DEM related input

Description

Clips, pre-processes and calculates or determines all input data related to the digital elevation model (DEM) in the broader sense: acc_inf, cha, dem, dir_inf, rds, slp_inf, and wsh.

Requires the WhiteboxTools binary (whitebox::install_whitebox) to be installed on your computer.

Usage

DEMrelatedInput(
  cv_dir,
  cs_dem,
  cs_cha,
  sp_msk,
  sp_olp,
  sp_sds,
  cs_rds = NULL,
  ns_cha = NULL,
  ns_brn = 50,
  is_adj = 1L,
  is_ths = 1L,
  ls_mD8 = FALSE,
  ls_tmp = FALSE
)

Arguments

Details

This function applies the following (pre-processing) steps to ensure hydrologic consistency of the generated input data:

• Stream burning and orientation of cells adjacent to channel cells approximately into the direction of channel cells (no effect with ns_brn = 0).

• Depression breaching.

• Tracing of downslope flowpaths from the provided channel sources.

When roads are provided, they are considered as flow obstacles breaking the continuity of the calculated flow accumulations.

ns_cha can be used to enhance the channel network obtained by the tracing of downslope flowpaths from the provided channel sources.

dem represents the breached DEM with reversed stream burning if applicable. The basis for the calculation of the D-infinity slopes provided by slp_inf, however, is the original DEM.

Value

A two column numeric matrix specifying one or more catchment outlet coordinates and side effects in the form of raster files.

References

Lindsay, J.B., 2016. Efficient hybrid breaching-filling sink removal methods for flow path enforcement in digital elevation models. Hydrological Processes 30, 846–857. https://doi.org/10.1002/hyp.10648

Tarboton, D.G., 1997. A new method for the determination of flow directions and upslope areas in grid digital elevation models. Water Resour. Res. 33, 309–319. https://doi.org/10.1029/96WR03137

See Also

RPhosFate, catchment

Examples

## Not run: 
# obtain temporary project root directory
cv_dir <- normalizePath(
  tempfile("cmt"),
  winslash = .Platform$file.sep,
  mustWork = FALSE
)
# obtain directory holding "large" rasters and other required data sets
cs_dir_lrg <- system.file("tinytest", "largeData", package = "RPhosFate")

nm_olc <- DEMrelatedInput(
  cv_dir = cv_dir,
  cs_dem = file.path(cs_dir_lrg, "dem_lrg.tif"),
  cs_cha = file.path(cs_dir_lrg, "cha_lrg.tif"),
  sp_msk = terra::vect(file.path(cs_dir_lrg, "msk.shp")),
  sp_olp = terra::vect(file.path(cs_dir_lrg, "olp.shp")),
  sp_sds = terra::vect(file.path(cs_dir_lrg, "sds.shp")),
  cs_rds = file.path(cs_dir_lrg, "rds_lrg.tif"),
  ls_tmp = TRUE
)
## End(Not run)

Initialise project

Description

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.

Usage

RPhosFate(...)

catchment(...)

Arguments

Value

An S4 RPhosFate river catchment object.

Input subdirectory

This directory holds all possible user input raster data (flow obstacles like roads must be considered during the generation of the flow accumulation layer and must also be cut out from it in order to be properly respected):

• acc_inf: D-infinity flow accumulations in number of upslope grid cells required for everything.

• 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_inf: D-infinity flow directions in azimuth degrees measured from north (0 to 360 clockwise) 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_inf: D-infinity slopes in % required for everything.

• wsh: Watershed (optional).

Intermediate subdirectory

This directory holds intermediate calculations:

• inl: Cells representing inlets at roads (storm drains).

• LFa: L-factors.

• rip: Cells representing the riparian zones within channel cells.

• SFa: RUSLE S-factors.

• slp_cap: Capped slopes in %.

Result subdirectory

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.

Data management and processing arguments

• 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_ths: An integer scalar holding the number of threads to use for processing (defaults to 1).

• 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).

Model parameter arguments

• ns_slp_min: A numeric scalar specifying the minimum bounding slope in % (defaults to 1.0).

• 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).

• 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)

Monte Carlo simulation mode

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.

