https://github.com/tom-n-walker/uphill-plants-soil-carbon
Revision 5c297ab275e1dd929f9b8db7c86d957ddf0fd6dd authored by Tom Walker on 07 September 2021, 14:31:53 UTC, committed by Tom Walker on 07 September 2021, 14:31:53 UTC
1 parent bd5cb92
Tip revision: 5c297ab275e1dd929f9b8db7c86d957ddf0fd6dd authored by Tom Walker on 07 September 2021, 14:31:53 UTC
Added all analyses, streamlined pipelines and improved statistical models.
Added all analyses, streamlined pipelines and improved statistical models.
Tip revision: 5c297ab
drake_plan.R
################################################################################
#### Project: SNF field experiment
#### Title: Drake plan
#### Author: Tom Walker (thomas.walker@usys.ethz.ch)
#### Date: 26 March 2021
#### ---------------------------------------------------------------------------
#### PROLOGUE ------------------------------------------------------------------
## Options ----
# remove objects from global environment
rm(list = ls())
# configure default R session options (no factors, bias against scientific #s)
options(stringsAsFactors = F,
scipen = 6)
## Libraries ----
source("packages.r")
## Code ----
sapply(list.files("./r_code",full.names = T), source)
#### PLANS ---------------------------------------------------------------------
## Load data ----
load_plan <- drake_plan(
raw_relevees = load_relevees(),
raw_soil = load_soil(),
flux_data = load_fluxes(),
full_try = load_try(),
gh_plants = load_gh_plants(),
gh_soil = load_gh_soil()
)
## Format field data ----
field_plan <- drake_plan(
cover_data = format_relevees(
raw_relevees = raw_relevees
),
trait_data = process_try(
cover_data = cover_data,
full_try = full_try
),
field_data = combine_field_data(
cover_data = cover_data,
trait_data = trait_data,
raw_soil = raw_soil
),
field_data_subset = subset_field_plants(
field_data = field_data
)
)
# ## Write all data to file ----
# export_plan <- drake_plan(
# localExport = target(
# command = {
# save(
# # Original species information
# edAllSpp,
# # Species information
# pfSpecies, edSpecies,
# # Phylogenies
# pfPhylogeny, edPhylogeny,
# # Trait data
# pfTraits, edTraits,
# pfTraitsPCA, edTraitsPCA,
# # Metabolite data
# pfMtbs, edMtbs,
# pfMtbsDiv, edMtbsDiv,
# pfMtbsPCoA, edMtbsPCoA,
# # Biogeography data
# pfBioGeo, edBioGeo,
# pfClimPCA, edClimPCA,
# # Output
# file = file_out("./data/exported/all_data.RData")
# )
# save(
# # Full biogeographic data for plotting
# pfBioGeoAll, edBioGeoAll,
# # Output
# file = file_out("./data/exported/geo_data.RData")
# )
#
# }
# )
# )
#### MAKE ----------------------------------------------------------------------
## Collate plans ----
weAreGo <- bind_rows(
load_plan,
field_plan
)
## Make ----
make(weAreGo)
Computing file changes ...