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_soil.R
################################################################################
#### Project: Lowland plant migrations alpine soil C loss
#### Title: Function | Load soil data
#### Author: Tom Walker (thomas.walker@usys.ethz.ch)
#### Date: 26 May 2021
#### ---------------------------------------------------------------------------
load_soil <- function(){
# load pools
pools <- fread("./data/field_soil_data.csv") %>%
# edit treatment and column names, remove species data
mutate(Treatment = substr(Treatment, nchar(Treatment), nchar(Treatment))) %>%
mutate(Site = tolower(Site)) %>%
# add leading zero to block
mutate(Block = ifelse(
nchar(Block) == 3,
Block,
paste0(substr(Block, 1, 1), "0", substr(Block, 2, 2))
)) %>%
# sort column names and select variables
dplyr::rename_with(.cols = Sample:Treatment, tolower) %>%
select(-sample) %>%
as.data.frame
# load lavey extra data and combine
lav <- fread("./data/field_deep_soil_data.csv") %>%
as.data.frame %>%
select(Block:Elevation, MR.ugC.g.h:CUE) %>%
rename_with(.cols = Block:Elevation, tolower) %>%
mutate(site = "lavey") %>%
# add leading zero to block
mutate(block = ifelse(
nchar(block) == 3,
block,
paste0(substr(block, 1, 1), "0", substr(block, 2, 2))
)) %>%
mutate(treatment = substr(treatment, nchar(treatment), nchar(treatment)))
# combine
out <- pools %>%
left_join(., lav, by = c("site", "block", "treatment", "elevation")) %>%
# setup proper units
rename(Rm = MR.ugC.g.h,
Gm = MG.ugC.g.h,
RmM = MRm.ugCmic.g.h,
GmM = MGm.ugCmic.g.h) %>%
mutate(Cmic = Cmic/1000,
CUE = CUE*100,
RmM = RmM * 1000,
GmM = GmM * 1000)
# return
return(out)
}
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