Initialises a project from scratch or loads the state of an existing one utilising GeoTIFF (*.tif) raster files from, by convention, the following three project root subdirectories:
Input
Intermediate
Result
See subdirectory sections for further information.
catchment is an alias for RPhosFate.
RPhosFate(...)
catchment(...)Arguments used to initialise the project. See argument sections for further information.
An S4 RPhosFate river catchment object.
This directory holds all possible user input raster data (flow obstacles like roads must be considered during generation of the flow accumulation layers and also be cut out from them in order to be properly respected):
acc: Flow accumulations required for transportCalcOrder.
acc_wtd: Weighted flow accumulations required for everything (can be equal to acc).
CFa: (R)USLE C-factors required for erosion.
cha: Channel cells required for everything (1: channel cell, NA: no
channel cell).
clc: Clay contents of top soils in % required for substance
emissions.
dem: Digital elevation model in m a.s.l. (optional).
dir: D8 flow directions required for transportPrerequisites and
substance transport.
fid: Field IDs (optional).
KFa: (R)USLE K-factors required for erosion.
lue: Land use classes (optional).
man: Manning's roughness coefficients required for substance
transport.
xxc: Substance contents of top soils in mg/kg required for substance
emissions, for example, ppc for PP top soil contents.
rds: Road cells required for transportPrerequisites (0: road cell
without subsurface drainage, 1: road cell with subsurface drainage, NA:
no road cell).
RFa: (R)USLE R-factors required for erosion.
slp: Slopes in % required for everything.
wsh: Watershed (optional).
This directory holds intermediate calculations:
inl: Cells representing inlets at roads (storm drains).
LFa: L-factors.
rhy: Hydraulic radii in m.
rip: Cells representing the riparian zones within channel cells.
SFa: RUSLE S-factors.
slp_cap: Capped slopes in %.
This directory holds the model results:
ero: Erosion in t/cell/yr.
xxe: Substance emissions in kg/cell/yr, for example, ppe for PP emissions.
xxr: Substance retentions in t/cell/yr (SS) or kg/cell/yr, for example, ppr for PP retentions.
xxt: Substance transports in t/cell/yr (SS) or kg/cell/yr, for example, ppt for PP transports.
xxt_cld: Substance cell loads in t/cell/yr (SS) or kg/cell/yr, for example, ppt_cld for PP cell loads.
xxt_ctf: Substance cell transfers in t/cell/yr (SS) or kg/cell/yr, for example, ppt_ctf for PP transfers.
xxt_inp: Substance inputs into surface waters in t/cell/yr (SS) or kg/cell/yr, for example, ppt_inp for PP inputs into surface waters.
xxt_out: Substance outlet loads of subsurface drainages in t/cell/yr (SS) or kg/cell/yr, for example, ppt_out for PP outlet loads.
cv_dir: A character vector specifying the project root (first position)
and optionally the Monte Carlo input data directory (second position).
ls_ini: A logical scalar specifying if the state of an existing project
shall be loaded from disk (defaults to FALSE). Parameters or substance
parameter values specified via the ... argument take precedence over loaded
ones.
is_MCi: An integer scalar specifying the current Monte Carlo iteration if
applicable (defaults to integer(), which means Monte Carlo simulation mode
is disabled).
cv_MCl: A character vector specifying the names of the layers, which
shall be written to disk with the associated Monte Carlo iteration in their
filenames upon calling the appropriate methods (defaults to "xxt"; no
effect in case Monte Carlo simulation mode is disabled).
ns_slp_min: A numeric scalar specifying the minimum bounding slope in %
(defaults to 0.001).
ns_slp_max: A numeric scalar specifying the maximum bounding slope in %
(defaults to 999.0).
ns_rhy_a: A numeric scalar specifying a network constant depending on the
discharge frequency needed for the calculation of the hydraulic radius, which
in turn is a prerequisite for substance transport (defaults to 0.09
representing a discharge frequency of approximately six years).
ns_rhy_b: A numeric scalar specifying a geometry scaling exponent
depending on the discharge frequency needed for the calculation of the
hydraulic radius, which in turn is a prerequisite for substance transport
(defaults to 0.50 representing a discharge frequency of approximately six
years).
ns_cha_rto: A numeric scalar specifying the ratio of the channel to the
cell width determining the widths of the riparian zones required for
substance transport (defaults to 0.5).
ns_man_rip: A numeric scalar specifying Manning's roughness coefficient
of the riparian zones within channel cells required for substance
transport (defaults to 0.32).
ns_man_cha: A numeric scalar specifying Manning's roughness coefficient
of the channel within channel cells required for substance transport
(defaults to 0.04).
ns_dep_ovl: A numeric scalar specifying the overland deposition rate per
second required for substance transport (calibration parameter; no
default).
ns_dep_cha: A numeric scalar specifying the channel deposition rate per
second required for substance transport (calibration parameter; no
default).
nv_tfc_inl: A named numeric vector specifying the inlet transfer
coefficients required for substance transport, for example, c(SS = 0.6, PP = 0.6) (no default).
nv_enr_rto A named numeric vector specifying the substance enrichment
ratios required for substance except SS transport, for example, c(PP = 2.0) (calibration parameter; no default).
iv_fDo: An integer vector specifying the outflow direction vector
required for substance transport (defaults to ArcGIS codes).
nm_olc: A two column numeric matrix specifying one or more catchment
outlet coordinates required for the in-channel retention ratio of
calibrationQuality (no default).
df_cdt: A data.frame with calibration data, which must have at least
the following three columns and one or more columns with substance river
loads in t/yr (no default):
ID: ID(s) of the gauge(s)
x: x-coordinate(s) of the gauge(s)
y: y-coordinate(s) of the gauge(s)
This mode can make use of repeated random samples, i.e. raster data, of distributions of about all input data. The filenames of the Monte Carlo input raster data must contain the specified iteration, for example, CFa12.tif for the twelfth iteration of the C-factors input data, and can reside in a separate directory. In case no Monte Carlo raster file is found for a certain layer in the designated directory, the respective project root subdirectory is searched for one and finally the “normal” project input raster data is utilised.
# \donttest{
# temporary demonstration project copy
cv_dir <- demoProject()
#> Warning: A folder called "demoProject" already exists and is left as is.
# initialise project from scratch
x <- RPhosFate(
cv_dir = cv_dir,
ns_dep_ovl = 25e-4,
ns_dep_cha = 0.0,
nv_tfc_inl = c(SS = 0.6, PP = 0.6),
nv_enr_rto = c(PP = 2.0),
nm_olc = matrix(c(4704255, 2795195), ncol = 2L),
df_cdt = read.table(
file.path(cv_dir, "cdt.txt"),
header = TRUE,
stringsAsFactors = FALSE
)
)
# load state of existing project in Monte Carlo simulation mode
x <- RPhosFate(
cv_dir = c(
cv_dir,
system.file("tinytest", "testProject", package = "RPhosFate")
),
ls_ini = TRUE,
is_MCi = 1L,
cv_MCl = c("xxt", "xxt_cld")
)# }