diff --git a/dev/CONTRIBUTING.html b/dev/CONTRIBUTING.html index b9e1d31..76eee74 100644 --- a/dev/CONTRIBUTING.html +++ b/dev/CONTRIBUTING.html @@ -3,7 +3,7 @@ - +
@@ -25,7 +25,7 @@
- +
@@ -121,15 +121,15 @@

Commit message guidelines

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/dev/LICENSE.html b/dev/LICENSE.html index cdd3e5e..7ded7b7 100644 --- a/dev/LICENSE.html +++ b/dev/LICENSE.html @@ -3,7 +3,7 @@ - +
@@ -25,7 +25,7 @@
- +
@@ -298,15 +298,15 @@

AGPL License

-

Site built with pkgdown 2.0.9.

+

Site built with pkgdown 2.1.1.

- - + + diff --git a/dev/articles/basicWorkflow.html b/dev/articles/basicWorkflow.html index 7a0ad13..165d417 100644 --- a/dev/articles/basicWorkflow.html +++ b/dev/articles/basicWorkflow.html @@ -12,7 +12,6 @@ - - +
@@ -43,7 +42,7 @@
  • - +
  • @@ -52,7 +51,7 @@
    • - +
    @@ -110,9 +109,9 @@

    Basic modelling workflow

    Gerold Hepp

    -

    2024-05-25

    +

    2024-12-15

    - Source: vignettes/basicWorkflow.Rmd + Source: vignettes/basicWorkflow.Rmd
    @@ -217,7 +216,7 @@

    Calibrate PP

    Save state

    -

    Write parameters and transport calculation order to disk:

    +

    Write parameters to disk:

    @@ -238,9 +237,7 @@

    Return to the calibrat +

    @@ -253,16 +250,16 @@

    Return to the calibrat

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/dev/articles/index.html b/dev/articles/index.html index 05b8f57..d650c1c 100644 --- a/dev/articles/index.html +++ b/dev/articles/index.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +
    @@ -97,15 +97,15 @@

    All vignettes

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/dev/authors.html b/dev/authors.html index 2d86459..f6ee25b 100644 --- a/dev/authors.html +++ b/dev/authors.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +
    @@ -82,16 +82,16 @@

    Authors and Citation

    - +

    Citation

    - Source: inst/CITATION + Source: inst/CITATION
    @@ -140,15 +140,15 @@

    Citation

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/dev/index.html b/dev/index.html index f1e8ad0..4817ffa 100644 --- a/dev/index.html +++ b/dev/index.html @@ -12,7 +12,7 @@ - + - +
    @@ -43,7 +43,7 @@
  • - +
  • @@ -52,7 +52,7 @@
    • - +
    @@ -181,16 +181,16 @@

    Developers

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/dev/news/index.html b/dev/news/index.html index 786fcc0..3b55845 100644 --- a/dev/news/index.html +++ b/dev/news/index.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    Changelog

    - Source: NEWS.md + Source: NEWS.md
    -

    RPhosFate v1.0.4.9000

    -
    • Switched to utilising the SpatRaster and SpatVector classes from the terra package instead of the RasterLayer class from the raster and the Spatial*DataFrame classes from the sp packages.
      • -
    • Added ns_cha argument to DEMrelatedInput() function: allows for specifying the minimum (weighted) flow accumulation determining a channel.
      • -
    • Added is_ths argument to RPhosFate() and catchment() constructors: allows for specifying the number of threads to use for processing, where applicable.
      • +

      RPhosFate v1.0.4.9004

      +

      This version introduces several breaking changes into RPhosFate.

      +
      +

      Overview

      +
      • Use of the D-infinity instead of the D8 flow method, however, the D8 flow method can still be mimicked by rounding the D-infinity flow directions to the nearest multiple of 45 degrees.
        • +
      • Weighted flow accumulations are no longer supported for the time being.
        • +
      • The basis for the calculation of the D-infinity slopes is the original digital elevation model and not the breached one with reversed stream burning any longer.
        • +
      • The default value for the parameter holding the minimum bounding slope (ns_slp_min) is now 1 instead of 0.001%.
        • +
      • The L factor is now calculated using the original equation (9) developed by Desmet and Govers (1996) and not the adjusted one from Kovacs (2013).
        • +
      • The channel retentions of the substance outlet loads of subsurface drainages are now calculated analogous to the overland retentions of the local emissions, i.e. by using half of the flow path lengths.
        • +
      • +RPhosFate now utilises the terra instead of the raster package.
      • Ceased support for ERDAS IMAGINE (*.img) raster files. img2tif() can be used to convert all ERDAS IMAGINE raster files in a directory and its subdirectories into GeoTIFF raster files.
      • Dropped backward compatibility to major version zero.
        • +
      +
      +

