vignettes/macrounchainedfocusgw-manual.Rmd
macrounchainedfocusgw-manual.RmdIf macrounchained is already installed on your computer, and need to run MACRO In FOCUS groundwater simulations, you can use the function macrounchained::macrounchainedFocusGW_ui(), and don’t need to read the rest of this document.
macrounchained::macrounchainedFocusGW_ui() is a text-based user interface for macrounchainedFocusGW().
With this interface the user can:
Obtain a copy of the Excel example files for the input parameters (including a documentation of these parameters).
Import an Excel file containing input parameters, as prepared by the user, and start macrounchainedFocusGW(), after a couple of simple questions.
The user simply needs to start R and type the following command:
and then follow the instructions.
Notice that the function requires the R package readxl to be installed (for importing the parameters from an Excel file). It can be installed by typing:
In the text below i use macrounchained to indicate the package, and macrounchained() to indicate the function named macrounchained in that package.
More generally, names followed by () are function names. For example, macrounchainedFocusGW() is used for the function named macrounchainedFocusGW.
In code examples, calls such as macrounchained::macrounchainedFocusGW(), i.e. two names separated by two colons (::), should be understood as “a call to the function macrounchainedFocusGW in the package macrounchained”.
Users not familiar to R should be aware that it is not possible to use backslashes (\) as a separator when giving a path. Although backslash is the default separator in Windows, it is a reserved character in R. Instead, slashes (/) or double backslashes (\\) should be used. As an example, defining a path like this: path <- "C:\swash\macro" will cause an error, while path <- "C:/swash/macro" or path <- "C:\\swash\\macro" are correctly interpreted by R.
In the code examples below, when a path is displayed, some Windows variables like %USERPROFILE% may appear instead of the actual path (something like C:\Users\username). This is a way to avoid the user name to be displayed in a public document. The same is true for the operation log produced by macrounchainedFocusGW(), as the user name is hidden behind relevant Windows variables.
macrounchained is a package for the program R.
macrounchainedFocusGW() is a higher level function of the package macrounchained. It is build on top of the more generic function macrounchained(). It is specifically designed to perform groundwater simulations like MACRO In FOCUS.
macrounchainedFocusGW() is not as user friendly as the graphical user interface (GUI) of MACRO In FOCUS, but it allows the simulation of Nth-order metabolites (MACRO In FOCUS GUI only allows 1st order metabolites), and of large batches of simulations. macrounchainedFocusGW() also reduces the total number of simulations to be run when simulating several degradation products of the same substance, compared to MACRO In FOCUS GUI, by avoiding to re-run the same “intermediate” simulation multiple time.
macrounchained is based on a collection of four R packages (codeinfo, macroutils2, rmacrolite and macrounchained). All need to be installed (see below).
macrounchained does not embed any executable for MACRO or MACRO In FOCUS, and neither for the so called exeparfile tool. So MACRO or MACRO In FOCUS need to be installed on the computer for macrounchained to work. macrounchained also needs to know where MACRO or MACRO in FOCUS is installed, and how the MACRO-executable and the exeparfile are called. macrounchained look for this information in the following order:
It is therefore possible to use (alternatively) different versions of MACRO (for example MACRO In FOCUS or MACRO 5.2) on the same computer.
It is possible for the user or its system administrator to define three Windows Environment Variables that will be used by macrounchained to know where MACRO or MACRO in FOCUS is installed, and how the MACRO-executable and the executables are called.
On Windows 10, the Windows Environment Variables can be accessed via the Control Panel > System and Security > System > Advanced System Settings > Advanced Tab > “Environment Variables…” System Variables. There, it is possible to define three variables:
rmacrolite_macro_exe, for example set to Macro52Model.exe.rmacrolite_macro_exeparfile, for example set to exeparfile.exe.rmacrolite_macro_path, for example set to C:/swash/macro.Once they have been defined, the values attributed to these variables can be accessed by typing:
Before using macrounchainedFocusGW(), the user can manually set the path and/ or the executable names, in R. This setting is only valid for the current R cession (i.e. until R is closed), and must therefore be re-set for every new R cession.
rmacrolite::rmlPar( "macro_path" = "Macro52Model.exe",
"macro_exe" = "exeparfile.exe",
"macro_exeparfile" = "C:/swash/macro" ) You may for example replace "C:/swash/macro" with "C:/Program Files (x86)/MACRO52" if you want to use MACRO 5.2.
As can be seen from the code above, the settings occur to be in the package rmacrolite which provide all the lower level functions used by macrounchained.
About the example: The example given below is for a parent substance, called here GW-M, a primary metabolite Met-M1, formed from the degradation of GW-M, and a secondary metabolite Met-M2, formed from the degradation of Met-M1.
Notice that it is perfectly possible to run several simulations with unrelated substances, i.e. just a batch of simulations with different parameters.
In the examples below, the substance is applied every year. In this case, the user does not need to indicate the number of years interval between application-years, and it will be set internally to one year (application every year, the default). For applications every other year or every third year, an additional column needs to be given in the parameter table, years_interval, set to 2 or 3, respectively. It can vary from substance to substance. An example is given further down.
Some example Excel-files with substance properties and application patterns are shipped with macrounchained. The list of Excel examples can be obtained by typing the following command in R prompt:
#> [1] "%USERPROFILE%/Documents/R/win-library/3.5/macrounchained/ xlsx"and the list of files in this folder can be seen with the following command:
list.files( system.file( package = "macrounchained", "xlsx" ) )
#> [1] "macrounchainedFocusGW-documentation.xlsx"
#> [2] "macrounchainedFocusGW-every-other-year.xlsx"
#> [3] "macrounchainedFocusGW-multiple-applications.xlsx"
#> [4] "macrounchainedFocusGW-multiple-paths.xlsx"
#> [5] "macrounchainedFocusGW-with-met.xlsx"
#> [6] "macrounchainedFocusGW-with-more-met.xlsx"Copy one of these files and edit the content of sheet s (do not edit directly the file in the package installation directory!).
In order to be able to import an Excel file containing MACRO In FOCUS parameters, the package readxl needs to be installed. You can check if readxl is installed by typing the following command in R prompt:
If it returns TRUE, the package is installed, and if it returns FALSE, it is not installed. If needed, it can be installed with the following command:
The parameters contained in an Excel file can be imported with the following command:
# Fetch the path to the Excel file and save it in an R
# object called "xl"
xl <- system.file( package = "macrounchained", "xlsx",
"macrounchainedFocusGW-with-met.xlsx" )
# Import the sheet 's' in that Excel file
param1 <- readxl::read_excel( path = xl, sheet = "s" )
# Inspect the content of the table
as.data.frame( param1 )
#> soil crop id name kfoc nf dt50 dt50_ref_temp dt50_pf
#> 1 chateaudun cereals, winter 1 GW-M 12 1.0 23 20 2
#> 2 chateaudun cereals, winter 2 Met-M1 114 0.9 19 20 2
#> 3 chateaudun cereals, winter 3 Met-M2 46 0.9 136 20 2
#> exp_temp_resp exp_moist_resp crop_upt_f diff_coef parent_id g_per_mol
#> 1 0.0948 0.49 0.5 5e-10 NA 381
#> 2 0.0948 0.49 0.5 5e-10 1 183
#> 3 0.0948 0.49 0.5 5e-10 2 140
#> transf_f g_as_per_ha app_j_day
#> 1 NA 6 309
#> 2 0.2 0 309
#> 3 1.0 0 309The reason for as.data.frame( param1 ) is that param1 is of class tibble, which is the format output by readxl::read_excel(), but not the standard format in R. macrounchainedFocusGW() can handle both formats, when it comes to input parameters.
A real world Example would rather look like this:
# Import the sheet 's' in that Excel file
param1 <- readxl::read_excel(
path = "C:/path/to/userexcelfile.xlsx",
sheet = "s" ) where "C:/path/to/userexcelfile.xlsx" is the path and the name of an Excel file somewhere on the computer.
