend Detection Anaysis

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(TDA)
library(tidyverse)
library(lubridate)

Load in data from package and select sites with at least 8 years of data

data(all_bibi_data)

sites_with_8plus_years<-all_bibi_data %>%
  group_by(Sites) %>%
  summarise(n=length(Year)) %>%
  filter(n>=8) %>%
  pull(Sites)

Set up a threshold for the trend magnitude of ecological significance

threshold=-1*0.5

Complete trend and power analysis

power_out<-all_bibi_data %>%
  filter(Sites %in% sites_with_8plus_years) %>%
  #filter(Sites %in% sites_with_8plus_years[1:5]) %>%
  select(Sites,Year,BIBI=`Overall Score`) %>%
  with(.,TDA_Power(value=BIBI,year=Year,site=Sites,trend.magnitude.threshold = threshold))

Let's peak at that table

knitr::kable(
head(power_out) 
)

power_out %>%
  mutate(Result=factor(Result,levels=c('Decreasing','Inadequate Data','Maintaining','Increasing'),
                       labels=c('Degrading','Inadequate Data','Maintaining','Improving'))) %>%
  ggplot()+
  geom_bar(aes(x=1,fill=Result),col='black',position = position_stack())+
  theme_bw()+
  theme(axis.text.x = element_blank(),
        axis.title.x = element_blank(),
        axis.ticks.x=element_blank())