      Details

      +
      • Input data changes: +
        • Removed the layers holding the (weighted) D8 flow accumulations (acc and acc_wtd) and added acc_inf holding the D-infinity flow accumulations.
          • +
        • Removed the layer holding the D8 flow directions (dir) and added dir_inf holding the D-infinity flow directions.
          • +
        • Removed the layer holding the D8 slopes (slp) and added slp_inf holding the D-infinity slopes.
          • +
        • +
      • +DEMrelatedInput() function changes: +
        • Adjusted it to reflect the aforementioned input data changes.
          • +
        • Added ns_cha argument to it: allows for specifying the minimum D8 flow accumulation determining a channel.
          • +
        • Added ls_fD8 argument to it: allows for mimicking D8 flow directions by rounding the D-infinity flow directions to the nearest multiple of 45 degrees. Please note that this treatment is always applied to channel cells independently of this argument.
          • +
        • Removed the cs_wgs and cs_dir arguments from it: These input data are no longer supported for the time being.
          • +
        • +
      • Switched to utilising the SpatRaster and SpatVector classes from the terra package instead of the RasterLayer class from the raster and the Spatial*DataFrame classes from the sp packages.
        • +
      • Added is_ths argument to the RPhosFate() and catchment() constructors: allows for specifying the number of threads to use for processing, where applicable.
        • +
      • Removed the layer holding the hydraulic radii (rhy), as the calculation of the hydraulic radii is now integrated into the transport() method. This implies that the transportPrerequisites() method does not save it to disk any longer.
        • +
      • Removed the parameter holding the D8 outflow direction vector (iv_fDo). Existing parameter files (parameters.yaml) containing it can still be used, but the parameter is removed upon saving a project’s state.
        • +
      • Removed the transportCalcOrder() method, as the determination of the cell transport calculation order is now integrated into the transport() method. This implies that the firstRun() as well as subsequentRun() methods do not call it any longer and the saveState() method does not save the transport calculation order to disk any longer.
        • +
      • The calibrationQuality() method now returns its return value invisibly.
        • +
      • Considerably revised the internal RPhosFateHelpers class.
      • Removed spatstat.geom from imported packages list (utilised functionality is now also provided by terra).
        • -
      • Bumped minimum tested R version from 4.2.3 to 4.3.2 using the corresponding Posit public package manager snapshot.
        • +
      • Bumped the minimum tested R version from 4.2.3 to 4.3.2 using the corresponding Posit public package manager snapshot.
      • Slightly improved documentation.
      • Major internal code improvements.
      +

    RPhosFate v1.0.42023-10-07

    -
    • The current raster package does not compress GeoTIFF raster files any longer by default. This is probably due to the switch from rgdal to terra and has been fixed by generally using the LZW algorithm.
      • -
    • Fixed warning “GDAL Message 6: driver GTiff does not support creation option COMPRESSED” curiously only occurring in the reference on GitHub Pages.
      • -
    • Removed hydroGOF from imported packages list (maptools is retiring and hydroGOF depends on it via hydroTSM). Thanks to Roger Bivand for raising this issue (#17).
      • -
    • Bumped minimum tested R version from 4.2.2 to 4.2.3 using the corresponding Posit public package manager snapshot.
      • +
      • Removed hydroGOF from imported packages list (maptools is retiring and hydroGOF depends on it via hydroTSM). Thanks to Roger Bivand for raising this issue (#17).
        • +
      • Bumped the minimum tested R version from 4.2.2 to 4.2.3 using the corresponding Posit public package manager snapshot.
      • Slightly improved documentation.

    RPhosFate v1.0.32023-03-06

    • Removed rgdal from suggested packages list and set minimum required version of the raster package to ≥ 3.6.3 (rgdal is retiring and raster ≥ 3.6.3 does not depend on it any longer). Thanks to Roger Bivand for raising this issue (#17).
      • -
    • Bumped minimum tested R version from 4.1.2 to 4.2.2 using the corresponding MRAN repository snapshot.
      • +
    • Bumped the minimum tested R version from 4.1.2 to 4.2.2 using the corresponding MRAN repository snapshot.
    • Slightly improved documentation.
    • Minor internal code improvements.
    @@ -152,11 +181,10 @@

    RPhosFate v0

    RPhosFate v0.10.0

    -
    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/dev/pkgdown.yml b/dev/pkgdown.yml index bff539e..bc81368 100644 --- a/dev/pkgdown.yml +++ b/dev/pkgdown.yml @@ -1,10 +1,9 @@ pandoc: 3.1.11 -pkgdown: 2.0.9 +pkgdown: 2.1.1 pkgdown_sha: ~ articles: basicWorkflow: basicWorkflow.html -last_built: 2024-05-25T17:22Z +last_built: 2024-12-15T19:06Z urls: reference: https://gisler.github.io/RPhosFate/reference article: https://gisler.github.io/RPhosFate/articles - diff --git a/dev/reference/DEMrelatedInput.html b/dev/reference/DEMrelatedInput.html index 862b4a9..421376b 100644 --- a/dev/reference/DEMrelatedInput.html +++ b/dev/reference/DEMrelatedInput.html @@ -1,15 +1,14 @@ DEM related input — DEMrelatedInput • RPhosFate - +
    @@ -31,7 +30,7 @@
    - +

    DEM related input

    - Source: R/input.R + Source: R/input.R

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

    -

    Requires TauDEM -5.3.7 and the +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.

    +(whitebox::install_whitebox) to be installed on your computer.

    @@ -108,92 +106,88 @@

    DEM related input

    sp_olp, sp_sds, cs_rds = NULL, - cs_wgs = NULL, - cs_dir = NULL, ns_cha = NULL, ns_brn = 50, is_adj = 1L, is_ths = 1L, + ls_fD8 = FALSE, ls_tmp = FALSE )

    Arguments

    -
    cv_dir
    + + +
    cv_dir

    A character vector specifying the desired project root directory (first position).

