Last updated: 2021-07-06
Checks: 7 0
Knit directory: emlr_mod_v_XXX/
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Ignored: .Rhistory
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Untracked files:
Untracked: doc_prepare/
Untracked: docs_1982-1999_2000-2012_GC_0.5/
Untracked: docs_1982-1999_2000-2012_GV_1.0/
Untracked: docs_1982-1999_2000-2012_RC_3.1/
Untracked: docs_1982-1999_2000-2012_RC_SO_1.6/
Untracked: docs_1982-1999_2000-2012_RV_3.4/
Untracked: docs_1982-1999_2000-2012_RV_SO_1.8/
Untracked: docs_2000-2009_2010-2019_GC_1.3/
Untracked: docs_2000-2009_2010-2019_GV_1.5/
Untracked: docs_2000-2009_2010-2019_RV_1.2/
Unstaged changes:
Modified: data/auxillary/params_local.rds
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| Rmd | 8e8abf5 | Jens Müller | 2020-12-18 | Initial commit |
The following local parametrisations (i.e. relevant for this sensitivity run) were defined to run the analysis:
# neutral density thresholds to cut the Atlantic ocean into slabs
slabs_Atl <-
c(
-Inf,
26.00,
26.50,
26.75,
27.00,
27.25,
27.50,
27.75,
27.85,
27.95,
28.05,
28.10,
28.15,
28.20,
Inf
)
# neutral density thresholds to cut the Indo-Pacific ocean into slabs [increase 28.20, 28.30]
slabs_Ind_Pac <-
c(-Inf,
26.00,
26.50,
26.75,
27.00,
27.25,
27.50,
27.75,
27.85,
27.95,
28.05,
28.10,
28.20,
28.30,
Inf)
# Predictors for MLR model
MLR_predictors <- c(
"sal",
"temp",
# "oxygen",
"aou",
"nitrate",
"silicate",
# "silicate_star",
"phosphate",
"phosphate_star")
params_local <-
lst(
# the GOBM used for subsetting, currently with options of CESM ("") or NorESM ("NorESM/") or FESOM_REcoM_LR ("FESOM_REcoM_LR/")
GOBM = "",
# model climate forcing with options of variable ("AD") or constant ("CB")
model_runs = "CB",
# model subsetting with options of "GLODAP" or "random"
subsetting = "random",
# random subsetting with options of "grid" or "lat"
random = "lat",
# ID of current sensitivity run
Version_ID = "v_XXX",
# f flags accepted for GLODAP data
flag_f = c(2, 0),
# qc flags accepted for GLODAP data
flag_qc = c(1, 0),
# Should A16 cruise from 2013/14 be included in middle era (y/n)
A16_GO_SHIP = "n",
# Shallowest depth for data to be included in MLR fitting
depth_min = 150,
# Shallowest water depth for data to be included in MLR fitting
bottomdepth_min = 0,
# Lowest neutral density to map Cant with eMLR approach (in surface layer?)
gamma_min = 26,
# break years for eras, numbers indicate the upper end of the respective era
era_breaks_GLODAP_start = c(1982, 2000, 2010),
era_breaks_GLODAP_end = c(1999, 2009, 2019),
era_breaks_random_start = c(1982, 2000, 2010),
era_breaks_random_end = c(1999, 2009, 2019),
# era_breaks_GLODAP = c(1981, 1999, 2009, Inf),
# era_breaks_random = c(1981, 1999, 2009, Inf),
# whether use median year as the tref
median_tref = "y",
# ID for basins for MLR fits: 2, 5, SO, AIP
MLR_basins = "2",
# Select the target variable for MLR, either "tco2", "cstar" or "cstar_tref"
MLR_target = "cstar_tref",
# see above
MLR_predictors = MLR_predictors,
# Maximum number of MLR predictors
MLR_predictors_max = 5,
# Minimum number of MLR predictors
MLR_predictors_min = 2,
# Total number of MLR fits taken into account
MLR_number = 10,
# Fitted model type rlm or lm
MLR_type = "lm",
# Criterion to select best MLR fits, either "rmse" or "aic" or "rank"
MLR_criterion = "rmse",
# VIF threshold (set vif = 1000 to apply slightly vif filter)
vif_max = 1000,
# see above
slabs_Atl = slabs_Atl,
# see above
slabs_Ind_Pac = slabs_Ind_Pac,
# Stoichiometric ratio of C to P
rCP = 117,
# Stoichiometric ratio of N to P
rNP = 16,
# Stoichiometric ratio of P to O (PO4* calculation)
rPO = 170,
# Offset P to O (PO4* calculation)
rPO_offset = 1.95,
# surface DIC calculation with options of "revelle factor" or "atmospheric equilibrium" or "atmospheric pCO2 increase"
surface_DIC_calculation = "revelle factor",
# Preindustrial atmospheric pCO2
preind_atm_pCO2 = 280,
# generate a high number of diagnostic plots while running the analysis (y/n)
plot_all_figures = "n"
)Parameterization criteria are locally stored and used throughout this sensitivty case.
params_local %>%
write_rds(here::here("data/auxillary",
"params_local.rds"))Folders for each new sensitivity run are automatically created.
sessionInfo()R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: openSUSE Leap 15.2
Matrix products: default
BLAS: /usr/local/R-4.0.3/lib64/R/lib/libRblas.so
LAPACK: /usr/local/R-4.0.3/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] forcats_0.5.0 stringr_1.4.0 dplyr_1.0.5 purrr_0.3.4
[5] readr_1.4.0 tidyr_1.1.2 tibble_3.0.4 ggplot2_3.3.3
[9] tidyverse_1.3.0 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] tidyselect_1.1.0 xfun_0.20 haven_2.3.1 colorspace_2.0-0
[5] vctrs_0.3.6 generics_0.1.0 htmltools_0.5.0 yaml_2.2.1
[9] blob_1.2.1 rlang_0.4.10 later_1.1.0.1 pillar_1.4.7
[13] withr_2.3.0 glue_1.4.2 DBI_1.1.0 dbplyr_1.4.4
[17] readxl_1.3.1 modelr_0.1.8 lifecycle_1.0.0 cellranger_1.1.0
[21] munsell_0.5.0 gtable_0.3.0 rvest_0.3.6 evaluate_0.14
[25] knitr_1.30 httpuv_1.5.4 fansi_0.4.1 broom_0.7.5
[29] Rcpp_1.0.5 promises_1.1.1 backports_1.1.10 scales_1.1.1
[33] jsonlite_1.7.2 fs_1.5.0 hms_0.5.3 digest_0.6.27
[37] stringi_1.5.3 rprojroot_2.0.2 grid_4.0.3 here_1.0.1
[41] cli_2.2.0 tools_4.0.3 magrittr_2.0.1 crayon_1.3.4
[45] whisker_0.4 pkgconfig_2.0.3 ellipsis_0.3.1 xml2_1.3.2
[49] reprex_0.3.0 lubridate_1.7.9 assertthat_0.2.1 rmarkdown_2.5
[53] httr_1.4.2 rstudioapi_0.13 R6_2.5.0 git2r_0.27.1
[57] compiler_4.0.3