It is of course possible to create the parameter table directly in R. Here is how to create the same table as the one imported above from an Excel file:
param2 <- data.frame(
"soil" = "chateaudun",
"crop" = "cereals, winter",
"id" = c( 1L, 2L, 3L ),
"name" = c( "GW-M", "Met-M1", "Met-M2" ),
"kfoc" = c( 12, 114, 46 ),
"nf" = c( 1, 0.9, 0.9 ),
"dt50" = c( 23, 19, 136 ),
"dt50_ref_temp" = 20,
"dt50_pf" = 2,
"exp_temp_resp" = 0.0948,
"exp_moist_resp" = 0.49,
"crop_upt_f" = 0.5,
"diff_coef" = 5E-10,
"parent_id" = c( NA, 1L, 2L ),
"g_per_mol" = c( 381, 183, 140 ),
"transf_f" = c( NA, 0.2, 1.0 ), # mol met formed / mol parent degraded
"g_as_per_ha" = c( 6, 0, 0 ),
"app_j_day" = 309,
stringsAsFactors = FALSE
) Note (1): In the example above, each input-row represent what will be a column (a variable) in the final table and each column will be a row (a parameter set). It is not necessary to use spaces, nor to align the columns, but it makes the code more readable.
Note (2): In the example above, only one value is given for some variables (instead of three, one per parameter set). These are variables that are identically for all parameter sets, and R will automatically repeat the value for each parameter set.
We can check that the two solutions are identical:
A 3rd alternative method to prepare a table of parameters is to enter the table as a “fixed width format”, with a variable number of spaces as a column separator. It is not the most common way of defining a table in R, but it has the advantage of being more human readable.
param3 <- read.table( header = TRUE, text = "
soil crop id name kfoc nf dt50 dt50_ref_temp dt50_pf exp_temp_resp exp_moist_resp crop_upt_f diff_coef parent_id g_per_mol transf_f g_as_per_ha app_j_day
'chateaudun' 'cereals, winter' 1 'GW-M' 12 1.0 23 20 2 0.0948 0.49 0.5 5e-10 NA 381 NA 6 309
'chateaudun' 'cereals, winter' 2 'Met-M1' 114 0.9 19 20 2 0.0948 0.49 0.5 5e-10 1 183 0.2 0 309
'chateaudun' 'cereals, winter' 3 'Met-M2' 46 0.9 136 20 2 0.0948 0.49 0.5 5e-10 2 140 1.0 0 309
", stringsAsFactors = FALSE )Note: In the example above, notice that the the whole input-table is placed between double quotes ("). For this reason, text strings in the input-table need to be placed between single quotes ('), and not double quotes. It can be done the other way round.
In the code below, the table of properties is imported from an example Excel file and saved in param1, and the function macrounchainedFocusGW() is called. Notice that this is a dry-run, meaning that all the parametrisation is performed, but the three simulations are not run. As a consequence, the results of the simulations is not analysed either (i.e., the PECs are not calculated).
# Fetch the path to the Excel file and save it in an R
# object called "xl"
xl <- system.file( package = "macrounchained", "xlsx",
"macrounchainedFocusGW-with-met.xlsx" )
# Import the sheet 's' in that Excel file
param1 <- readxl::read_excel( path = xl, sheet = "s" )
library("macrounchained")
# Dry run:
macrounchainedFocusGW(
s = param1,
overwrite = TRUE,
run = FALSE ) # Set to TRUE to run the simulations
#> <2019-05-30|07:28:46> Temporary log-file
#> %USERPROFILE%/AppData/Local/Temp/RtmpCoJU5N/rml_log_2c4c3e9a7fa7.txt
#> ********************************************************************************
#> <2019-05-30|07:28:46> Parametrise MACRO simulations
#> ********************************************************************************
#> <2019-05-30|07:28:46> Fetch MACRO executables names and location
#> <2019-05-30|07:28:46> Fetch MACRO version
#> <2019-05-30|07:28:46> Check input parameter-table ('s')
#> <2019-05-30|07:28:46> The parameter table ('s') contains soil/crop scenario
#> <2019-05-30|07:28:46> * Look for scenario-templates and crop-parameters for
#> MACRO In FOCUS version '5.5.4'
#> <2019-05-30|07:28:46> * Import base information on sites/scenario
#> <2019-05-30|07:28:46> * Import crop parameter values
#> <2019-05-30|07:28:46> * Import crop parameter map
#> <2019-05-30|07:28:46> * Match scenario(s) and crop(s) requested by the user
#> with FOCUS scenario and crops
#> <2019-05-30|07:28:46> * Find-out the relevant soil/scenario-template
#> par-file(s)
#> <2019-05-30|07:28:46> Import par-file id 1
#> (%USERPROFILE%/Documents/R/win-library/3.5/macrounchained/focus_scenario/5.5.4/
#> soils/chateaudun.par)
#> <2019-05-30|07:28:46> Find-out order of simulations (metabolite(s)
#> transformation pathway)
#> <2019-05-30|07:28:46> Prepare a list of operations (incl. metabolite(s)
#> intermediate output)
#> <2019-05-30|07:28:46> Identified 5 simulations for 3 substances (2
#> intermediate-outputs)
#> <2019-05-30|07:28:46> Substance properties (updated):
#> soil crop id name kfoc nf dt50 dt50_ref_temp dt50_pf
#> 1 chateaudun cereals, winter 1 GW-M 12 1.0 23 20 2
#> 2 chateaudun cereals, winter 2 Met-M1 114 0.9 19 20 2
#> 3 chateaudun cereals, winter 3 Met-M2 46 0.9 136 20 2
#> exp_temp_resp exp_moist_resp crop_upt_f diff_coef parent_id g_per_mol
#> 1 0.0948 0.49 0.5 5e-10 NA 381
#> 2 0.0948 0.49 0.5 5e-10 1 183
#> 3 0.0948 0.49 0.5 5e-10 2 140
#> transf_f g_as_per_ha app_j_day f_int years_interval focus_soil
#> 1 NA 6 309 0 1 Chateaudun
#> 2 0.2 0 309 0 1 Chateaudun
#> 3 1.0 0 309 0 1 Chateaudun
#> focus_crop focus_index parfile_id as_id met_level f_conv has_met
#> 1 Cereals, winter 2 1 1 0 NA TRUE
#> 2 Cereals, winter 2 1 1 2 0.09606299 TRUE
#> 3 Cereals, winter 2 1 1 2 0.76502732 FALSE
#> <2019-05-30|07:28:46> Table of par-file(s):
#> [1] 1
#> <2019-05-30|07:28:46> Operations register:
#> id run_id is_as is_met is_inter par_file drivingfile
#> 1 1 1 TRUE FALSE FALSE rml_001.par rml_000_inter.bin
#> 2 1 4 TRUE FALSE TRUE rml_001_inter.par rml_000_inter.bin
#> 3 2 2 FALSE TRUE FALSE rml_002.par rml_001_inter.bin
#> 4 2 5 FALSE TRUE TRUE rml_002_inter.par rml_001_inter.bin
#> 5 3 3 FALSE TRUE FALSE rml_003.par rml_002_inter.bin
#> output_macro output_rename indump_rename summary_file
#> 1 MACRO001.BIN rml_001.bin rml_001_indump.tmp rml_001_summary.txt
#> 2 MACRO004.BIN rml_001_inter.bin rml_004_indump.tmp <NA>
#> 3 MACRO002.BIN rml_002.bin rml_002_indump.tmp rml_002_summary.txt
#> 4 MACRO005.BIN rml_002_inter.bin rml_005_indump.tmp <NA>
#> 5 MACRO003.BIN rml_003.bin rml_003_indump.tmp rml_003_summary.txt
#> merge_inter_first
#> 1 FALSE
#> 2 FALSE
#> 3 FALSE
#> 4 FALSE
#> 5 FALSE
#> <2019-05-30|07:28:47> All output-files will be now saved in C:/swash/macro
#> <2019-05-30|07:28:47> Log-file continues in C:/swash/macro/rml_001-005_log.txt