    -
    cs_dem
    +
    cs_dem

    A character string specifying a path to a potentially large raster digital elevation model.

    -
    cs_cha
    +
    cs_cha

    A character string specifying a path to a potentially large raster providing channels.

    -
    sp_msk
    +
    sp_msk

    A terra::SpatVector providing a somewhat oversized catchment polygon mask used to clip the potentially large input rasters for further processing.

    -
    sp_olp
    +
    sp_olp

    A terra::SpatVector providing the desired catchment outlet point(s).

    -
    sp_sds
    +
    sp_sds

    A terra::SpatVector providing channel source points.

    -
    cs_rds
    +
    cs_rds

    An optional character string specifying a path to a potentially large raster providing roads.

    -
    cs_wgs
    -

    An optional character string specifying a path to a potentially -large raster providing flow accumulation weights.

    +
    ns_cha
    +

    An optional numeric scalar specifying the minimum D8 flow +accumulation in number of upslope grid cells determining a channel.

    -
    cs_dir
    -

    An optional character string specifying a path to a potentially -large raster providing D8 flow directions using ArcGIS codes.

    - - -
    ns_cha
    -

    An optional numeric scalar specifying the minimum (weighted) -flow accumulation determining a channel.

    - - -
    ns_brn
    +
    ns_brn

    A numeric scalar specifying the stream burning step size in m.

    -
    is_adj
    +
    is_adj

    A numeric scalar specifying how many cells adjacent to channels shall be burnt.

    -
    is_ths
    +
    is_ths

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

    -
    ls_tmp
    +
    ls_fD8
    +

    A logical scalar specifying if D8 flow directions shall be +mimicked, i.e. the D-infinity flow directions are rounded to the nearest +multiple of 45 degrees. Please note that this treatment is always applied +to channel cells independently of this argument.

    + + +
    ls_tmp

    A logical scalar specifying if the temporary files created during computation shall be kept.

    Value

    - - -

    A two column numeric matrix specifying one or more catchment +

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

    @@ -205,23 +199,20 @@

    Details

  • 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.

    -

    In case no flow accumulation weights are provided, acc and acc_wtd -are identical.

    -

    Providing existing flow directions prevents calculating them, which, for -example, may be useful in case the effect of tillage directions has been -enforced on topographic flow directions in advance. Please note that doing so -renders stream burning and depression breaching without effect.

    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. -This processed DEM also serves as the basis for the calculation of the D8 -slopes provided by slp.

    +The basis for the calculation of the D-infinity slopes provided by +slp_inf, however, is the original DEM.

    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.

    +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

    @@ -230,7 +221,7 @@

    See also

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 # obtain temporary project root directory
 cv_dir <- normalizePath(
   tempfile("cmt"),
@@ -248,9 +239,8 @@ 
    Examples
    
   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"),
-  cs_wgs = file.path(cs_dir_lrg, "wgs_lrg.tif"),
   ls_tmp = TRUE
-)}
+)} # }
    @@ -266,15 +256,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/dev/reference/RPhosFate-class.html b/dev/reference/RPhosFate-class.html index db505d8..2f353f5 100644 --- a/dev/reference/RPhosFate-class.html +++ b/dev/reference/RPhosFate-class.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    RPhosFate class

    - Source: R/aaa.R + Source: R/aaa.R
    @@ -90,7 +90,7 @@

    RPhosFate class

    Slots

    - +
    cv_dir

    A character vector holding the project root (first position) and @@ -162,15 +162,15 @@

    See also

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

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    @@ -26,7 +26,7 @@
    - +

    One dimensional automatic model calibration

    - Source: R/interface.R + Source: R/interface.R
    @@ -90,7 +90,7 @@

    One dimensional automatic model calibration

    - 
    # S4 method for RPhosFate
+    
    # S4 method for class 'RPhosFate'
 autoCalibrate(
   x,
   substance,
@@ -104,35 +104,37 @@ 
    One dimensional automatic model calibration
    
 
     
    
     
    Arguments
    
-    
    x
    
+
+
+
    x
    
 
    An S4 RPhosFate river catchment object.
    
 
 
-
    substance
    
+
    substance
    
 
    A character string specifying the substance to calculate.
    
 
 
-
    col
    
+
    col
    
 
    A character string specifying the calibration data column with the
 respective substance river loads.
    
 
 
-
    interval
    
+
    interval
    
 
    A numeric vector specifying the end-points of the interval to
 be searched.
    
 
 
-
    metric
    
+
    metric
    
 
    A character string specifying the metric to optimise. See
 calibrationQuality for available metrics.
    
 
 
-
    tol
    
+
    tol
    
 
    A numeric scalar specifying the desired accuracy of the parameter
 used for optimisation (not the metric).
    
 
 
-
    parameter
    
+
    parameter
    
 
    By default, SS are calibrated utilising the overland
 deposition rate and all other substances are calibrated utilising their
 respective enrichment ratio. This argument can be used to specify a
@@ -142,9 +144,7 @@ 
    Arguments
    
 
    
     
    
     
    Value
    
-    
-
-
    An S4 RPhosFate river catchment object and side effects in
+    
    An S4 RPhosFate river catchment object and side effects in
 the form of raster files.
    
