https://github.com/tom-n-walker/uphill-plants-soil-carbon
Tip revision: 05e1672664e587a3808d326d6f78d29ca5e44c01 authored by Tom Walker on 07 September 2021, 14:31:53 UTC
Added all analyses, streamlined pipelines and improved statistical models. Removed data export (all done via drake cache).
Added all analyses, streamlined pipelines and improved statistical models. Removed data export (all done via drake cache).
Tip revision: 05e1672
compute_cover.R
################################################################################
#### Project: Lowland plant migrations alpine soil C loss
#### Title: Function | Basic formatting of relevee data
#### Author: Tom Walker (thomas.walker@usys.ethz.ch)
#### Date: 26 May 2021
#### ---------------------------------------------------------------------------
compute_cover <- function(raw_relevees){
## Filter for 2017 year only ----
quad_2017 <- lapply(raw_relevees$quadrats, function(x) x %>% filter(year == 2017))
rele_2017 <- lapply(raw_relevees$relevees, function(x) x %>% filter(year == 2017))
## Match quadrants and relevees to collar data ----
# quadrants
quad_matched <- lapply(
quad_2017,
semi_join,
y = raw_relevees$collars,
by = "grid_id"
)
# relevees
rele_matched <- lapply(
rele_2017,
semi_join,
y = raw_relevees$collars,
by = "grid_id"
)
## Quantify bare ground and species cover ----
# bare ground
quad_bare <- lapply(
quad_matched,
function(x){
x %>%
filter(quadrant_fail != "M") %>%
group_by(grid_id) %>%
summarize(total_cover = sum(cover_cm2_bare_soil, na.rm = T)) %>%
ungroup %>%
as.data.frame %>%
mutate(species = "bare ground")
}
)
# species covers
rele_sum <- lapply(
rele_matched,
function(x){
x %>%
group_by(grid_id, species) %>%
summarize(total_cover = sum(cover_cm2, na.rm = T)) %>%
ungroup %>%
as.data.frame
}
)
## Format output ----
# unlist to data frames
bare_long <- do.call(rbind, quad_bare)
rele_long <- do.call(rbind, rele_sum)
all_long <- rbind(bare_long, rele_long)
# identify site information
hilo_id <- substr(all_long$grid_id, 1, 3)
calanda <- hilo_id %in% c("Cal", "Nes")
# combine, add site_id, rearrange
all_out <- all_long %>%
mutate(site = if_else(calanda, "calanda", "lavey")) %>%
arrange(grid_id, species) %>%
remove_rownames
# return
return(all_out)
}