#> <2019-05-30|07:28:47> Exporting updated substance parameters:
#> rml_001-005_s_updated.csv
#> <2019-05-30|07:28:47> Exporting operation register:
#> rml_001-005_operation_register.csv
#> <2019-05-30|07:28:47> Exporting par-file template(s):
#> <2019-05-30|07:28:47> * parfile id 1 (rml_001-005_par_template_id1.par)
#> ================================================================================
#> <2019-05-30|07:28:47> Parametrising and exporting par-files
#> ================================================================================
#> --------------------------------------------------------------------------------
#> <2019-05-30|07:28:47> Simulation 1/5
#> --------------------------------------------------------------------------------
#> <2019-05-30|07:28:47> Substance GW-M. id 1, run id 1
#> <2019-05-30|07:28:47> FOCUS: Chateaudun; Cereals, winter; Irrigated
#> <2019-05-30|07:28:47> Set substance properties:
#> <2019-05-30|07:28:47> * Run id
#> <2019-05-30|07:28:47> * Application rate and date (Julian day) and crop
#> interception
#> <2019-05-30|07:28:47> * Simulation type
#> <2019-05-30|07:28:47> * Simulation identified as: parent
#> <2019-05-30|07:28:47> * Sorption parameters
#> <2019-05-30|07:28:47> * Degradation parameters
#> <2019-05-30|07:28:47> * Crop uptake factor
#> <2019-05-30|07:28:47> * Diffusion coefficient
#> <2019-05-30|07:28:47> * Set FOCUS-crop parameters
#> <2019-05-30|07:28:47> * Information section (end of par-file)
#> <2019-05-30|07:28:47> Exporting the par-file (rml_001.par)
#> <2019-05-30|07:28:47> Generate indump.tmp
#> <2019-05-30|07:28:47> Run MACRO simulation: SKIPPED
#> <2019-05-30|07:28:47> Rename indump.tmp to rml_001_indump.tmp
#> --------------------------------------------------------------------------------
#> <2019-05-30|07:28:47> Simulation 2/5
#> --------------------------------------------------------------------------------
#> <2019-05-30|07:28:47> Substance GW-M. id 1, run id 4
#> <2019-05-30|07:28:47> FOCUS: Chateaudun; Cereals, winter; Irrigated
#> <2019-05-30|07:28:47> Set substance properties:
#> <2019-05-30|07:28:47> * Run id
#> <2019-05-30|07:28:47> * Application rate and date (Julian day) and crop
#> interception
#> <2019-05-30|07:28:48> * Simulation type
#> <2019-05-30|07:28:48> * Simulation identified as: parent, intermediate
#> <2019-05-30|07:28:48> * Sorption parameters
#> <2019-05-30|07:28:48> * Degradation parameters
#> <2019-05-30|07:28:48> * Crop uptake factor
#> <2019-05-30|07:28:48> * Diffusion coefficient
#> <2019-05-30|07:28:48> * Set FOCUS-crop parameters
#> <2019-05-30|07:28:48> * Information section (end of par-file)
#> <2019-05-30|07:28:48> Exporting the par-file (rml_001_inter.par)
#> <2019-05-30|07:28:48> Generate indump.tmp
#> <2019-05-30|07:28:48> Run MACRO simulation: SKIPPED
#> <2019-05-30|07:28:48> Rename indump.tmp to rml_004_indump.tmp
#> --------------------------------------------------------------------------------
#> <2019-05-30|07:28:48> Simulation 3/5
#> --------------------------------------------------------------------------------
#> <2019-05-30|07:28:48> Substance Met-M1. id 2, run id 2
#> <2019-05-30|07:28:48> FOCUS: Chateaudun; Cereals, winter; Irrigated
#> <2019-05-30|07:28:48> Set substance properties:
#> <2019-05-30|07:28:48> * Run id
#> <2019-05-30|07:28:48> * Application rate and date (Julian day) and crop
#> interception
#> <2019-05-30|07:28:48> * Simulation type
#> <2019-05-30|07:28:48> * Simulation identified as: metabolite
#> <2019-05-30|07:28:48> * Sorption parameters
#> <2019-05-30|07:28:49> * Degradation parameters
#> <2019-05-30|07:28:49> * Crop uptake factor
#> <2019-05-30|07:28:49> * Diffusion coefficient
#> <2019-05-30|07:28:49> * Set FOCUS-crop parameters
#> <2019-05-30|07:28:49> * Information section (end of par-file)
#> <2019-05-30|07:28:49> Exporting the par-file (rml_002.par)
#> <2019-05-30|07:28:49> Generate indump.tmp
#> <2019-05-30|07:28:49> Run MACRO simulation: SKIPPED
#> <2019-05-30|07:28:49> Rename indump.tmp to rml_002_indump.tmp
#> --------------------------------------------------------------------------------
#> <2019-05-30|07:28:49> Simulation 4/5
#> --------------------------------------------------------------------------------
#> <2019-05-30|07:28:49> Substance Met-M1. id 2, run id 5
#> <2019-05-30|07:28:49> FOCUS: Chateaudun; Cereals, winter; Irrigated
#> <2019-05-30|07:28:49> Set substance properties:
#> <2019-05-30|07:28:49> * Run id
#> <2019-05-30|07:28:49> * Application rate and date (Julian day) and crop
#> interception
#> <2019-05-30|07:28:49> * Simulation type
#> <2019-05-30|07:28:49> * Simulation identified as: metabolite, intermediate
#> <2019-05-30|07:28:49> * Sorption parameters
#> <2019-05-30|07:28:49> * Degradation parameters
#> <2019-05-30|07:28:49> * Crop uptake factor
#> <2019-05-30|07:28:50> * Diffusion coefficient
#> <2019-05-30|07:28:50> * Set FOCUS-crop parameters
#> <2019-05-30|07:28:50> * Information section (end of par-file)
#> <2019-05-30|07:28:50> Exporting the par-file (rml_002_inter.par)
#> <2019-05-30|07:28:50> Generate indump.tmp
#> <2019-05-30|07:28:50> Run MACRO simulation: SKIPPED
#> <2019-05-30|07:28:50> Rename indump.tmp to rml_005_indump.tmp
#> --------------------------------------------------------------------------------
#> <2019-05-30|07:28:50> Simulation 5/5
#> --------------------------------------------------------------------------------
#> <2019-05-30|07:28:50> Substance Met-M2. id 3, run id 3
#> <2019-05-30|07:28:50> FOCUS: Chateaudun; Cereals, winter; Irrigated
#> <2019-05-30|07:28:50> Set substance properties:
#> <2019-05-30|07:28:50> * Run id
#> <2019-05-30|07:28:50> * Application rate and date (Julian day) and crop
#> interception
#> <2019-05-30|07:28:50> * Simulation type
#> <2019-05-30|07:28:50> * Simulation identified as: metabolite
#> <2019-05-30|07:28:50> * Sorption parameters
#> <2019-05-30|07:28:50> * Degradation parameters
#> <2019-05-30|07:28:50> * Crop uptake factor
#> <2019-05-30|07:28:50> * Diffusion coefficient
#> <2019-05-30|07:28:50> * Set FOCUS-crop parameters
#> <2019-05-30|07:28:51> * Information section (end of par-file)
#> <2019-05-30|07:28:51> Exporting the par-file (rml_003.par)
#> <2019-05-30|07:28:51> Generate indump.tmp
#> <2019-05-30|07:28:51> Run MACRO simulation: SKIPPED
#> <2019-05-30|07:28:51> Rename indump.tmp to rml_003_indump.tmp
#> ================================================================================