See Also

saveState, demoProject

Examples

# temporary demonstration project copy
cv_dir <- demoProject()

# 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")
)

RPhosFate class

Description

An S4 object representing a river catchment.

Slots

cv_dir

A character vector holding 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 was loaded from disk.

is_ths

An integer scalar holding the number of threads to use for processing, where applicable.

is_MCi

An integer scalar holding the current Monte Carlo iteration if applicable.

cv_MCl

A character vector holding 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.

parameters

An S4 object holding the model parameters.

topo

An S4 object holding the raster layers related to topography in the broader sense.

erosion

An S4 object holding the raster layers related to erosion.

transport

An S4 object holding raster layers required for modelling transport.

substances

An S4 object holding the substance raster layer containers.

helpers

An S4 object holding helper data.

See Also

RPhosFate, catchment

One dimensional automatic model calibration

Description

Automatically calibrates the model with the help of a combination of golden section search and successive parabolic interpolation.

Usage

## S4 method for signature 'RPhosFate'
autoCalibrate(
  x,
  substance,
  col,
  interval,
  metric,
  tol = min(interval) * 0.1,
  parameter = NULL
)

Arguments

Value

An S4 RPhosFate river catchment object and side effects in the form of raster files.

See Also

snapGauges, optimize

Examples

# temporary demonstration project copy
cv_dir <- demoProject()
# load temporary demonstration project
x <- RPhosFate(
  cv_dir = cv_dir,
  ls_ini = TRUE
)
# presupposed method calls
x <- firstRun(x, "SS")
x <- snapGauges(x)

x <- autoCalibrate(
  x,
  "SS",
  col = "SS_load",
  interval = c(1e-3, 2e-3),
  metric = "KGE"
)

Two dimensional automatic model calibration

Description

Automatically calibrates the model with the help of a general-purpose optimisation function. In contrast to autoCalibrate, this method always utilises the overland and channel deposition rate at the same time and never the respective enrichment ratio for calibration. Beware of local optima and parameters approximately within the convergence tolerance of interval end-points.

Usage

## S4 method for signature 'RPhosFate'
autoCalibrate2(
  x,
  substance,
  col,
  metric,
  method = "Nelder-Mead",
  lower = 0,
  upper = 0.1,
  control = list(fnscale = if (metric %in% c("NSE", "mNSE", "KGE")) -1 else 1)
)

Arguments

Value

An S4 RPhosFate river catchment object and side effects in the form of raster files.

See Also

snapGauges

Examples

# temporary demonstration project copy
cv_dir <- demoProject()
# load temporary demonstration project
x <- RPhosFate(
  cv_dir = cv_dir,
  ls_ini = TRUE
)
# presupposed method calls
x <- firstRun(x, "SS")
x <- snapGauges(x)

x <- autoCalibrate2(
  x,
  "SS",
  col = "SS_load",
  metric = "KGE",
  method = "L-BFGS-B",
  lower = c(1e-3, 0),
  upper = c(2e-3, 2e-3),
  control = list(fnscale = -1, parscale = c(1e-3, 1e-3), factr = 1e12)
)

Calibration quality

Description

Assesses the model's calibration quality with the help of the pairwise complete modelled as well as observed loads and the following metrics:

• NSE: Nash-Sutcliffe Efficiency

• mNSE: Modified Nash-Sutcliffe Efficiency (j = 1)

• KGE: Modified Kling-Gupta Efficiency

• RMSE: Root Mean Square Error

• PBIAS: Percent Bias

• RSR: Ratio of the RMSE to the standard deviation of the observations

• RCV: Ratio of the coefficients of variation

• GMRAE: Geometric Mean Relative Absolute Error

• MdRAE: Median Relative Absolute Error

In addition, a scatter plot with the observed river loads on the x- and the modelled river loads on the y-axis is displayed and provides a visual impression of the model performance. Other elements of this plot are an identity line (solid) and plus/minus 30% deviation lines (dashed).

Usage

## S4 method for signature 'RPhosFate'
calibrationQuality(x, substance, col)

Arguments

Value

A named numeric vector containing the assessed metrics along with the in-channel retention ratio (one minus sum of xxt at catchment outlet(s) divided by sum of xxt_inp).

