https://github.com/tom-n-walker/uphill-plants-soil-carbon
Revision 05e1672664e587a3808d326d6f78d29ca5e44c01 authored by Tom Walker on 07 September 2021, 14:31:53 UTC, committed by Tom Walker on 07 September 2021, 14:32:33 UTC
1 parent bd5cb92
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
load_gh_soil.R
################################################################################
#### Project: Lowland plant migrations alpine soil C loss
#### Title: Function | Load glasshouse pot data
#### Author: Tom Walker (thomas.walker@usys.ethz.ch)
#### Date: 26 May 2021
#### ---------------------------------------------------------------------------
load_gh_soil <- function(){
# load pot level data
pots <- fread("./data/glasshouse_pot_data.csv") %>%
as.data.frame %>%
# drop mixed treatment
filter(Treatment != "Mixed") %>%
# rename treatments
mutate(Treatment = substr(Treatment, 1, 1)) %>%
rename_with(.cols = Pot:Block, tolower)
# load fluxes
fluxes <- fread("./data/glasshouse_incubation_co2.csv") %>%
as.data.frame %>%
# remove mixed treatment
filter(Treatment != "M") %>%
# constrain to 6 weeks
filter(Hours < (6 * 7 * 24 + 0.2)) %>%
select(Day, Hours, Sample:R.ugC.g.h)
# load soil model and add to pot data
twoPool <- fread("./data/glasshouse_soil_pool_model.csv") %>%
as.data.frame %>%
filter(!is.na(p)) %>%
# drop mixed treatment
filter(treatment != "M") %>%
# bind to pot data
select(sample, p:b)
# subset and collate data
soil <- pots %>%
select(pot:block, Cmic.ugC.g:baseMR.ugC.g.h, DOM.a350:DOM.C6) %>%
left_join(., twoPool, by = c("pot" = "sample"))
pots <- pots %>%
select(pot:block, AGB.g:cGS.umol.m2.s) %>%
filter(treatment != "B")
# return
out <- list(
pot_plants = pots,
pot_soil = soil,
mic_resp = fluxes
)
return(out)
}
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