#> <2019-05-30|07:28:51> Post-processing operations
#> ================================================================================
#> --------------------------------------------------------------------------------
#> <2019-05-30|07:28:51> Information (traceability & reproducibility)
#> --------------------------------------------------------------------------------
#> <2019-05-30|07:28:51> Call from package: 'macrounchained'
#> <2019-05-30|07:28:51> Model: FOCUS_MACRO_5.5.4; core-model version: v. 5 (=
#> 5.2)
#> <2019-05-30|07:28:51> Information on system, packages and executables
#> $r
#> variable value
#> 1 OS Windows 10 x64 (build 17134)
#> 2 system x86_64, mingw32
#> 3 R_version R version 3.5.1 (2018-07-02)
#> 4 GUI RTerm
#>
#> $packages
#> package version revision date_packaged
#> 1 macrounchained 0.13.0 93b0f40 2019-05-26
#> 2 rmacrolite 0.9.7 9a38321 2019-04-15
#> 3 macroutils2 2.2.3 ef26fd7 2019-04-17
#> 4 codeinfo 0.1.3 a595b27 2019-05-13
#> checksums_checksum
#> 1 97b9addd9d2a360fec8cdbb758ec44d0
#> 2 945f371b037b8aa18b057b82096ee0fd
#> 3 6356c0f3f25b6abd9402e6546c5ab0ef
#> 4 6829117696319b3d3a508d95d8c4420d
#>
#> $files
#> files md5_checksums
#> 1 adodb.dll c0f0651ac9610796599e87fbb3142802
#> 2 AxInterop.MSFlexGridLib.dll ec00ebacae2846394a22eb67f394a0ea
#> 3 conv.exe 921d18f1097802c6f4bfde51f66f37d6
#> 4 exeparfile.exe 29651b9fbbb7ad8fef04d2b7b0056ac5
#> 5 Interop.MSDBGrid.dll b78fb118568484eff04030e52ecc4040
#> 6 Interop.MSFlexGridLib.dll 967cb46d107518c79433f077de3620fa
#> 7 Interop.Threed.dll 149a47480822e743460efbfac396a2c0
#> 8 m2t.exe c9f39e7986008d5b22f062a7253bd36c
#> 9 MACRO_FOCUS.exe 5ae35eecbdd04a021f2a3cbbd54f2b1c
#> 10 MACRO5.dll 1b8f57d0e3746789c4f585b911a3a84c
#> 11 Macro52Model.exe 35f9cd21522402dc3f0dda2e4e6b814e
#>
#> $objects
#> name md5_checksums class environment
#> 1 analyse 0192420d2b2ecea4fef91b7736935cc8 function macroutils2
#> 2 analyse_summary 93c7497ef335b47b01f485fd3af6176c function macrounchained
#> <2019-05-30|07:28:51> Original call:
#> <2019-05-30|07:28:51> macrounchainedFocusGW(s = param1, overwrite = TRUE, run =
#> FALSE)
#> --------------------------------------------------------------------------------
#> <2019-05-30|07:28:52> Final step(s)
#> --------------------------------------------------------------------------------
#> <2019-05-30|07:28:52> Formatting output
#> <2019-05-30|07:28:52> Internal clean-up
#> <2019-05-30|07:28:52> Total operation time at this point: 0.087 mins
#> <2019-05-30|07:28:52> FINAL STEP: Calculate md5-checksums for generated files
#> (rml_001-005_md5.txt) and archive them (rml_001-005_archive.tar.gz)When the simulations are run, that is when the argument run is set to TRUE or omitted (default value is TRUE), more output will be visible in the operation log, and the simulation results is analysed “on the fly” and shown. The results will then include something like:
<2019-01-23|18:03:43> MACRO runtime 23.13 min
<2019-01-23|18:03:43> Rename MACRO output from MACRO001.BIN to rml_001.bin
<2019-01-23|18:03:43> Analyse simulation results:
$info_general
conc_percentile rank_period1 rank_period2 method nb_sim_yrs_used
1 80 16 17 focus 20
nb_yrs_per_period nb_yrs_warmup neg_conc_set_to_0
1 1 6 TRUE
$info_period
period_index from_year to_year
1 1 1907 1907
2 2 1908 1908
3 3 1909 1909
4 4 1910 1910
5 5 1911 1911
6 6 1912 1912
7 7 1913 1913
8 8 1914 1914
9 9 1915 1915
10 10 1916 1916
11 11 1917 1917
12 12 1918 1918
13 13 1919 1919
14 14 1920 1920
15 15 1921 1921
16 16 1922 1922
17 17 1923 1923
18 18 1924 1924
19 19 1925 1925
20 20 1926 1926
$water_target_layer_by_period
period_index mm_mic mm_mac mm_tot
1 1 235.470763 0 235.470763
2 2 25.219577 0 25.219577
3 3 249.413842 0 249.413842
4 4 210.212175 0 210.212175
5 5 313.436020 0 313.436020
6 6 203.400054 0 203.400054
7 7 256.735007 0 256.735007
8 8 237.177154 0 237.177154
9 9 142.302469 0 142.302469
10 10 313.514879 0 313.514879
11 11 102.166490 0 102.166490
12 12 133.547061 0 133.547061
13 13 185.370237 0 185.370237
14 14 228.786978 0 228.786978
15 15 45.906557 0 45.906557
16 16 8.512096 0 8.512096
17 17 85.944210 0 85.944210
18 18 113.385342 0 113.385342
19 19 73.593095 0 73.593095
20 20 99.801542 0 99.801542
$solute_target_layer_by_period
period_index mg_per_m2_mic mg_per_m2_mac mg_per_m2_tot ug_per_L
1 1 0.0130986457 0 0.0130986457 0.05562748
2 2 -0.0012073002 0 -0.0012073002 0.00000000
3 3 0.0303878063 0 0.0303878063 0.12183689
4 4 0.0326010108 0 0.0326010108 0.15508622
5 5 0.0640291599 0 0.0640291599 0.20428143
6 6 0.0289145618 0 0.0289145618 0.14215612
7 7 0.0360325941 0 0.0360325941 0.14034936
8 8 0.0185321498 0 0.0185321498 0.07813632
9 9 0.0194373138 0 0.0194373138 0.13659154
10 10 0.0301531842 0 0.0301531842 0.09617784
11 11 0.0096938342 0 0.0096938342 0.09488272
12 12 0.0111410579 0 0.0111410579 0.08342421
13 13 0.0120960097 0 0.0120960097 0.06525325
14 14 0.0318550546 0 0.0318550546 0.13923456
15 15 0.0009124727 0 0.0009124727 0.01987674
16 16 -0.0033259016 0 -0.0033259016 0.00000000
17 17 0.0011909045 0 0.0011909045 0.01385672
18 18 0.0020206876 0 0.0020206876 0.01782142
19 19 0.0039686604 0 0.0039686604 0.05392708
20 20 0.0056017143 0 0.0056017143 0.05612853
$water_perc_by_period
period_index mm
1 1 236.47974
2 2 19.49554
3 3 250.39844
4 4 200.46625
5 5 318.68542
6 6 202.45740
7 7 256.35547
8 8 237.01562
9 9 153.94165
10 10 307.54321
11 11 107.05884
12 12 127.01587
13 13 186.15771
14 14 234.07593
15 15 38.68237
16 16 15.55029
17 17 88.74512
18 18 109.76221
19 19 71.59131
20 20 102.41870
$conc_target_layer
ug_per_L ug_per_L_rnd index_period1 index_period2 f_solute_mac f_solute_mic
1 0.139792 0.14 14 7 0 1
--------------------------------------------------------------------------------
<2019-01-23|18:03:43> Simulation 2/5
--------------------------------------------------------------------------------Where ug_per_L_rnd in the item conc_target_layer is the PECgw as MACRO In FOCUS would calculate it (rounded to three significant figures).
The commands for a real-world example may rather look like this:
Compared to the case above (one application per year, every year), the case of several application per year, every year will differ in the way the columns g_as_per_ha and app_j_day in the parameter table are specified.
The example Excel file macrounchainedFocusGW-multiple-applications.xlsx shows how this must be done in Excel (enter several values in the same cell by separating with with a vertical bar |).