References

Nash, J.E., Sutcliffe, J.V., 1970. River flow forecasting through conceptual models part I – a discussion of principles. Journal of Hydrology 10, 282–290. https://doi.org/10.1016/0022-1694(70)90255-6

Legates, D.R., McCabe Jr., G.J., 1999. Evaluating the use of “goodness-of-fit” measures in hydrologic and hydroclimatic model validation. Water Resources Research 35, 233–241. https://doi.org/10.1029/1998WR900018

Kling, H., Fuchs, M., Paulin, M., 2012. Runoff conditions in the upper Danube basin under an ensemble of climate change scenarios. Journal of Hydrology 424–425, 264–277. https://doi.org/10.1016/j.jhydrol.2012.01.011

Moriasi, D.N., Arnold, J.G., Van Liew, M.W., Bingner, R.L., Harmel, R.D., Veith, T.L., 2007. Model evaluation guidelines for systematic quantification of accuracy in watershed simulations. Transactions of the ASABE 50, 885–900.

See Also

snapGauges, autoCalibrate, autoCalibrate2

Examples

# temporary demonstration project copy
cv_dir <- demoProject()
# load temporary demonstration project
x <- RPhosFate(
  cv_dir = cv_dir,
  ls_ini = TRUE
)
# presupposed method calls
x <- firstRun(x, "SS")
x <- snapGauges(x)

calibrationQuality(x, "SS", "SS_load")

Demonstration project

Description

Copies a demonstration project to an existing or a temporary directory.

The demonstration project data are a derivative of the

• Geoland.at (digital elevation model),

• AMA (field data; utilised dataset with the ID 35e36014-ec69-439b-8629-389f52ffaa92 was removed from Offene Daten Österreich),

• BMLRT (channel data) and

• GIP.at (road data)

data sets, used and licensed under (CC BY 4.0) by Gerold Hepp.

While the data represent a real catchment (HOAL), some of them are fictitious, but plausible. These are, among others, R- and C-factors, soil and related data, existence of subsurface drainage at road embankments as well as substance river loads.

Usage

demoProject(cs_dir = tempdir(TRUE))

Arguments

Value

A character string containing the demonstration project root directory.

See Also

RPhosFate, catchment

Examples

demoProject()

Emission

Description

Calculates and writes substance emissions to disk.

Usage

## S4 method for signature 'RPhosFate'
emission(x, substance = "PP")

Arguments

Value

An S4 RPhosFate river catchment object and side effects in the form of raster files.

See Also

firstRun, subsequentRun

Examples

# temporary demonstration project copy
cv_dir <- demoProject()
# load temporary demonstration project
x <- RPhosFate(
  cv_dir = cv_dir,
  ls_ini = TRUE
)
# presupposed method calls
x <- erosionPrerequisites(x)
x <- erosion(x)

x <- emission(x, "PP")

Erosion

Description

Calculates and writes (R)USLE erosion to disk.

Usage

## S4 method for signature 'RPhosFate'
erosion(x)

Arguments

Value

An S4 RPhosFate river catchment object and side effects in the form of raster files.

References

Renard, K.G., Foster, G.R., Weesies, G.A., McCool, D.K., Yoder, D.C., 1997. Predicting soil erosion by water: a guide to conservation planning with the Revised Universal Soil Loss Equation (RUSLE), Agriculture Handbook. U.S. Government Printing Office, Washington, DC.

Wischmeier, W.H., Smith, D.D., 1978. Predicting rainfall erosion losses. A guide to conservation planning, Agriculture Handbook. U.S. Government Printing Office, Washington, DC.

See Also

firstRun, subsequentRun

Examples

# temporary demonstration project copy
cv_dir <- demoProject()
# load temporary demonstration project
x <- RPhosFate(
  cv_dir = cv_dir,
  ls_ini = TRUE
)
# presupposed method call
x <- erosionPrerequisites(x)

x <- erosion(x)

Erosion prerequisites

Description

Calculates and writes capped slopes, L- and RUSLE S-factors (equations for summer conditions and slopes \geq 15 ft) to disk.