     
    
     
    
@@ -170,106 +170,106 @@ 
    Examples
    
   x,
   "SS",
   col = "SS_load",
-  interval = c(10e-4, 20e-4),
-  metric = "NSE"
+  interval = c(1e-3, 2e-3),
+  metric = "KGE"
 )# }
-#> NSE:   0.9202848
-#> mNSE:  0.7948886
-#> KGE:   0.8813162
-#> RMSE:  3.013774
-#> PBIAS: 11.4
-#> RSR:   0.2305286
-#> RCV:   0.974027
-#> GMRAE: 0.07787891
-#> MdRAE: 0.05117665
+#> NSE:   0.9692195
+#> mNSE:  0.8404272
+#> KGE:   0.8993928
+#> RMSE:  1.872744
+#> PBIAS: 6.3
+#> RSR:   0.1432493
+#> RCV:   0.9220409
+#> GMRAE: 0.1541012
+#> MdRAE: 0.06190472
 #> 
-#> In-channel retention ratio: -4.440892e-16
+#> In-channel retention ratio: -2.220446e-16
 #> 
 
-#> NSE:   0.9481625
-#> mNSE:  0.7967036
-#> KGE:   0.931081
-#> RMSE:  2.430313
-#> PBIAS: -6.2
-#> RSR:   0.1858987
-#> RCV:   0.9769786
-#> GMRAE: 0.1784269
-#> MdRAE: 0.3456409
+#> NSE:   0.9171912
+#> mNSE:  0.7903329
+#> KGE:   0.8649407
+#> RMSE:  3.071698
+#> PBIAS: -11.6
+#> RSR:   0.2349593
+#> RCV:   0.9316332
+#> GMRAE: 0.0867775
+#> MdRAE: 0.2116875
 #> 
-#> In-channel retention ratio: -6.661338e-16
+#> In-channel retention ratio: 3.330669e-16
 #> 
 
-#> NSE:   0.8845115
-#> mNSE:  0.7383309
-#> KGE:   0.8475804
-#> RMSE:  3.627519
-#> PBIAS: -14.9
-#> RSR:   0.277475
-#> RCV:   0.9772123
-#> GMRAE: 0.1727009
-#> MdRAE: 0.2020938
+#> NSE:   0.8659469
+#> mNSE:  0.640928
+#> KGE:   0.7769389
+#> RMSE:  3.908217
+#> PBIAS: 20.5
+#> RSR:   0.298946
+#> RCV:   0.9127025
+#> GMRAE: 0.3730323
+#> MdRAE: 0.2531637
 #> 
-#> In-channel retention ratio: -2.220446e-16
+#> In-channel retention ratio: -8.881784e-16
 #> 
 
-#> NSE:   0.961589
-#> mNSE:  0.8081648
-#> KGE:   0.9681348
-#> RMSE:  2.09203
-#> PBIAS: -1
-#> RSR:   0.1600229
-#> RCV:   0.9764393
-#> GMRAE: 0.1737914
-#> MdRAE: 0.2273883
+#> NSE:   0.972409
+#> mNSE:  0.8372972
+#> KGE:   0.9246256
+#> RMSE:  1.773064
+#> PBIAS: -1.2
+#> RSR:   0.1356246
+#> RCV:   0.9263376
+#> GMRAE: 0.1616979
+#> MdRAE: 0.2276317
 #> 
-#> In-channel retention ratio: -4.440892e-16
+#> In-channel retention ratio: -6.661338e-16
 #> 
 
-#> NSE:   0.9615765
-#> mNSE:  0.8134918
-#> KGE:   0.9661575
-#> RMSE:  2.09237
-#> PBIAS: 1.4
-#> RSR:   0.1600489
-#> RCV:   0.9760944
-#> GMRAE: 0.1602222
-#> MdRAE: 0.1731449
+#> NSE:   0.9653981
+#> mNSE:  0.8360763
+#> KGE:   0.9180164
+#> RMSE:  1.985594
+#> PBIAS: -3.7
+#> RSR:   0.1518814
+#> RCV:   0.9277124
+#> GMRAE: 0.1410067
+#> MdRAE: 0.2846086
 #> 
-#> In-channel retention ratio: 4.440892e-16
+#> In-channel retention ratio: -2.220446e-16
 #> 
 
-#> NSE:   0.9579342
-#> mNSE:  0.8030787
-#> KGE:   0.9554299
-#> RMSE:  2.189297
-#> PBIAS: -3.3
-#> RSR:   0.167463
-#> RCV:   0.9767136
-#> GMRAE: 0.1804247
-#> MdRAE: 0.2796064
+#> NSE:   0.975304
+#> mNSE:  0.8384925
+#> KGE:   0.9226028
+#> RMSE:  1.677466
+#> PBIAS: 1.5
+#> RSR:   0.1283122
+#> RCV:   0.9248487
+#> GMRAE: 0.1723862
+#> MdRAE: 0.1682604
 #> 
-#> In-channel retention ratio: -6.661338e-16
+#> In-channel retention ratio: -2.220446e-16
 #> 
 