In R, the parameter table can be entered as follow:
param2 <- data.frame(
"soil" = "chateaudun",
"crop" = "cereals, winter",
"id" = c( 1, 2 ),
"name" = c( "GW-C", "Met-C" ),
"kfoc" = c( 172, 52 ),
"nf" = c( 0.9, 0.9 ),
"dt50" = c( 20, 100 ),
"dt50_ref_temp" = 20,
"dt50_pf" = 2,
"exp_temp_resp" = 0.079,
"exp_moist_resp" = c( 0.49, 0.7 ),
"crop_upt_f" = 0.5,
"diff_coef" = c( 5e-10, 5e-10 ),
"parent_id" = c( NA, 1 ),
"g_per_mol" = c( 200, 150 ),
"transf_f" = c( NA, .53/.75 ),
"g_as_per_ha" = c( "1000|950", "0|0" ),
"app_j_day" = c( "298|305", "298|305" ),
stringsAsFactors = FALSE ) The columns g_as_per_ha and app_j_day now contains character strings in which several values have been written, separated by a vertical bar (|). macrounchainedFocusGW() will internally convert these into numeric values.
param3 <- read.table( header = TRUE, text = "
soil crop id name kfoc nf dt50 dt50_ref_temp dt50_pf exp_temp_resp exp_moist_resp crop_upt_f diff_coef parent_id g_per_mol transf_f g_as_per_ha app_j_day
'chateaudun' 'cereals, winter' 1 'GW-C' 172 0.9 20 20 2 0.079 0.49 0.5 5e-10 NA 200 NA '1000|950' '298|305'
'chateaudun' 'cereals, winter' 2 'Met-C' 52 0.9 100 20 2 0.079 0.70 0.5 5e-10 1 150 0.7066667 '0|0' '298|305'
", stringsAsFactors = FALSE )In the example below, the parameter table is imported from Excel and macrounchainedFocusGW() is called with these parameters:
# Fetch the path to the Excel file and save it in an R
# object called "xl"
xl <- system.file( package = "macrounchained", "xlsx",
"macrounchainedFocusGW-multiple-applications.xlsx" )
# Import the sheet 's' in that Excel file
param1 <- readxl::read_excel( path = xl, sheet = "s" )
library("macrounchained")
# Dry run:
macrounchainedFocusGW(
s = param1,
overwrite = TRUE,
run = FALSE ) # Set to TRUE to run the simulations
#> <2019-05-30|07:28:52> Temporary log-file
#> %USERPROFILE%/AppData/Local/Temp/RtmpCoJU5N/rml_log_2c4c248712b.txt
#> ********************************************************************************
#> <2019-05-30|07:28:52> Parametrise MACRO simulations
#> ********************************************************************************
#> <2019-05-30|07:28:52> Fetch MACRO executables names and location
#> <2019-05-30|07:28:52> Fetch MACRO version
#> <2019-05-30|07:28:52> Check input parameter-table ('s')
#> <2019-05-30|07:28:52> The parameter table ('s') contains soil/crop scenario
#> <2019-05-30|07:28:52> * Look for scenario-templates and crop-parameters for
#> MACRO In FOCUS version '5.5.4'
#> <2019-05-30|07:28:52> * Import base information on sites/scenario
#> <2019-05-30|07:28:52> * Import crop parameter values
#> <2019-05-30|07:28:52> * Import crop parameter map
#> <2019-05-30|07:28:52> * Match scenario(s) and crop(s) requested by the user
#> with FOCUS scenario and crops
#> <2019-05-30|07:28:52> * Find-out the relevant soil/scenario-template
#> par-file(s)
#> <2019-05-30|07:28:52> Import par-file id 1
#> (%USERPROFILE%/Documents/R/win-library/3.5/macrounchained/focus_scenario/5.5.4/
#> soils/chateaudun.par)
#> <2019-05-30|07:28:52> Find-out order of simulations (metabolite(s)
#> transformation pathway)
#> <2019-05-30|07:28:52> Prepare a list of operations (incl. metabolite(s)
#> intermediate output)
#> <2019-05-30|07:28:52> Identified 3 simulations for 2 substances (1
#> intermediate-outputs)
#> <2019-05-30|07:28:52> Substance properties (updated):
#> soil crop id name kfoc nf dt50 dt50_ref_temp dt50_pf
#> 1 chateaudun cereals, winter 3 GW-C 172 0.9 20 20 2
#> 2 chateaudun cereals, winter 4 Met-C 52 0.9 100 20 2
#> exp_temp_resp exp_moist_resp crop_upt_f diff_coef parent_id g_per_mol
#> 1 0.079 0.49 0.5 5e-10 NA 200
#> 2 0.079 0.70 0.5 5e-10 3 150
#> transf_f g_as_per_ha app_j_day f_int years_interval focus_soil
#> 1 NA 1000, 950 298, 305 0 1 Chateaudun
#> 2 0.7066667 0, 0 298, 305 0 1 Chateaudun
#> focus_crop focus_index parfile_id as_id met_level f_conv has_met
#> 1 Cereals, winter 2 1 3 0 NA TRUE
#> 2 Cereals, winter 2 1 3 1 0.53 FALSE
#> <2019-05-30|07:28:52> Table of par-file(s):
#> [1] 1
#> <2019-05-30|07:28:52> Operations register:
#> id run_id is_as is_met is_inter par_file drivingfile
#> 1 3 3 TRUE FALSE FALSE rml_003.par rml_000_inter.bin
#> 2 3 5 TRUE FALSE TRUE rml_003_inter.par rml_000_inter.bin
#> 3 4 4 FALSE TRUE FALSE rml_004.par rml_003_inter.bin
#> output_macro output_rename indump_rename summary_file
#> 1 MACRO003.BIN rml_003.bin rml_003_indump.tmp rml_003_summary.txt
#> 2 MACRO005.BIN rml_003_inter.bin rml_005_indump.tmp <NA>
#> 3 MACRO004.BIN rml_004.bin rml_004_indump.tmp rml_004_summary.txt
#> merge_inter_first
#> 1 FALSE
#> 2 FALSE
#> 3 FALSE
#> <2019-05-30|07:28:52> All output-files will be now saved in C:/swash/macro
#> <2019-05-30|07:28:52> Log-file continues in C:/swash/macro/rml_003-005_log.txt
#> <2019-05-30|07:28:52> Exporting updated substance parameters:
#> rml_003-005_s_updated.csv
#> <2019-05-30|07:28:52> Exporting operation register:
#> rml_003-005_operation_register.csv
#> <2019-05-30|07:28:52> Exporting par-file template(s):
#> <2019-05-30|07:28:52> * parfile id 1 (rml_003-005_par_template_id1.par)
#> ================================================================================
#> <2019-05-30|07:28:52> Parametrising and exporting par-files
#> ================================================================================
#> --------------------------------------------------------------------------------
#> <2019-05-30|07:28:52> Simulation 1/3
#> --------------------------------------------------------------------------------
#> <2019-05-30|07:28:52> Substance GW-C. id 3, run id 3
#> <2019-05-30|07:28:52> FOCUS: Chateaudun; Cereals, winter; Irrigated
#> <2019-05-30|07:28:52> Set substance properties:
#> <2019-05-30|07:28:52> * Run id
#> <2019-05-30|07:28:52> * Application rate and date (Julian day) and crop
#> interception
#> <2019-05-30|07:28:52> * Simulation type
#> <2019-05-30|07:28:52> * Simulation identified as: parent
#> <2019-05-30|07:28:52> * Sorption parameters
#> <2019-05-30|07:28:52> * Degradation parameters
#> <2019-05-30|07:28:52> * Crop uptake factor
#> <2019-05-30|07:28:52> * Diffusion coefficient
#> <2019-05-30|07:28:52> * Set FOCUS-crop parameters
#> <2019-05-30|07:28:52> * Information section (end of par-file)
#> <2019-05-30|07:28:52> Exporting the par-file (rml_003.par)
#> <2019-05-30|07:28:52> Generate indump.tmp
#> <2019-05-30|07:28:53> Run MACRO simulation: SKIPPED
#> <2019-05-30|07:28:53> Rename indump.tmp to rml_003_indump.tmp
#> --------------------------------------------------------------------------------
#> <2019-05-30|07:28:53> Simulation 2/3
#> --------------------------------------------------------------------------------
#> <2019-05-30|07:28:53> Substance GW-C. id 3, run id 5
#> <2019-05-30|07:28:53> FOCUS: Chateaudun; Cereals, winter; Irrigated
#> <2019-05-30|07:28:53> Set substance properties:
