diversity
Antonio J Perez-Luque
2021-05-03
Last updated: 2021-05-20
Checks: 7 0
Knit directory: booksn_dispersantes/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | b847df4 | Antonio J Perez-Luque | 2021-05-20 | Build site. |
| Rmd | 6724023 | Antonio J Perez-Luque | 2021-05-20 | filter Delichon urbicum |
| html | 4d72c1e | Antonio J Perez-Luque | 2021-05-10 | Build site. |
| Rmd | dee25a5 | Antonio J Perez-Luque | 2021-05-10 | update diversity index |
| html | 684a3f9 | Antonio J Perez-Luque | 2021-05-07 | Build site. |
| html | ce17a57 | Antonio J Perez-Luque | 2021-05-07 | Build site. |
| Rmd | 73addc3 | Antonio J Perez-Luque | 2021-05-07 | add richness analysis |
| html | dad5db5 | Antonio J Perez-Luque | 2021-05-06 | Build site. |
| Rmd | 4ef40a7 | Antonio J Perez-Luque | 2021-05-06 | compare diversity by temporal steps |
| html | 12af27d | Antonio J Perez-Luque | 2021-05-03 | Build site. |
| Rmd | 5306189 | Antonio J Perez-Luque | 2021-05-03 | compute diversity (alpha) analysis |
Diversity analysis
- Compute Simpson and Shannon diversity index. See diversity functions in vegan pkg.
knitr::opts_chunk$set(echo = TRUE,
warning = FALSE,
message = FALSE)library("tidyverse")
library("here")
library("vegan")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))
df <- passerine.ab %>%
unite("site", habitat:year, sep="_", remove = FALSE) %>%
dplyr::select(-sd, -se, -n) %>%
pivot_wider(names_from = sp,
values_from = ab_avg,
values_fill = 0)Create a function to compute Simpson and Shannon diversity indices
computeDiversity <- function(d, hab, ...){
df.habitat <- d %>%
filter(habitat == hab) %>%
dplyr::select(-habitat, -site) %>%
dplyr::select_if(
negate(function(x) is.numeric(x) && sum(x) == 0)) %>%
column_to_rownames("year")
shannon <- diversity(df.habitat, "shannon") %>%
as.data.frame() %>% rownames_to_column("year") %>%
rename(shannon = starts_with("."))
simpson <- diversity(df.habitat, "simpson") %>%
as.data.frame() %>%
rownames_to_column("year") %>%
rename(simpson = starts_with("."))
diver <- shannon %>%
inner_join(simpson) %>%
mutate(habitat = hab)
return(diver)
}- Compute diversity index for each site
diver.summits <- computeDiversity(df, "cumbres")
diver.juniper <- computeDiversity(df, "enebral")
diver.robledal <- computeDiversity(df, "robledal")
diversity_index <- bind_rows(diver.summits, diver.juniper, diver.robledal)
write_csv(diversity_index, here::here("output/diversity/alfa_diversity.csv"))diversity_plot <- diversity_index %>%
filter(!(habitat == "cumbres" & year == 2013)) %>%
ggplot(
aes(x=year, y=shannon, colour=habitat, group=habitat)) +
geom_point() + geom_line() +
geom_smooth(method = "lm",
se=FALSE, size = .5, linetype="dashed") +
ylab("Shannon Index (H')") +
theme_bw() +
theme(
panel.grid = element_blank(),
#panel.grid.major.x = element_blank(),
strip.background = element_blank()
)
ggsave(here::here("output/diversity/diversity_habitat.pdf"),
width = 18, height = 12, units = "cm")
diversity_plot
dev.off()null device
1 Compare three temporal times
- Generate three temporal times: 1983; 2009: mean for 2008 - 2009; and 2018: mean for 2017 - 2018.
