Batch run MACRO simulations with different substance
properties and application patterns, starting from a
template imported MACRO par-file, including metabolites.
s |
A data.frame containing different sets
of substance properties and application patterns to be
simulated. Each row is a substance. The order of the
column has no importance, but the order of the row
will steer the simulation order. Substances deriving
from the same applied substance will nonetheless be
simulated together. The following columns
must or can be provided
"soil"(optional) Name of the FOCUS-scenario (soil/ site)
to be used for the parameter set. Can only be
used when the argument focus_mode is set
to "gw" . When the column "soil" is
provided, the column
"crop" should be provided too (see below),
but the argument parfile should not be
used, and neither the optional column
"parfile" , as the template
par-file is determined internally.
Partial matching and
transliteration are
used, and casing is ignored, and so that input
like "Ch\^{a}teaudun" , "chateaudun" or
"chat" will all refer to the same
"Ch\^{a}teaudun" FOCUS-scenario. An
error will be raised in
case of multiple matches or no match.
"crop"(optional) Name of the FOCUS-crop
to be used for the parameter set. Can only be
used when the argument focus_mode is set
to "gw" . When the column "crop" is
provided, the column
"soil" should be provided too (see above).
Partial matching and
transliteration are
used, and casing is ignored. Important qualifiers
such as "winter" and "spring" (for
cereals and oil seed rape), or "bulb" ,
"fruiting" , "leafy" and "root"
(for vegetables), should be separated from the
crop name by a comma (as in MACRO In FOCUS user
interface), but the can come either before or
after the crop name. Spaces are otherwise ignored.
Input like "Cereals, Winter" ,
"cereals, winter" , "cer, win" or
even "win, cer" will all refer to the same
Winter cereals FOCUS-crop. "Sugar beets"
is equivalent to "sugarbeets" .
An error will be raised in
case of multiple matches or no match.
"id"Integer-value, between 1 and 998. Unique
identifier of the substance. Will also be used as
a Run ID.
"name"Character-string. Name of the substance.
Names don't need to be unique, but it may be a
good idea if they are.
"kfoc"Numeric-value. [L/kg]. Freundlich
adsorption coefficient of the substance.
"nf"Numeric-value. [-]. Freundlich exponent
of the substance.
"dt50"Numeric-value. [days]. Half-life of
the substance in soil.
"dt50_ref_temp"Numeric-value. [Degrees Celsius].
Reference temperature at which the half-life was
measured.
"dt50_pf"Integer-value. [log10(cm)]. pF at
which the DT50 was measured.
"exp_temp_resp"Numeric-value. [-]. Exponent
of the temperature response (effect of temperature
on degradation).
"exp_moist_resp"Numeric-value. [-]. Exponent
of the moisture response (effect of soil water
content on degradation).
"crop_upt_f"Numeric-value. [-]. Crop uptake
factor. Between 0 (no root uptake of the substance)
and 1 (passive uptake of the substance with root
water uptake).
"diff_coef"Numeric-value. [m2/s]. Substance
diffusion coefficient (in water).
"parent_id"Integer-value. Only for metabolites.
Leave empty (NA_integer_ ) for substances
that are not the degradation product of another
substance. id of the parent substance, i.e.
the substance that degrades into the metabolite
described in this row. For secondary metabolites
(and further), the "parent" will also be a
metabolite.
"g_per_mol"Numeric-value. [g/mol]. Molar mass
of the substance. Only needed when the substance
is degrading into a degradation product or is
the degradation product of another substance.
Leave empty (NA_integer_ ) otherwise.
"g_as_per_ha"Numeric-value or, in case of
multiple applications, character string. [g/ha].
Application
rate (in g substance per hectare) of the substance.
Set to 0 g/ha if the substance is a degradation
product. In case of several applications per year,
give the values separated with a vertical bar
(see https://en.wikipedia.org/wiki/Vertical_bar).
Do quote the values. For example, for two
applications of 1000g/ha and 90g/ha, respectively,
type "1000|900" .
"app_j_day"Integer-value or, in case of
multiple applications, character string. Between
1 and 365.
[Julian day]. Application date of the substance.
Use the application date of the applied substance
(the top parent) if the substance is a
degradation product. In case of several
applications per year, give the values separated
with a vertical bar (see https://en.wikipedia.org/wiki/Vertical_bar).
Do quote the values. For example, for two
applications on Julian days 298 and 305,
respectively, type "298|305"
"f_int"Numeric-value. [-]. Fraction of the
applied product that is intercepted by the crop
canopy.
The columns "parent_id" and "g_per_mol" can
be entirely skipped (missing), and should at least be
only NA when no metabolite is to be simulated. |
… |
Additional parameters passed to specific methods.
Currently not used. |
parfile |
A macroParFile , as imported with
rmacroliteImportParFile-methods |
verbose |
Single integer value. If set to a value < 1 ,
the program is silent (except on errors or warnings). If
set to 1 , the program outputs messages. Values
> 1 may also activate messages from lower level
functions (for debugging purpose). |
indump |
Single logical value. If TRUE (the default),
the so called indump.tmp parameter file is produced.
Must be TRUE when run is TRUE . |
run |
Single logical value. If TRUE (the default),
the parametrised simulations are run. |
overwrite |
Single logical value. If FALSE (the default),
the function will check that the files to be created
do not exist yet, and will stop if
some of the files already exist. Set to TRUE to
silently overwrite existing files. |
analyse |
Single R function . Function to be
used by macrounchained to analyse the results of
MACRO simulations. An example of such function is
macroutilsFocusGWConc .
Notice that the appropriate function depends on what
output needs to be analysed and what parameters are
exported from MACRO, as defined in parfile , so
there is no generic all purpose function to be used here.
When analyse is NULL (the default), MACRO
output is not analysed. |
analyse_args |
A list containing named-items to
be passed as arguments to analyse . An example
of use is analyse_args = list( "quiet" = TRUE ) . |
analyse_summary |
Single R function . Function to be
used by macrounchained to summarise all the results
of MACRO simulations, as output by analyse .
An example of such function is
macroutilsFocusGWConc_summary .
Notice that the appropriate function depends on what
output needs to be summarised and what output analyse
is returning, so there is no generic all purpose function
to be used here. |
dt50_depth_f |
See rmacroliteDegradation . |
keep0conc |
See rmacroliteApplications . |
focus_mode |
See rmacroliteApplications . |
anonymise |
Single boolean value. If TRUE , the function
tries to replace USERNAME, HOMEPATH and USERPROFILE
(i.e Windows environment variables) in paths displayed
in messages by their environment variables, in order
to preserve the user anonymity in the logs produced. |
archive |
Single boolean value. If TRUE , all the files
generated are archived in a .tar.gz -file when
all other operations are finished. Default to
FALSE . |
TO BE WRITTEN.