Usage

## S4 method for signature 'RPhosFate'
erosionPrerequisites(x)

Arguments

Value

An S4 RPhosFate river catchment object and side effects in the form of raster files.

References

Desmet, P.J.J., Govers, G., 1996. A GIS procedure for automatically calculating the USLE LS factor on topographically complex landscape units. Journal of Soil and Water Conservation 51, 427–433.

Renard, K.G., Foster, G.R., Weesies, G.A., McCool, D.K., Yoder, D.C., 1997. Predicting soil erosion by water: a guide to conservation planning with the Revised Universal Soil Loss Equation (RUSLE), Agriculture Handbook. U.S. Government Printing Office, Washington, DC.

See Also

firstRun, subsequentRun

Examples

# temporary demonstration project copy
cv_dir <- demoProject()
# load temporary demonstration project
x <- RPhosFate(
  cv_dir = cv_dir,
  ls_ini = TRUE
)

x <- erosionPrerequisites(x)

First run

Description

Calls erosionPrerequisites, erosion, emission, transportPrerequisites and transport in the mentioned order. While transport is called for the specified substance only, emission is called for all substances whose top soil concentrations have been provided.

Usage

## S4 method for signature 'RPhosFate'
firstRun(x, substance = "PP")

Arguments

Value

An S4 RPhosFate river catchment object and side effects in the form of raster files.

See Also

subsequentRun

Examples

# temporary demonstration project copy
cv_dir <- demoProject()
# load temporary demonstration project
x <- RPhosFate(
  cv_dir = cv_dir,
  ls_ini = TRUE
)

x <- firstRun(x, "SS")

Get layer

Description

Obtains a project raster layer for further analysis.

Usage

## S4 method for signature 'RPhosFate'
getLayer(x, i, j = NULL)

## S4 method for signature 'RPhosFate,ANY,ANY'
x[i, j]

Arguments

Value

A terra::SpatRaster object.

Input subdirectory

This directory holds all possible user input raster data (flow obstacles like roads must be considered during the generation of the flow accumulation layer and must also be cut out from it in order to be properly respected):

• acc_inf: D-infinity flow accumulations in number of upslope grid cells required for everything.

• 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_inf: D-infinity flow directions in azimuth degrees measured from north (0 to 360 clockwise) 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_inf: D-infinity slopes in % required for everything.

• wsh: Watershed (optional).

Intermediate subdirectory

This directory holds intermediate calculations:

• inl: Cells representing inlets at roads (storm drains).

• LFa: L-factors.

• rip: Cells representing the riparian zones within channel cells.

• SFa: RUSLE S-factors.

• slp_cap: Capped slopes in %.

Result subdirectory

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.

Examples

# temporary demonstration project copy
cv_dir <- demoProject()
# load temporary demonstration project
x <- RPhosFate(
  cv_dir = cv_dir,
  ls_ini = TRUE
)
# presupposed method call
x <- firstRun(x, "SS")

getLayer(x, "dir_inf")
getLayer(x, "xxt", "SS")
getLayer(x, "xxe", "PP")

Get parameter(s)

Description

Obtains a single model parameter or all model parameters at once.

Usage

## S4 method for signature 'RPhosFate'
getParameter(x, parameter = NULL)

Arguments

Value

Depends on the queried parameter or a list in case of all parameters. See model parameter arguments section for further information.

Model parameter arguments

• ns_slp_min: A numeric scalar specifying the minimum bounding slope in % (defaults to 1.0).

• 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).

• 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)

See Also

setParameter

Examples

# temporary demonstration project copy
cv_dir <- demoProject()
# load temporary demonstration project
x <- RPhosFate(
  cv_dir = cv_dir,
  ls_ini = TRUE
)

getParameter(x)
getParameter(x, "ns_dep_ovl")

Convert ERDAS IMAGINE to GeoTIFF raster files

Description

Converts all ERDAS IMAGINE raster files in a directory and its subdirectories into GeoTIFF raster files.

Usage

img2tif(cs_dir, cs_crs = NULL)

Arguments

Value

A character vector containing the paths to the processed ERDAS IMAGINE raster files.

Save state

Description

Saves parameters (parameters.yaml) to disk.