-#> NSE:   0.961589
-#> mNSE:  0.8081648
-#> KGE:   0.9681348
-#> RMSE:  2.09203
-#> PBIAS: -1
-#> RSR:   0.1600229
-#> RCV:   0.9764393
-#> GMRAE: 0.1737914
-#> MdRAE: 0.2273883
+#> NSE:   0.972409
+#> mNSE:  0.8372972
+#> KGE:   0.9246256
+#> RMSE:  1.773064
+#> PBIAS: -1.2
+#> RSR:   0.1356246
+#> RCV:   0.9263376
+#> GMRAE: 0.1616979
+#> MdRAE: 0.2276317
 #> 
-#> In-channel retention ratio: -4.440892e-16
+#> In-channel retention ratio: -6.661338e-16
 #> 
 
 #> $maximum
-#> [1] 0.001540684
+#> [1] 0.00147171
 #> 
 #> $objective
-#>      NSE 
-#> 0.961589 
+#>       KGE 
+#> 0.9246256 
 #> 
 
 
    
@@ -286,15 +286,15 @@ 
    Examples
    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

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a/dev/reference/autoCalibrate2-RPhosFate-method.html +++ b/dev/reference/autoCalibrate2-RPhosFate-method.html @@ -8,7 +8,7 @@ - +
    @@ -30,7 +30,7 @@
    - +

    Two dimensional automatic model calibration

    - Source: R/interface.R + Source: R/interface.R
    @@ -98,7 +98,7 @@

    Two dimensional automatic model calibration

    - 
    # S4 method for RPhosFate
+    
    # S4 method for class 'RPhosFate'
 autoCalibrate2(
   x,
   substance,
@@ -113,50 +113,50 @@ 
    Two dimensional automatic model calibration
    
 
     
    
     
    Arguments
    
-    
    x
    
+
+
+
    x
    
 
    An S4 RPhosFate river catchment object.
    
 
 
-
    substance
    
+
    substance
    
 
    A character string specifying the substance to calculate.
    
 
 
-
    col
    
+
    col
    
 
    A character string specifying the calibration data column with the
 respective substance river loads.
    
 
 
-
    metric
    
+
    metric
    
 
    A character string specifying the metric to optimise. See
 calibrationQuality for available metrics.
    
 
 
-
    method
    
+
    method
    
 
    A character string specifying the utilised optimisation method.
 See optim for further information (use autoCalibrate instead of
 method "Brent").
    
 
 
-
    lower
    
+
    lower
    
 
    A numeric scalar or vector specifying the lower end-point(s) of
 the interval(s) to be searched.
    
 
 
-
    upper
    
+
    upper
    
 
    A numeric scalar or vector specifying the upper end-point(s) of
 the interval(s) to be searched.
    
 
 
-
    control
    
+
    control
    
 
    A list of control parameters passed on to optim. See
 optim for further information.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    An S4 RPhosFate river catchment object and side effects in
+    
    An S4 RPhosFate river catchment object and side effects in
 the form of raster files.
    
     
    
     
    
@@ -183,410 +183,475 @@ 
    Examples
    
   x,
   "SS",
   col = "SS_load",
-  metric = "NSE",
+  metric = "KGE",
   method = "L-BFGS-B",
-  lower = c(10e-4, 0),
-  upper = c(20e-4, 20e-4),
+  lower = c(1e-3, 0),
+  upper = c(2e-3, 2e-3),
   control = list(fnscale = -1, parscale = c(1e-3, 1e-3), factr = 1e12)
 )# }
-#> NSE:   0.7191828
-#> mNSE:  0.5345233
-#> KGE:   0.7323813
-#> RMSE:  5.656556
-#> PBIAS: -26.6
-#> RSR:   0.4326794
-#> RCV:   0.9761362
-#> GMRAE: 0.3842057
-#> MdRAE: 0.8072484
+#> NSE:   0.6071161
+#> mNSE:  0.4420663
+#> KGE:   0.6753664
+#> RMSE:  6.690713
+#> PBIAS: -31.9
+#> RSR:   0.5117838
+#> RCV:   0.9389487
+#> GMRAE: 0.3970503
+#> MdRAE: 0.9200186
 #> 
-#> In-channel retention ratio: -4.440892e-16
+#> In-channel retention ratio: -2.220446e-16
 #> 
-#> NSE:   0.7191828
-#> mNSE:  0.5345233
-#> KGE:   0.7323813
-#> RMSE:  5.656556
-#> PBIAS: -26.6
-#> RSR:   0.4326794
-#> RCV:   0.9761362
-#> GMRAE: 0.3842057
-#> MdRAE: 0.8072484
+
+#> NSE:   0.6071161
+#> mNSE:  0.4420663
+#> KGE:   0.6753664
+#> RMSE:  6.690713
+#> PBIAS: -31.9
+#> RSR:   0.5117838
+#> RCV:   0.9389487
+#> GMRAE: 0.3970503
+#> MdRAE: 0.9200186
 #> 
-#> In-channel retention ratio: -4.440892e-16
+#> In-channel retention ratio: -2.220446e-16
 #> 
-
-#> NSE:   0.7199797
-#> mNSE:  0.5352918
-#> KGE:   0.7328179
-#> RMSE:  5.648524
-#> PBIAS: -26.5
-#> RSR:   0.432065
-#> RCV:   0.9761435
-#> GMRAE: 0.3835328
-#> MdRAE: 0.8062524
+#> NSE:   0.6080637
+#> mNSE:  0.4428216
+#> KGE:   0.6757878
+#> RMSE:  6.682639
+#> PBIAS: -31.8
+#> RSR:   0.5111662
+#> RCV:   0.9389382
+#> GMRAE: 0.3963558
+#> MdRAE: 0.919039
 #> 
-#> In-channel retention ratio: -4.440892e-16
+#> In-channel retention ratio: 1.221245e-15
 #> 
 
