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library(tidyverse)
library(lubridate)

1 Definition

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
  )

2 Write file

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 18363)

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