A function to read and inspect the isobxr master files and obtain a master formatted list.
read.isobxr_master(
workdir,
isobxr_master_file = "0_ISOBXR_MASTER",
inspect = TRUE,
export_rds = FALSE
)Working directory of isobxr excel master file and where output files will be stored if exported by user. (character string)
Name of isobxr excel master file. (without file "xlsx" extension). Default is "0_ISOBXR_MASTER".
If TRUE, checks all inputs from isobxr master file for format
and structure errors.
Default is TRUE.
If TRUE, exports rds version of isobxr master file
to working directory.
Default is FALSE.
A formatted list of data frames containing constants, box, fluxes and fractionation coefficients descriptions.
read.isobxr_master(workdir = "/Users/username/Documents/1_ABC_tutorial",
isobxr_master_file = "0_ISOBXR_MASTER",
export_rds = FALSE,
inspect = TRUE)
#> $CONSTANTS
#> ELEMENT RATIO_STANDARD NUMERATOR DENOMINATOR MASS_UNIT TIME_UNIT
#> 1 Ca 3.20297 44 42 mg d
#>
#> $BOXES
#> BOX_ID INFINITE LAYOUT_X LAYOUT_Y
#> 1 A FINITE 0 10
#> 2 B FINITE 10 10
#> 3 D FINITE 0 0
#> 4 C FINITE 10 0
#> 5 SOURCE INFINITE 0 15
#> 6 SINK INFINITE 10 15
#>
#> $FLUXES
#> SIZE_or_FLUX FROM TO BOX_ID Fx1_ABC_bal Fx2_ABC_unbal Fx3_ABC_unbal
#> 1 FLUX A B NaN 5e+01 5.0e+01 5.0e+01
#> 2 FLUX A C NaN 5e+01 5.0e+01 5.0e+01
#> 3 FLUX A D NaN 0e+00 0.0e+00 0.0e+00
#> 4 FLUX B A NaN 6e+01 6.0e+01 6.0e+01
#> 5 FLUX B C NaN 0e+00 0.0e+00 0.0e+00
#> 6 FLUX B D NaN 0e+00 0.0e+00 0.0e+00
#> 7 FLUX C A NaN 4e+01 4.1e+01 3.9e+01
#> 8 FLUX C B NaN 1e+01 1.0e+01 1.0e+01
#> 9 FLUX C D NaN 0e+00 0.0e+00 0.0e+00
#> 10 FLUX D A NaN 0e+00 0.0e+00 0.0e+00
#> 11 FLUX D B NaN 0e+00 0.0e+00 0.0e+00
#> 12 FLUX D C NaN 0e+00 0.0e+00 0.0e+00
#> 13 FLUX SOURCE A NaN 0e+00 0.0e+00 0.0e+00
#> 14 FLUX B SINK NaN 0e+00 0.0e+00 0.0e+00
#> 15 FLUX D SINK NaN 0e+00 0.0e+00 0.0e+00
#> 16 SIZE NaN NaN A 2e+03 2.0e+03 2.0e+03
#> 17 SIZE NaN NaN B 2e+03 2.0e+03 2.0e+03
#> 18 SIZE NaN NaN C 2e+03 2.0e+03 2.0e+03
#> 19 SIZE NaN NaN D 2e+03 2.0e+03 2.0e+03
#> 20 SIZE NaN NaN SOURCE 1e+15 1.0e+15 1.0e+15
#> 21 SIZE NaN NaN SINK 1e+15 1.0e+15 1.0e+15
#> Fx4_ABCD_bal Fx5_ABCD_unbal Fx6_ABC_open_bal Fx7_ABC_open_unbal fluxes_FINnD
#> 1 5.0e+01 5.5e+01 5.5e+01 6.5e+01 0e+00
#> 2 5.0e+01 5.0e+01 5.0e+01 5.0e+01 9e+00
#> 3 0.0e+00 0.0e+00 0.0e+00 0.0e+00 5e+00
#> 4 6.0e+01 6.0e+01 6.0e+01 6.0e+01 0e+00
#> 5 0.0e+00 0.0e+00 0.0e+00 0.0e+00 0e+00
#> 6 0.0e+00 0.0e+00 0.0e+00 0.0e+00 0e+00
#> 7 4.0e+01 4.0e+01 4.0e+01 4.0e+01 0e+00
#> 8 0.0e+00 0.0e+00 1.0e+01 1.0e+01 1e+01
#> 9 1.5e+01 1.5e+01 0.0e+00 0.0e+00 0e+00
#> 10 0.0e+00 0.0e+00 0.0e+00 0.0e+00 4e+00
#> 11 1.0e+01 1.0e+01 0.0e+00 0.0e+00 0e+00
#> 12 5.0e+00 5.0e+00 0.0e+00 0.0e+00 1e+00
#> 13 0.0e+00 0.0e+00 5.0e+00 5.0e+00 1e+01
#> 14 0.0e+00 0.0e+00 5.0e+00 5.0e+00 1e+01
#> 15 0.0e+00 0.0e+00 0.0e+00 0.0e+00 0e+00
#> 16 2.0e+03 2.0e+03 2.0e+03 2.0e+03 1e+02
#> 17 2.0e+03 2.0e+03 2.0e+03 2.0e+03 1e+02
#> 18 2.0e+03 2.0e+03 2.0e+03 2.0e+03 1e+02
#> 19 2.0e+03 2.0e+03 2.0e+03 2.0e+03 1e+02
#> 20 1.0e+15 1.0e+15 1.0e+15 1.0e+15 1e+15
#> 21 1.0e+15 1.0e+15 1.0e+15 1.0e+15 1e+15
#>
#> $COEFFS
#> FROM TO a0 a1 a2 a3 a4 b1 b2 b3 b4 true_coeff_FINnD
#> 1 A B 1 0.999 0.999 0.9990 1.00 0.999 0.9995 1 1.0005 1.0000000
#> 2 B A 1 1.000 1.001 1.0010 1.00 1.000 1.0000 1 1.0000 1.0000000
#> 3 C A 1 1.000 1.000 0.9997 1.00 1.000 1.0000 1 1.0000 1.0000000
#> 4 C D 1 1.000 1.000 1.0000 0.99 1.000 1.0000 1 1.0000 1.0000000
#> 5 A D 1 1.000 1.000 1.0000 1.00 1.000 1.0000 1 1.0000 0.9995001
#> 6 D A 1 1.000 1.000 1.0000 1.00 1.000 1.0000 1 1.0000 1.0005001
#> 7 C B 1 1.000 1.000 1.0000 1.00 1.000 1.0000 1 1.0000 1.0010005
#> sweep_coeff_FINnD
#> 1 1.0000
#> 2 1.0000
#> 3 1.0000
#> 4 1.0000
#> 5 1.0000
#> 6 1.0005
#> 7 1.0000
#>
#> $bx.groups
#> $bx.groups$all
#> [1] "A" "B" "C" "D" "SINK" "SOURCE"
#>
#> $bx.groups$all.n
#> [1] 6
#>
#> $bx.groups$called_in_FLUXES
#> [1] "A" "B" "C" "D" "SOURCE" "SINK"
#>
#> $bx.groups$called_in_SIZES
#> [1] "A" "B" "C" "D" "SOURCE" "SINK"
#>
#> $bx.groups$called_in_COEFFS
#> [1] "A" "B" "C" "D"
#>
#>