-#> NSE:   0.7175584
-#> mNSE:  0.533252
-#> KGE:   0.7316275
-#> RMSE:  5.672893
-#> PBIAS: -26.7
-#> RSR:   0.433929
-#> RCV:   0.9758995
-#> GMRAE: 0.3849627
-#> MdRAE: 0.8095904
-#> 
-#> In-channel retention ratio: 0.001423537
+#> NSE:   0.6064526
+#> mNSE:  0.4416167
+#> KGE:   0.675093
+#> RMSE:  6.69636
+#> PBIAS: -31.9
+#> RSR:   0.5122157
+#> RCV:   0.9388427
+#> GMRAE: 0.3972695
+#> MdRAE: 0.9208093
+#> 
+#> In-channel retention ratio: 0.0005159496
 #> 
 
-#> NSE:   0.7191828
-#> mNSE:  0.5345233
-#> KGE:   0.7323813
-#> RMSE:  5.656556
-#> PBIAS: -26.6
-#> RSR:   0.4326794
-#> RCV:   0.9761362
-#> GMRAE: 0.3842057
-#> MdRAE: 0.8072484
+#> NSE:   0.6071161
+#> mNSE:  0.4420663
+#> KGE:   0.6753664
+#> RMSE:  6.690713
+#> PBIAS: -31.9
+#> RSR:   0.5117838
+#> RCV:   0.9389487
+#> GMRAE: 0.3970503
+#> MdRAE: 0.9200186
 #> 
-#> In-channel retention ratio: -4.440892e-16
+#> In-channel retention ratio: -2.220446e-16
 #> 
 
-#> NSE:   0.6910678
-#> mNSE:  0.4945718
-#> KGE:   0.7090686
-#> RMSE:  5.932966
-#> PBIAS: 28.9
-#> RSR:   0.4538224
-#> RCV:   0.9680198
-#> GMRAE: 0.3447724
-#> MdRAE: 0.4399217
+#> NSE:   0.9377421
+#> mNSE:  0.8298658
+#> KGE:   0.885968
+#> RMSE:  2.663406
+#> PBIAS: -9
+#> RSR:   0.2037284
+#> RCV:   0.9303839
+#> GMRAE: 0.04548961
+#> MdRAE: 0.01767349
 #> 
-#> In-channel retention ratio: -4.440892e-16
+#> In-channel retention ratio: -2.220446e-16
 #> 
 
-#> NSE:   0.6931383
-#> mNSE:  0.4965049
-#> KGE:   0.7101685
-#> RMSE:  5.91305
-#> PBIAS: 28.7
-#> RSR:   0.4522991
-#> RCV:   0.9680672
-#> GMRAE: 0.3428975
-#> MdRAE: 0.4374743
+#> NSE:   0.9372657
+#> mNSE:  0.8288419
+#> KGE:   0.8854508
+#> RMSE:  2.673578
+#> PBIAS: -9
+#> RSR:   0.2045064
+#> RCV:   0.930417
+#> GMRAE: 0.04929736
+#> MdRAE: 0.02270224
 #> 
-#> In-channel retention ratio: -2.220446e-16
+#> In-channel retention ratio: 7.771561e-16
 #> 
 
-#> NSE:   0.6889864
-#> mNSE:  0.4926358
-#> KGE:   0.7079669
-#> RMSE:  5.952919
-#> PBIAS: 29
-#> RSR:   0.4553487
-#> RCV:   0.9679721
-#> GMRAE: 0.3466493
-#> MdRAE: 0.4423725
+#> NSE:   0.9382161
+#> mNSE:  0.8308907
+#> KGE:   0.886484
+#> RMSE:  2.653249
+#> PBIAS: -8.9
+#> RSR:   0.2029514
+#> RCV:   0.9303506
+#> GMRAE: 0.04080259
+#> MdRAE: 0.01340401
 #> 
-#> In-channel retention ratio: -4.440892e-16
+#> In-channel retention ratio: 1.110223e-16
 #> 
 
-#> NSE:   0.69327
-#> mNSE:  0.496767
-#> KGE:   0.7102749
-#> RMSE:  5.911782
-#> PBIAS: 28.7
-#> RSR:   0.452202
-#> RCV:   0.9677696
-#> GMRAE: 0.3435011
-#> MdRAE: 0.4358584
-#> 
-#> In-channel retention ratio: 0.001404835
+#> NSE:   0.9374155
+#> mNSE:  0.8292696
+#> KGE:   0.8856287
+#> RMSE:  2.670384
+#> PBIAS: -9
+#> RSR:   0.2042621
+#> RCV:   0.9302727
+#> GMRAE: 0.04700307
+#> MdRAE: 0.01944738
+#> 
+#> In-channel retention ratio: 0.0005129603
 #> 
 
