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library(tidyverse)
library(lubridate)Following parameterizations were are saved to an .rds file and will be used to run analysis and display results:
parameters <-
lst(
# flush duration after zeroing of the HydroC pCO2 sensor
HC_flush_duration = 600,
# mixing duration after zeroing of the HydroC pCO2 sensor
HC_mixing_duration = 20,
# date of switching between 1W- and 8W- pump
pump_switch = ymd_hms("2018-07-17;13:08:34"),
# duration of intervals to be used for tau determination
duration_intervals = seq(150,500,50),
# pCO2 residual limit for tau determination
pCO2_resid_lim = 1,
# window width in seconds used to smooth RT corrected pCO2
smoothing_duration = 30,
# scaling factors used to test optimization of tau determination
tau_factors = seq(0.8, 1.6, 0.2),
# scaling factor used to optimize tau
tau_factor_used = 1,
# ID used to produce example plots
example_ID = "180802",
# station used to produce example plots
example_station = "P03",
# width for vertical gridding of profiles
dep_grid = 1,
# max depth for data analysis
max_dep = 25,
# max depth for checking of data gaps
max_dep_gap = 20,
# max number of accepted data gaps
max_gap = 3,
# max depth threshold for entire profile to be included in RT quality assessment
RT_stats_dep_max = 30,
# max pCO2 for RT quality assessment
RT_stats_pCO2_max = 300,
# max sampling depth included for RT quality assessment
RT_stats_dep = 20,
# max depth considered for surface data
surface_dep = 6,
# integration depths tested for NCP quantification
fixed_integration_depths = seq(9,13,1),
# density thresholds for integration depths tested for NCP quantification
rho_lim_integration_depths = c(0.1,0.2,0.5),
# density thresholds for integration depths used for NCP quantification
rho_lim = 0.1,
# integration depth for NCP quantification
i_dep_lim = 12,
# maximum depth of vertical mixing event
i_dep_mix_lim = 17,
# stations not used in this study
stations_out = c("PX1", "PX2", "P14", "P13", "P01"),
# cruise dates not used in this study
dates_out = c("180616","180820"),
# profiling phases used for quality assessment and analysis
phases_in = c("down", "up"),
# box limits for inclusion of SOOP Finnmaid data
fm_box_lon = c(18.9, 19.5, 19.5, 18.9),
fm_box_lat = c(57.4, 57.2, 57.45, 57.61),
# box limits for map
map_lat_lo = 57.25,
map_lat_hi = 57.6,
map_lon_lo = 18.6,
map_lon_hi = 19.7,
# coordinates of Herrvik harbor
herrvik_lat = 57.421658,
herrvik_lon = 18.914558,
# coordinates of ICOS flux tower on Ostergarnsholm
ostergarn_lat = 57.430544,
ostergarn_lon = 18.984387,
# stations used for analysis of phytoplankton data
stations_in_phytoplankton = c("P07", "P10"),
# class of phytoplanktion data used
class_in_phytoplankton = "t",
# Finnmaid standard route ("E" or "W") used to select GETM model output
getm_select_route = "E",
# latitude limits for subsetting of GETM model data
getm_low_lat = 57.3,
getm_high_lat = 57.5,
# date limits for subsetting of GETM model data
getm_start_date = "2018-06-20",
getm_end_date = "2018-08-25",
# maximum depth used for integrations of GETM model data
getm_i_dep = 19
)parameters %>%
write_rds(here::here("data",
"parameters.rds"))
sessionInfo()R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)
Matrix products: default
locale:
[1] LC_COLLATE=English_Germany.1252 LC_CTYPE=English_Germany.1252
[3] LC_MONETARY=English_Germany.1252 LC_NUMERIC=C
[5] LC_TIME=English_Germany.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] lubridate_1.7.9.2 forcats_0.5.0 stringr_1.4.0 dplyr_1.0.2
[5] purrr_0.3.4 readr_1.4.0 tidyr_1.1.2 tibble_3.0.4
[9] ggplot2_3.3.3 tidyverse_1.3.0 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] tidyselect_1.1.0 xfun_0.19 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] rlang_0.4.10 later_1.1.0.1 pillar_1.4.7 withr_2.3.0
[13] glue_1.4.2 DBI_1.1.0 dbplyr_2.0.0 modelr_0.1.8
[17] readxl_1.3.1 lifecycle_0.2.0 munsell_0.5.0 gtable_0.3.0
[21] cellranger_1.1.0 rvest_0.3.6 evaluate_0.14 knitr_1.30
[25] ps_1.5.0 httpuv_1.5.4 fansi_0.4.1 broom_0.7.5
[29] Rcpp_1.0.5 promises_1.1.1 backports_1.2.1 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 assertthat_0.2.1 rmarkdown_2.6 httr_1.4.2
[53] rstudioapi_0.13 R6_2.5.0 git2r_0.27.1 compiler_4.0.3