Usage

## S4 method for signature 'RPhosFate'
saveState(x)

Arguments

Value

NULL invisibly and side effects in the form of files.

See Also

RPhosFate, catchment

Examples

# temporary demonstration project copy
cv_dir <- demoProject()
# load temporary demonstration project
x <- RPhosFate(
  cv_dir = cv_dir,
  ls_ini = TRUE
)

saveState(x)

Set parameter(s)

Description

Sets one or more model parameters or substance parameter values.

Usage

## S4 method for signature 'RPhosFate'
setParameter(x, ...)

Arguments

Value

An S4 RPhosFate river catchment object.

Model parameter arguments

• ns_slp_min: A numeric scalar specifying the minimum bounding slope in % (defaults to 1.0).

• 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).

• 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)

See Also

getParameter

Examples

# temporary demonstration project copy
cv_dir <- demoProject()
# load temporary demonstration project
x <- RPhosFate(
  cv_dir = cv_dir,
  ls_ini = TRUE
)

x <- setParameter(x, ns_dep_ovl = 15e-4)
x <- setParameter(
  x,
  nv_tfc_inl = c(SS = 0.6, PP = 0.6),
  nv_enr_rto = c(PP = 1.4)
)

Snap gauge(s)

Description

Snaps the coordinates of the provided calibration gauges to the respective midpoint of the nearest channel cell.

Usage

## S4 method for signature 'RPhosFate'
snapGauges(x)

Arguments

Value

An S4 RPhosFate river catchment object.

See Also

calibrationQuality, autoCalibrate, autoCalibrate2

Examples

# temporary demonstration project copy
cv_dir <- demoProject()
# load temporary demonstration project
x <- RPhosFate(
  cv_dir = cv_dir,
  ls_ini = TRUE
)

x <- snapGauges(x)

Subsequent run

Description

Calls transport for the specified substance and optionally erosionPrerequisites, erosion, emission and transportPrerequisites beforehand.

Usage

## S4 method for signature 'RPhosFate'
subsequentRun(
  x,
  substance = "PP",
  erosionPrerequisites = FALSE,
  erosion = FALSE,
  emission = FALSE,
  transportPrerequisites = FALSE
)

Arguments

Value

An S4 RPhosFate river catchment object and side effects in the form of raster files.

See Also

firstRun

Examples

# temporary demonstration project copy
cv_dir <- demoProject()
# load temporary demonstration project
x <- RPhosFate(
  cv_dir = cv_dir,
  ls_ini = TRUE
)
# presupposed method call
x <- firstRun(x, "SS")

x <- subsequentRun(x, "PP")

Transport

Description

Calculates and writes substance retentions, transports and cell loads as well as transfers to disk.

Usage

## S4 method for signature 'RPhosFate'
transport(x, substance = "PP")

Arguments

Value

An S4 RPhosFate river catchment object and side effects in the form of raster files.

References

Engman, E.T., 1986. Roughness coefficients for routing surface runoff. Journal of Irrigation and Drainage Engineering 112, 39–53.

Molnár, P., Ramírez, J.A., 1998. Energy dissipation theories and optimal channel characteristics of river networks. Water Resources Research 34, 1809–1818. https://doi.org/10.1029/98WR00983

See Also

firstRun, subsequentRun

Examples

# temporary demonstration project copy
cv_dir <- demoProject()
# load temporary demonstration project
x <- RPhosFate(
  cv_dir = cv_dir,
  ls_ini = TRUE
)
# presupposed method calls
x <- erosionPrerequisites(x)
x <- erosion(x)
x <- emission(x, "PP")
x <- transportPrerequisites(x)

x <- transport(x, "PP")

Transport prerequisites

Description

Determines cells representing inlets as well as riparian zones before writing them to disk.

Usage

## S4 method for signature 'RPhosFate'
transportPrerequisites(x)

Arguments

Value

An S4 RPhosFate river catchment object and side effects in the form of raster files.

See Also

firstRun, subsequentRun

Examples

# temporary demonstration project copy
cv_dir <- demoProject()
# load temporary demonstration project
x <- RPhosFate(
  cv_dir = cv_dir,
  ls_ini = TRUE
)

x <- transportPrerequisites(x)