-#> NSE:   0.6910678
-#> mNSE:  0.4945718
-#> KGE:   0.7090686
-#> RMSE:  5.932966
-#> PBIAS: 28.9
-#> RSR:   0.4538224
-#> RCV:   0.9680198
-#> GMRAE: 0.3447724
-#> MdRAE: 0.4399217
+#> NSE:   0.9377421
+#> mNSE:  0.8298658
+#> KGE:   0.885968
+#> RMSE:  2.663406
+#> PBIAS: -9
+#> RSR:   0.2037284
+#> RCV:   0.9303839
+#> GMRAE: 0.04548961
+#> MdRAE: 0.01767349
 #> 
-#> In-channel retention ratio: -4.440892e-16
+#> In-channel retention ratio: -2.220446e-16
 #> 
 
-#> NSE:   0.9575214
-#> mNSE:  0.8027044
-#> KGE:   0.9541649
-#> RMSE:  2.200014
-#> PBIAS: -3.4
-#> RSR:   0.1682827
-#> RCV:   0.9767316
-#> GMRAE: 0.1806504
-#> MdRAE: 0.2834657
-#> 
-#> In-channel retention ratio: 6.661338e-16
+#> NSE:   0.4664724
+#> mNSE:  0.2591888
+#> KGE:   0.5642745
+#> RMSE:  7.796841
+#> PBIAS: 42.3
+#> RSR:   0.5963934
+#> RCV:   0.8958417
+#> GMRAE: 0.7711987
+#> MdRAE: 0.7283918
+#> 
+#> In-channel retention ratio: 0
 #> 
 
-#> NSE:   0.957352
-#> mNSE:  0.8025559
-#> KGE:   0.9536547
-#> RMSE:  2.204395
-#> PBIAS: -3.5
-#> RSR:   0.1686178
-#> RCV:   0.9767387
-#> GMRAE: 0.1807294
-#> MdRAE: 0.2849978
+#> NSE:   0.4700652
+#> mNSE:  0.261723
+#> KGE:   0.565708
+#> RMSE:  7.770545
+#> PBIAS: 42.2
+#> RSR:   0.5943819
+#> RCV:   0.8959632
+#> GMRAE: 0.7685763
+#> MdRAE: 0.7252692
 #> 
-#> In-channel retention ratio: 0
+#> In-channel retention ratio: 5.551115e-16
 #> 
 
-#> NSE:   0.9576878
-#> mNSE:  0.8028532
-#> KGE:   0.9546712
-#> RMSE:  2.1957
-#> PBIAS: -3.4
-#> RSR:   0.1679527
-#> RCV:   0.9767245
-#> GMRAE: 0.1805653
-#> MdRAE: 0.2819319
+#> NSE:   0.4628606
+#> mNSE:  0.2566501
+#> KGE:   0.5628382
+#> RMSE:  7.823188
+#> PBIAS: 42.4
+#> RSR:   0.5984087
+#> RCV:   0.89572
+#> GMRAE: 0.7738261
+#> MdRAE: 0.7315197
 #> 
-#> In-channel retention ratio: 5.551115e-16
+#> In-channel retention ratio: 0
 #> 
 
-#> NSE:   0.9569899
-#> mNSE:  0.8018995
-#> KGE:   0.9532673
-#> RMSE:  2.213733
-#> PBIAS: -3.5
-#> RSR:   0.1693321
-#> RCV:   0.9764926
-#> GMRAE: 0.1809222
-#> MdRAE: 0.2865277
-#> 
-#> In-channel retention ratio: 0.001411743
+#> NSE:   0.467853
+#> mNSE:  0.2601182
+#> KGE:   0.5647587
+#> RMSE:  7.786747
+#> PBIAS: 42.2
+#> RSR:   0.5956212
+#> RCV:   0.8957155
+#> GMRAE: 0.7704267
+#> MdRAE: 0.726758
+#> 
+#> In-channel retention ratio: 0.0005136488
 #> 
 
-#> NSE:   0.9575214
-#> mNSE:  0.8027044
-#> KGE:   0.9541649
-#> RMSE:  2.200014
-#> PBIAS: -3.4
-#> RSR:   0.1682827
-#> RCV:   0.9767316
-#> GMRAE: 0.1806504
-#> MdRAE: 0.2834657
-#> 
-#> In-channel retention ratio: 6.661338e-16
+#> NSE:   0.4664724
+#> mNSE:  0.2591888
+#> KGE:   0.5642745
+#> RMSE:  7.796841
+#> PBIAS: 42.3
+#> RSR:   0.5963934
+#> RCV:   0.8958417
+#> GMRAE: 0.7711987
+#> MdRAE: 0.7283918
+#> 
+#> In-channel retention ratio: 0
 #> 
 
-#> NSE:   0.9552136
-#> mNSE:  0.8208966
-#> KGE:   0.9431924
-#> RMSE:  2.258985
-#> PBIAS: 4.8
-#> RSR:   0.1727935
-#> RCV:   0.9755208
-#> GMRAE: 0.129613
-#> MdRAE: 0.09851233
+#> NSE:   0.9707589
+#> mNSE:  0.836942
+#> KGE:   0.9234894
+#> RMSE:  1.825311
+#> PBIAS: -1.9
+#> RSR:   0.1396211
+#> RCV:   0.9267516
+#> GMRAE: 0.1566302
+#> MdRAE: 0.2445573
 #> 
 #> In-channel retention ratio: 0
 #> 
 