#> <2019-05-30|07:28:53> * Run id
#> <2019-05-30|07:28:53> * Application rate and date (Julian day) and crop
#> interception
#> <2019-05-30|07:28:53> * Simulation type
#> <2019-05-30|07:28:53> * Simulation identified as: parent, intermediate
#> <2019-05-30|07:28:53> * Sorption parameters
#> <2019-05-30|07:28:53> * Degradation parameters
#> <2019-05-30|07:28:53> * Crop uptake factor
#> <2019-05-30|07:28:53> * Diffusion coefficient
#> <2019-05-30|07:28:53> * Set FOCUS-crop parameters
#> <2019-05-30|07:28:53> * Information section (end of par-file)
#> <2019-05-30|07:28:53> Exporting the par-file (rml_003_inter.par)
#> <2019-05-30|07:28:53> Generate indump.tmp
#> <2019-05-30|07:28:54> Run MACRO simulation: SKIPPED
#> <2019-05-30|07:28:54> Rename indump.tmp to rml_005_indump.tmp
#> --------------------------------------------------------------------------------
#> <2019-05-30|07:28:54> Simulation 3/3
#> --------------------------------------------------------------------------------
#> <2019-05-30|07:28:54> Substance Met-C. id 4, run id 4
#> <2019-05-30|07:28:54> FOCUS: Chateaudun; Cereals, winter; Irrigated
#> <2019-05-30|07:28:54> Set substance properties:
#> <2019-05-30|07:28:54> * Run id
#> <2019-05-30|07:28:54> * Application rate and date (Julian day) and crop
#> interception
#> <2019-05-30|07:28:54> * Simulation type
#> <2019-05-30|07:28:54> * Simulation identified as: metabolite
#> <2019-05-30|07:28:54> * Sorption parameters
#> <2019-05-30|07:28:54> * Degradation parameters
#> <2019-05-30|07:28:54> * Crop uptake factor
#> <2019-05-30|07:28:54> * Diffusion coefficient
#> <2019-05-30|07:28:54> * Set FOCUS-crop parameters
#> <2019-05-30|07:28:54> * Information section (end of par-file)
#> <2019-05-30|07:28:54> Exporting the par-file (rml_004.par)
#> <2019-05-30|07:28:54> Generate indump.tmp
#> <2019-05-30|07:28:55> Run MACRO simulation: SKIPPED
#> <2019-05-30|07:28:55> Rename indump.tmp to rml_004_indump.tmp
#> ================================================================================
#> <2019-05-30|07:28:55> Post-processing operations
#> ================================================================================
#> --------------------------------------------------------------------------------
#> <2019-05-30|07:28:55> Information (traceability & reproducibility)
#> --------------------------------------------------------------------------------
#> <2019-05-30|07:28:55> Call from package: 'macrounchained'
#> <2019-05-30|07:28:55> Model: FOCUS_MACRO_5.5.4; core-model version: v. 5 (=
#> 5.2)
#> <2019-05-30|07:28:55> Information on system, packages and executables
#> $r
#> variable value
#> 1 OS Windows 10 x64 (build 17134)
#> 2 system x86_64, mingw32
#> 3 R_version R version 3.5.1 (2018-07-02)
#> 4 GUI RTerm
#>
#> $packages
#> package version revision date_packaged
#> 1 macrounchained 0.13.0 93b0f40 2019-05-26
#> 2 rmacrolite 0.9.7 9a38321 2019-04-15
#> 3 macroutils2 2.2.3 ef26fd7 2019-04-17
#> 4 codeinfo 0.1.3 a595b27 2019-05-13
#> checksums_checksum
#> 1 97b9addd9d2a360fec8cdbb758ec44d0
#> 2 945f371b037b8aa18b057b82096ee0fd
#> 3 6356c0f3f25b6abd9402e6546c5ab0ef
#> 4 6829117696319b3d3a508d95d8c4420d
#>
#> $files
#> files md5_checksums
#> 1 adodb.dll c0f0651ac9610796599e87fbb3142802
#> 2 AxInterop.MSFlexGridLib.dll ec00ebacae2846394a22eb67f394a0ea
#> 3 conv.exe 921d18f1097802c6f4bfde51f66f37d6
#> 4 exeparfile.exe 29651b9fbbb7ad8fef04d2b7b0056ac5
#> 5 Interop.MSDBGrid.dll b78fb118568484eff04030e52ecc4040
#> 6 Interop.MSFlexGridLib.dll 967cb46d107518c79433f077de3620fa
#> 7 Interop.Threed.dll 149a47480822e743460efbfac396a2c0
#> 8 m2t.exe c9f39e7986008d5b22f062a7253bd36c
#> 9 MACRO_FOCUS.exe 5ae35eecbdd04a021f2a3cbbd54f2b1c
#> 10 MACRO5.dll 1b8f57d0e3746789c4f585b911a3a84c
#> 11 Macro52Model.exe 35f9cd21522402dc3f0dda2e4e6b814e
#>
#> $objects
#> name md5_checksums class environment
#> 1 analyse 0192420d2b2ecea4fef91b7736935cc8 function macroutils2
#> 2 analyse_summary 93c7497ef335b47b01f485fd3af6176c function macrounchained
#> <2019-05-30|07:28:55> Original call:
#> <2019-05-30|07:28:55> macrounchainedFocusGW(s = param1, overwrite = TRUE, run =
#> FALSE)
#> --------------------------------------------------------------------------------
#> <2019-05-30|07:28:55> Final step(s)
#> --------------------------------------------------------------------------------
#> <2019-05-30|07:28:55> Formatting output
#> <2019-05-30|07:28:55> Internal clean-up
#> <2019-05-30|07:28:55> Total operation time at this point: 0.055 mins
#> <2019-05-30|07:28:55> FINAL STEP: Calculate md5-checksums for generated files
#> (rml_003-005_md5.txt) and archive them (rml_003-005_archive.tar.gz)Compared to the first case (one application per year, every year), the case of one application per year, every two years will only differ by one column in the table of properties. It needs to contain a column called "years_interval" that contains the number of years interval between application years (1 being for applications every year, 2 for applications every other year and 3 for applications every third year). Notice that, in the case of applications every year, the column can be missing and is internally set to 1 (i.e. applications every year is assumed).
# Fetch the path to the Excel file and save it in an R
# object called "xl"
xl <- system.file( package = "macrounchained", "xlsx",
"macrounchainedFocusGW-every-other-year.xlsx" )
# Import the sheet 's' in that Excel file
param1 <- readxl::read_excel( path = xl, sheet = "s" )
# Inspect the table
as.data.frame( param1 )
#> soil crop id name kfoc nf dt50 dt50_ref_temp dt50_pf
#> 1 chateaudun cereals, winter 1 GW-M 12 1.0 23 20 2
#> 2 chateaudun cereals, winter 2 Met-M1 114 0.9 19 20 2
#> 3 chateaudun cereals, winter 3 Met-M2 46 0.9 136 20 2
#> exp_temp_resp exp_moist_resp crop_upt_f diff_coef parent_id g_per_mol
#> 1 0.0948 0.49 0.5 5e-10 NA 381
#> 2 0.0948 0.49 0.5 5e-10 1 183
#> 3 0.0948 0.49 0.5 5e-10 2 140
#> transf_f g_as_per_ha app_j_day years_interval
#> 1 NA 6 309 2
#> 2 0.2 0 309 2
#> 3 1.0 0 309 2
library("macrounchained")
# Dry run:
macrounchainedFocusGW(
s = param1,
overwrite = TRUE,
run = FALSE ) # Set to TRUE to run the simulations
#> <2019-05-30|07:28:56> Temporary log-file
#> %USERPROFILE%/AppData/Local/Temp/RtmpCoJU5N/rml_log_2c4c5f681137.txt
#> ********************************************************************************
#> <2019-05-30|07:28:56> Parametrise MACRO simulations
#> ********************************************************************************
#> <2019-05-30|07:28:56> Fetch MACRO executables names and location
#> <2019-05-30|07:28:56> Fetch MACRO version
#> <2019-05-30|07:28:56> Check input parameter-table ('s')
#> <2019-05-30|07:28:56> The parameter table ('s') contains soil/crop scenario
#> <2019-05-30|07:28:56> * Look for scenario-templates and crop-parameters for
#> MACRO In FOCUS version '5.5.4'