shannon <- diversity_index %>%
filter(year %in% c(1981:1985, 2008:2009, 2017:2018)) %>%
mutate(yearF = case_when(
year %in% c(1981:1985) ~ as.character(1983),
year %in% c(2008:2009) ~ as.character(2009),
year %in% c(2017:2018) ~ as.character(2018)
)) %>%
group_by(yearF, habitat) %>%
summarise(mean = mean(shannon, na.rm=TRUE),
sd = sd(shannon, na.rm=TRUE),
se = sd/sqrt(length(shannon)))
shannon %>%
ggplot(aes(x=yearF, y=mean, group=1)) +
geom_point() +
geom_line() +
# geom_bar(stat="identity", fill="black") +
geom_errorbar(aes(ymax = mean + se, ymin= mean - se),
width = .2, size = .3) +
facet_wrap(~habitat, ncol = 1) +
theme_bw() +
theme(
panel.grid.minor = element_blank(),
strip.background = element_blank()
) +
ylab("Shannon Index (H')") + xlab("")
Richness
richness <- passerine.ab %>%
group_by(habitat, year) %>%
summarise(richness = length(sp))
write_csv(richness, here::here("output/diversity/richness.csv"))richness %>%
ggplot(aes(as.factor(year), richness)) +
geom_point() +
geom_path(aes(group=habitat)) +
facet_wrap(~habitat, nrow = 3) +
ylab("Richness (n sps)") + xlab("") +
theme_bw() +
theme(
panel.grid.minor = element_blank(),
strip.background = element_blank()
)
richness %>%
filter(year %in% c(1981:1985, 2008:2009, 2017:2018)) %>%
mutate(yearF = case_when(
year %in% c(1981:1985) ~ as.character(1983),
year %in% c(2008:2009) ~ as.character(2009),
year %in% c(2017:2018) ~ as.character(2018)
)) %>%
group_by(yearF, habitat) %>%
summarise(mean = mean(richness, na.rm=TRUE),
sd = sd(richness, na.rm=TRUE),
se = sd/sqrt(length(richness))) %>%
ggplot(aes(x=yearF, y=mean, group=1)) +
geom_point() +
geom_line() +
# geom_bar(stat="identity", fill="black") +
geom_errorbar(aes(ymax = mean + se, ymin= mean - se),
width = .2, size = .3) +
facet_wrap(~habitat, ncol = 1) +
theme_bw() +
theme(
panel.grid.minor = element_blank(),
strip.background = element_blank()
) 
sessionInfo()R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.3
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] vegan_2.5-7 lattice_0.20-41 permute_0.9-5 here_1.0.1
[5] forcats_0.5.1 stringr_1.4.0 dplyr_1.0.4 purrr_0.3.4
[9] readr_1.4.0 tidyr_1.1.2 tibble_3.0.6 ggplot2_3.3.3
[13] tidyverse_1.3.0 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 lubridate_1.7.10 assertthat_0.2.1 rprojroot_2.0.2
[5] digest_0.6.27 R6_2.5.0 cellranger_1.1.0 backports_1.2.1
[9] reprex_1.0.0 evaluate_0.14 highr_0.8 httr_1.4.2
[13] pillar_1.4.7 rlang_0.4.10 readxl_1.3.1 rstudioapi_0.13
[17] whisker_0.4 jquerylib_0.1.3 Matrix_1.3-2 rmarkdown_2.6.6
[21] labeling_0.4.2 splines_4.0.2 munsell_0.5.0 broom_0.7.4
[25] compiler_4.0.2 httpuv_1.5.5 modelr_0.1.8 xfun_0.20
[29] pkgconfig_2.0.3 mgcv_1.8-33 htmltools_0.5.1.1 tidyselect_1.1.0
[33] crayon_1.4.1 dbplyr_2.1.0 withr_2.4.1 later_1.1.0.1
[37] MASS_7.3-53 grid_4.0.2 nlme_3.1-152 jsonlite_1.7.2
[41] gtable_0.3.0 lifecycle_1.0.0 DBI_1.1.1 git2r_0.28.0
[45] magrittr_2.0.1 scales_1.1.1 cli_2.3.0 stringi_1.5.3
[49] farver_2.0.3 fs_1.5.0 promises_1.2.0.1 xml2_1.3.2
[53] bslib_0.2.4 ellipsis_0.3.1 generics_0.1.0 vctrs_0.3.6
[57] tools_4.0.2 glue_1.4.2 hms_1.0.0 parallel_4.0.2
[61] yaml_2.2.1 colorspace_2.0-0 cluster_2.1.0 rvest_0.3.6
[65] knitr_1.31 haven_2.3.1 sass_0.3.1