Last updated: 2021-05-07

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Introduction

knitr::opts_chunk$set(echo = TRUE, 
                      warning = FALSE, 
                      message = FALSE)
library("tidyverse")
library("here")
library("rtrim")
library("trend")
library("DT")
  • Read data and compute the abundance average by year
passerine <- read_csv(here::here("data/passerine.csv")) 
passerine_abbreviations <- read_csv(here::here("data/passerine_abbrev.csv")) 

passerine.ab <- passerine %>% 
  rename(sp = sp.abb) %>% 
  dplyr::select(-especie) %>% 
  group_by(sp, year, habitat) %>% 
  summarise(ab_avg = round(mean(den, na.rm=TRUE),2), 
            sd = sd(den, na.rm = TRUE), 
            se = sd/sqrt(length(den)), 
            n = length(den))

Explore Abundances as index

  • For each species we compute the abundance index, i.e. relative abundance comparing with initial values (\(ab_{index} = abundance_{time_{i}} / abundance_{time_{0}}\))

  • Data was exported as (data/passerine_ab.csv)

compute_abindex <- function(x){
  ab.base <- x %>% filter(year == min(x$year)) %>% pull(ab_avg)
  out <- x %>% mutate(ab.index = ab_avg/ab.base) %>% dplyr::select(year,ab.index)
  return(out)
}

cumbres <- passerine.ab %>% 
  filter(habitat == "cumbres") 
cumbres.index <- cumbres %>% 
  group_by(sp) %>% group_modify(
    ~ {compute_abindex(.x)})
cumbres <-cumbres %>%  inner_join(cumbres.index)


enebral <- passerine.ab %>% 
  filter(habitat == "enebral") 
enebral.index <- enebral %>% 
  group_by(sp) %>% group_modify(
    ~ {compute_abindex(.x)})
enebral <- enebral %>%  inner_join(enebral.index)

robledal <- passerine.ab %>% 
  filter(habitat == "robledal") 
robledal.index <- robledal %>% 
  group_by(sp) %>% group_modify(
    ~ {compute_abindex(.x)})
robledal <- robledal %>%  inner_join(robledal.index)

passerine.abindex <- bind_rows(cumbres, enebral, robledal) %>% 
  inner_join(passerine_abbreviations, by = c("sp" = "sp.abb"))

write_csv(passerine.abindex, here::here("data/passerine_ab.csv"))
bird_theme <- 
  ggplot2::theme_bw() + 
  ggplot2::theme(
    panel.grid.minor = element_blank(),
    strip.background = element_blank()
  )
# Generate functions to plot abundances and abundance index 
plotabundances <- function(df, myhabitat, selected_especies){
  df %>% 
  filter(habitat == myhabitat) %>% 
  filter(stringr::str_detect(especie, selected_especies)) %>%
  ggplot(aes(x=as.factor(year), y=ab_avg)) + 
  geom_errorbar(aes(ymin = ab_avg - se, 
                    ymax = ab_avg + se),
                width = 0.2) +
  geom_point() +
  geom_point(aes(x=as.factor(year), y=ab.index), color = "red", shape=15) + 
  geom_hline(yintercept = 1, colour="red", linetype = "dashed") + 
  facet_wrap(~especie) + 
  geom_line(aes(x=as.factor(year), y=ab.index, group=1), colour = "red") +
  ylab("abundance (ind / 10ha)") + xlab("") + 
  bird_theme + 
  ggtitle(myhabitat)
} 

plotabindex <- function(df, myhabitat, selected_especies){
  df %>% 
  filter(habitat == myhabitat) %>% 
  filter(stringr::str_detect(especie, selected_especies)) %>%
  ggplot(aes(x=as.factor(year), y=ab.index)) + 
  geom_point(color = "red", shape=15) + 
  geom_hline(yintercept = 1, colour="red", linetype = "dashed") + 
  facet_wrap(~especie) + 
  geom_line(aes(x=as.factor(year), y=ab.index, group=1), colour = "red") +
  ylab("abundance (ind / 10ha)") + xlab("") + 
  bird_theme + 
  ggtitle(myhabitat)
} 
sp_cumbres <- "Card|Oena|Phoeni|collaris"
sp_enebral <- "Alauda|Anthus|cannabina|Embe|Oena|Phoeni|collaris|conspici|Troglo"
sp_robledal <- "Aeg|cannabina|Certhia|Cyanis|Erith|Fringi|Garrulus|Lullula|Parus|Peripares|Phoeni|bonelli|Regulus|rubicola|serinus|Sitta|atricapilla|cantillans|merula|visci|Troglo"

# enebral rubicola
# robledal Lopho
plotabundances(df = passerine.abindex, 
           myhabitat = "cumbres",
           selected_especies = sp_cumbres)

plotabundances(df = passerine.abindex, 
           myhabitat = "enebral",
           selected_especies = sp_enebral)

plotabundances(df = passerine.abindex, 
           myhabitat = "robledal",
           selected_especies = sp_robledal)
plotabindex(df = passerine.abindex, 
           myhabitat = "cumbres",
           selected_especies = sp_cumbres)

Version Author Date
725547c Antonio J Perez-Luque 2021-05-05 
plotabindex(df = passerine.abindex, 
           myhabitat = "enebral",
           selected_especies = sp_enebral)

Version Author Date
725547c Antonio J Perez-Luque 2021-05-05 
plotabindex(df = passerine.abindex, 
           myhabitat = "robledal",
           selected_especies = sp_robledal)

Version Author Date
725547c Antonio J Perez-Luque 2021-05-05