#> <2019-05-30|07:28:56> * Import base information on sites/scenario
#> <2019-05-30|07:28:56> * Import crop parameter values
#> <2019-05-30|07:28:56> * Import crop parameter map
#> <2019-05-30|07:28:56> * Match scenario(s) and crop(s) requested by the user
#> with FOCUS scenario and crops
#> <2019-05-30|07:28:56> * Find-out the relevant soil/scenario-template
#> par-file(s)
#> <2019-05-30|07:28:56> Import par-file id 1
#> (%USERPROFILE%/Documents/R/win-library/3.5/macrounchained/focus_scenario/5.5.4/
#> soils/chateaudun.par)
#> <2019-05-30|07:28:56> Find-out order of simulations (metabolite(s)
#> transformation pathway)
#> <2019-05-30|07:28:56> Prepare a list of operations (incl. metabolite(s)
#> intermediate output)
#> <2019-05-30|07:28:56> Identified 5 simulations for 3 substances (2
#> intermediate-outputs)
#> <2019-05-30|07:28:56> Substance properties (updated):
#> soil crop id name kfoc nf dt50 dt50_ref_temp dt50_pf
#> 1 chateaudun cereals, winter 1 GW-M 12 1.0 23 20 2
#> 2 chateaudun cereals, winter 2 Met-M1 114 0.9 19 20 2
#> 3 chateaudun cereals, winter 3 Met-M2 46 0.9 136 20 2
#> exp_temp_resp exp_moist_resp crop_upt_f diff_coef parent_id g_per_mol
#> 1 0.0948 0.49 0.5 5e-10 NA 381
#> 2 0.0948 0.49 0.5 5e-10 1 183
#> 3 0.0948 0.49 0.5 5e-10 2 140
#> transf_f g_as_per_ha app_j_day years_interval f_int focus_soil
#> 1 NA 6 309 2 0 Chateaudun
#> 2 0.2 0 309 2 0 Chateaudun
#> 3 1.0 0 309 2 0 Chateaudun
#> focus_crop focus_index parfile_id as_id met_level f_conv has_met
#> 1 Cereals, winter 2 1 1 0 NA TRUE
#> 2 Cereals, winter 2 1 1 2 0.09606299 TRUE
#> 3 Cereals, winter 2 1 1 2 0.76502732 FALSE
#> <2019-05-30|07:28:56> Table of par-file(s):
#> [1] 1
#> <2019-05-30|07:28:56> Operations register:
#> id run_id is_as is_met is_inter par_file drivingfile
#> 1 1 1 TRUE FALSE FALSE rml_001.par rml_000_inter.bin
#> 2 1 4 TRUE FALSE TRUE rml_001_inter.par rml_000_inter.bin
#> 3 2 2 FALSE TRUE FALSE rml_002.par rml_001_inter.bin
#> 4 2 5 FALSE TRUE TRUE rml_002_inter.par rml_001_inter.bin
#> 5 3 3 FALSE TRUE FALSE rml_003.par rml_002_inter.bin
#> output_macro output_rename indump_rename summary_file
#> 1 MACRO001.BIN rml_001.bin rml_001_indump.tmp rml_001_summary.txt
#> 2 MACRO004.BIN rml_001_inter.bin rml_004_indump.tmp <NA>
#> 3 MACRO002.BIN rml_002.bin rml_002_indump.tmp rml_002_summary.txt
#> 4 MACRO005.BIN rml_002_inter.bin rml_005_indump.tmp <NA>
#> 5 MACRO003.BIN rml_003.bin rml_003_indump.tmp rml_003_summary.txt
#> merge_inter_first
#> 1 FALSE
#> 2 FALSE
#> 3 FALSE
#> 4 FALSE
#> 5 FALSE
#> <2019-05-30|07:28:56> All output-files will be now saved in C:/swash/macro
#> <2019-05-30|07:28:56> Log-file continues in C:/swash/macro/rml_001-005_log.txt
#> <2019-05-30|07:28:56> Exporting updated substance parameters:
#> rml_001-005_s_updated.csv
#> <2019-05-30|07:28:56> Exporting operation register:
#> rml_001-005_operation_register.csv
#> <2019-05-30|07:28:56> Exporting par-file template(s):
#> <2019-05-30|07:28:56> * parfile id 1 (rml_001-005_par_template_id1.par)
#> ================================================================================
#> <2019-05-30|07:28:56> Parametrising and exporting par-files
#> ================================================================================
#> --------------------------------------------------------------------------------
#> <2019-05-30|07:28:56> Simulation 1/5
#> --------------------------------------------------------------------------------
#> <2019-05-30|07:28:56> Substance GW-M. id 1, run id 1
#> <2019-05-30|07:28:56> FOCUS: Chateaudun; Cereals, winter; Irrigated
#> <2019-05-30|07:28:56> Set substance properties:
#> <2019-05-30|07:28:56> * Run id
#> <2019-05-30|07:28:56> * Application rate and date (Julian day) and crop
#> interception
#> <2019-05-30|07:28:56> * Simulation type
#> <2019-05-30|07:28:56> * Simulation identified as: parent
#> <2019-05-30|07:28:56> * Sorption parameters
#> <2019-05-30|07:28:56> * Degradation parameters
#> <2019-05-30|07:28:56> * Crop uptake factor
#> <2019-05-30|07:28:56> * Diffusion coefficient
#> <2019-05-30|07:28:56> * Set FOCUS-crop parameters
#> <2019-05-30|07:28:56> * Information section (end of par-file)
#> <2019-05-30|07:28:56> Exporting the par-file (rml_001.par)
#> <2019-05-30|07:28:56> Generate indump.tmp
#> <2019-05-30|07:28:57> Run MACRO simulation: SKIPPED
#> <2019-05-30|07:28:57> Rename indump.tmp to rml_001_indump.tmp
#> --------------------------------------------------------------------------------
#> <2019-05-30|07:28:57> Simulation 2/5
#> --------------------------------------------------------------------------------
#> <2019-05-30|07:28:57> Substance GW-M. id 1, run id 4
#> <2019-05-30|07:28:57> FOCUS: Chateaudun; Cereals, winter; Irrigated
#> <2019-05-30|07:28:57> Set substance properties:
#> <2019-05-30|07:28:57> * Run id
#> <2019-05-30|07:28:57> * Application rate and date (Julian day) and crop
#> interception
#> <2019-05-30|07:28:57> * Simulation type
#> <2019-05-30|07:28:57> * Simulation identified as: parent, intermediate
#> <2019-05-30|07:28:57> * Sorption parameters
#> <2019-05-30|07:28:57> * Degradation parameters
#> <2019-05-30|07:28:57> * Crop uptake factor
#> <2019-05-30|07:28:57> * Diffusion coefficient
#> <2019-05-30|07:28:57> * Set FOCUS-crop parameters
#> <2019-05-30|07:28:57> * Information section (end of par-file)
#> <2019-05-30|07:28:57> Exporting the par-file (rml_001_inter.par)
#> <2019-05-30|07:28:57> Generate indump.tmp
#> <2019-05-30|07:28:58> Run MACRO simulation: SKIPPED
#> <2019-05-30|07:28:58> Rename indump.tmp to rml_004_indump.tmp
#> --------------------------------------------------------------------------------
#> <2019-05-30|07:28:58> Simulation 3/5
#> --------------------------------------------------------------------------------
#> <2019-05-30|07:28:58> Substance Met-M1. id 2, run id 2
#> <2019-05-30|07:28:58> FOCUS: Chateaudun; Cereals, winter; Irrigated
#> <2019-05-30|07:28:58> Set substance properties:
#> <2019-05-30|07:28:58> * Run id
#> <2019-05-30|07:28:58> * Application rate and date (Julian day) and crop
#> interception
#> <2019-05-30|07:28:58> * Simulation type
#> <2019-05-30|07:28:58> * Simulation identified as: metabolite
#> <2019-05-30|07:28:58> * Sorption parameters
#> <2019-05-30|07:28:58> * Degradation parameters
#> <2019-05-30|07:28:58> * Crop uptake factor
#> <2019-05-30|07:28:58> * Diffusion coefficient
#> <2019-05-30|07:28:58> * Set FOCUS-crop parameters
#> <2019-05-30|07:28:58> * Information section (end of par-file)
#> <2019-05-30|07:28:58> Exporting the par-file (rml_002.par)
#> <2019-05-30|07:28:58> Generate indump.tmp
#> <2019-05-30|07:28:59> Run MACRO simulation: SKIPPED
#> <2019-05-30|07:28:59> Rename indump.tmp to rml_002_indump.tmp
#> --------------------------------------------------------------------------------
#> <2019-05-30|07:28:59> Simulation 4/5
#> --------------------------------------------------------------------------------
#> <2019-05-30|07:28:59> Substance Met-M1. id 2, run id 5
#> <2019-05-30|07:28:59> FOCUS: Chateaudun; Cereals, winter; Irrigated
#> <2019-05-30|07:28:59> Set substance properties:
#> <2019-05-30|07:28:59> * Run id
#> <2019-05-30|07:28:59> * Application rate and date (Julian day) and crop
#> interception
#> <2019-05-30|07:28:59> * Simulation type
#> <2019-05-30|07:28:59> * Simulation identified as: metabolite, intermediate
#> <2019-05-30|07:28:59> * Sorption parameters
#> <2019-05-30|07:28:59> * Degradation parameters
#> <2019-05-30|07:28:59> * Crop uptake factor
#> <2019-05-30|07:28:59> * Diffusion coefficient
#> <2019-05-30|07:28:59> * Set FOCUS-crop parameters
#> <2019-05-30|07:29:00> * Information section (end of par-file)
#> <2019-05-30|07:29:00> Exporting the par-file (rml_002_inter.par)
#> <2019-05-30|07:29:00> Generate indump.tmp
#> <2019-05-30|07:29:00> Run MACRO simulation: SKIPPED
#> <2019-05-30|07:29:00> Rename indump.tmp to rml_005_indump.tmp
#> --------------------------------------------------------------------------------
#> <2019-05-30|07:29:00> Simulation 5/5
#> --------------------------------------------------------------------------------
#> <2019-05-30|07:29:00> Substance Met-M2. id 3, run id 3
#> <2019-05-30|07:29:00> FOCUS: Chateaudun; Cereals, winter; Irrigated
#> <2019-05-30|07:29:00> Set substance properties:
#> <2019-05-30|07:29:00> * Run id
#> <2019-05-30|07:29:00> * Application rate and date (Julian day) and crop
#> interception
#> <2019-05-30|07:29:00> * Simulation type
#> <2019-05-30|07:29:00> * Simulation identified as: metabolite
#> <2019-05-30|07:29:01> * Sorption parameters
#> <2019-05-30|07:29:01> * Degradation parameters
#> <2019-05-30|07:29:01> * Crop uptake factor
#> <2019-05-30|07:29:01> * Diffusion coefficient
#> <2019-05-30|07:29:01> * Set FOCUS-crop parameters
#> <2019-05-30|07:29:01> * Information section (end of par-file)
#> <2019-05-30|07:29:01> Exporting the par-file (rml_003.par)
#> <2019-05-30|07:29:01> Generate indump.tmp
#> <2019-05-30|07:29:01> Run MACRO simulation: SKIPPED
#> <2019-05-30|07:29:01> Rename indump.tmp to rml_003_indump.tmp
#> ================================================================================
#> <2019-05-30|07:29:01> Post-processing operations
#> ================================================================================
#> --------------------------------------------------------------------------------
#> <2019-05-30|07:29:02> Information (traceability & reproducibility)
#> --------------------------------------------------------------------------------
#> <2019-05-30|07:29:02> Call from package: 'macrounchained'
#> <2019-05-30|07:29:02> Model: FOCUS_MACRO_5.5.4; core-model version: v. 5 (=
#> 5.2)
#> <2019-05-30|07:29:02> Information on system, packages and executables
#> $r
#> variable value
#> 1 OS Windows 10 x64 (build 17134)
#> 2 system x86_64, mingw32
#> 3 R_version R version 3.5.1 (2018-07-02)
#> 4 GUI RTerm
#>
#> $packages
#> package version revision date_packaged
#> 1 macrounchained 0.13.0 93b0f40 2019-05-26
#> 2 rmacrolite 0.9.7 9a38321 2019-04-15
#> 3 macroutils2 2.2.3 ef26fd7 2019-04-17
#> 4 codeinfo 0.1.3 a595b27 2019-05-13
#> checksums_checksum
#> 1 97b9addd9d2a360fec8cdbb758ec44d0
#> 2 945f371b037b8aa18b057b82096ee0fd
#> 3 6356c0f3f25b6abd9402e6546c5ab0ef
#> 4 6829117696319b3d3a508d95d8c4420d
#>
#> $files
#> files md5_checksums
#> 1 adodb.dll c0f0651ac9610796599e87fbb3142802
#> 2 AxInterop.MSFlexGridLib.dll ec00ebacae2846394a22eb67f394a0ea
#> 3 conv.exe 921d18f1097802c6f4bfde51f66f37d6
#> 4 exeparfile.exe 29651b9fbbb7ad8fef04d2b7b0056ac5
#> 5 Interop.MSDBGrid.dll b78fb118568484eff04030e52ecc4040
#> 6 Interop.MSFlexGridLib.dll 967cb46d107518c79433f077de3620fa
#> 7 Interop.Threed.dll 149a47480822e743460efbfac396a2c0
#> 8 m2t.exe c9f39e7986008d5b22f062a7253bd36c
#> 9 MACRO_FOCUS.exe 5ae35eecbdd04a021f2a3cbbd54f2b1c
#> 10 MACRO5.dll 1b8f57d0e3746789c4f585b911a3a84c
#> 11 Macro52Model.exe 35f9cd21522402dc3f0dda2e4e6b814e
#>
#> $objects
#> name md5_checksums class environment
#> 1 analyse 0192420d2b2ecea4fef91b7736935cc8 function macroutils2
#> 2 analyse_summary 93c7497ef335b47b01f485fd3af6176c function macrounchained
#> <2019-05-30|07:29:02> Original call:
#> <2019-05-30|07:29:02> macrounchainedFocusGW(s = param1, overwrite = TRUE, run =
#> FALSE)
#> --------------------------------------------------------------------------------
#> <2019-05-30|07:29:02> Final step(s)
#> --------------------------------------------------------------------------------
#> <2019-05-30|07:29:02> Formatting output
#> <2019-05-30|07:29:02> Internal clean-up
#> <2019-05-30|07:29:02> Total operation time at this point: 0.099 mins
#> <2019-05-30|07:29:02> FINAL STEP: Calculate md5-checksums for generated files
#> (rml_001-005_md5.txt) and archive them (rml_001-005_archive.tar.gz)As visible in the operation log outputs of macrounchainedFocusGW(), above, the package macrounchained gives quite extensive information on R-version, the system on which the code was run, and not least on the version of the different key R packages. Besides the package version, are also returned package revision and a package MD5-checksum. The version is defined by the package developer(s). The revision is machine generated hash that can be related to a version of the source code on GitHub. The package MD5 checksum can be used to make sure that the original code was not altered on the computer used for the calculations.
In macrounchainedFocusGW() operation log is also indicated Call from package: 'macrounchained'. The later would be different (likely 'R_GlobalEnv' instead of 'macrounchained') if the function macrounchainedFocusGW() would have been defined by an R script instead of a package.
Finally, the operation log also contains the version and the MD5 checksum of the MACRO executable that was used to run the simulations.
None of these features are fully error- or fool-proof, but they altogether should provide a rather robust way to trace what version of macrounchainedFocusGW() and MACRO were used to generate the simulation results.
The user can obtain the same information by using the function codeinfo() in the package codeinfo:
library("codeinfo")
codeinfo( r = TRUE, packages = c( "macrounchained",
"rmacrolite", "macroutils2", "codeinfo" ) )
#> $r
#> variable value
#> 1 OS Windows 10 x64 (build 17134)
#> 2 system x86_64, mingw32
#> 3 R_version R version 3.5.1 (2018-07-02)
#> 4 GUI RTerm
#>
#> $packages
#> package version revision date_packaged
#> 1 macrounchained 0.13.0 93b0f40 2019-05-26
#> 2 rmacrolite 0.9.7 9a38321 2019-04-15
#> 3 macroutils2 2.2.3 ef26fd7 2019-04-17
#> 4 codeinfo 0.1.3 a595b27 2019-05-13
#> checksums_checksum
#> 1 97b9addd9d2a360fec8cdbb758ec44d0
#> 2 945f371b037b8aa18b057b82096ee0fd
#> 3 6356c0f3f25b6abd9402e6546c5ab0ef
#> 4 6829117696319b3d3a508d95d8c4420d