-#> NSE:   0.9554464
-#> mNSE:  0.8207224
-#> KGE:   0.9438469
-#> RMSE:  2.253107
-#> PBIAS: 4.7
-#> RSR:   0.1723439
-#> RCV:   0.9755355
-#> GMRAE: 0.1305188
-#> MdRAE: 0.1002579
-#> 
-#> In-channel retention ratio: 0
+#> NSE:   0.9705705
+#> mNSE:  0.8369055
+#> KGE:   0.9233325
+#> RMSE:  1.831183
+#> PBIAS: -2
+#> RSR:   0.1400703
+#> RCV:   0.9267934
+#> GMRAE: 0.1560648
+#> MdRAE: 0.2462799
+#> 
+#> In-channel retention ratio: 3.330669e-16
 #> 
 
-#> NSE:   0.9549765
-#> mNSE:  0.8210711
-#> KGE:   0.9425341
-#> RMSE:  2.264957
-#> PBIAS: 4.8
-#> RSR:   0.1732503
-#> RCV:   0.975506
-#> GMRAE: 0.1286952
-#> MdRAE: 0.09676464
-#> 
-#> In-channel retention ratio: -2.220446e-16
+#> NSE:   0.9709438
+#> mNSE:  0.8369785
+#> KGE:   0.923639
+#> RMSE:  1.819532
+#> PBIAS: -1.8
+#> RSR:   0.139179
+#> RCV:   0.9267096
+#> GMRAE: 0.1571871
+#> MdRAE: 0.2428326
+#> 
+#> In-channel retention ratio: 3.330669e-16
 #> 
 
-#> NSE:   0.955245
-#> mNSE:  0.8200235
-#> KGE:   0.9438916
-#> RMSE:  2.258193
-#> PBIAS: 4.7
-#> RSR:   0.172733
-#> RCV:   0.9752798
-#> GMRAE: 0.1308989
-#> MdRAE: 0.1018291
-#> 
-#> In-channel retention ratio: 0.001409039
+#> NSE:   0.9705897
+#> mNSE:  0.8366748
+#> KGE:   0.9232838
+#> RMSE:  1.830586
+#> PBIAS: -2
+#> RSR:   0.1400246
+#> RCV:   0.9266386
+#> GMRAE: 0.15667
+#> MdRAE: 0.2456889
+#> 
+#> In-channel retention ratio: 0.0005125375
 #> 
 
-#> NSE:   0.9552136
-#> mNSE:  0.8208966
-#> KGE:   0.9431924
-#> RMSE:  2.258985
-#> PBIAS: 4.8
-#> RSR:   0.1727935
-#> RCV:   0.9755208
-#> GMRAE: 0.129613
-#> MdRAE: 0.09851233
+#> NSE:   0.9707589
+#> mNSE:  0.836942
+#> KGE:   0.9234894
+#> RMSE:  1.825311
+#> PBIAS: -1.9
+#> RSR:   0.1396211
+#> RCV:   0.9267516
+#> GMRAE: 0.1566302
+#> MdRAE: 0.2445573
 #> 
 #> In-channel retention ratio: 0
 #> 
 
-#> NSE:   0.962066
-#> mNSE:  0.8106337
-#> KGE:   0.969484
-#> RMSE:  2.079
-#> PBIAS: 0.2
-#> RSR:   0.1590262
-#> RCV:   0.9762867
-#> GMRAE: 0.1683249
-#> MdRAE: 0.2021909
+#> NSE:   0.9752522
+#> mNSE:  0.8384166
+#> KGE:   0.9230168
+#> RMSE:  1.679224
+#> PBIAS: 1.3
+#> RSR:   0.1284466
+#> RCV:   0.924948
+#> GMRAE: 0.1720404
+#> MdRAE: 0.1721504
 #> 
 #> In-channel retention ratio: 1.110223e-16
 #> 
 
-#> NSE:   0.9620605
-#> mNSE:  0.8104743
-#> KGE:   0.9695189
-#> RMSE:  2.079151
-#> PBIAS: 0.1
-#> RSR:   0.1590377
-#> RCV:   0.9762969
-#> GMRAE: 0.1687208
-#> MdRAE: 0.2038152
+#> NSE:   0.9752215
+#> mNSE:  0.8383812
+#> KGE:   0.9231968
+#> RMSE:  1.680266
+#> PBIAS: 1.2
+#> RSR:   0.1285264
+#> RCV:   0.9249941
+#> GMRAE: 0.1718613
+#> MdRAE: 0.1739629
 #> 
-#> In-channel retention ratio: -2.220446e-16
+#> In-channel retention ratio: 0
 #> 
 
-#> NSE:   0.962068
-#> mNSE:  0.8107934
-#> KGE:   0.969432
-#> RMSE:  2.078945
-#> PBIAS: 0.2
-#> RSR:   0.159022
-#> RCV:   0.9762764
-#> GMRAE: 0.1679225
-#> MdRAE: 0.2005647
-#> 
-#> In-channel retention ratio: 2.220446e-16
+#> NSE:   0.9752788
+#> mNSE:  0.838452
+#> KGE:   0.9228283
+#> RMSE:  1.678322
+#> PBIAS: 1.4
+#> RSR:   0.1283777
+#> RCV:   0.9249017
+#> GMRAE: 0.1722083
+#> MdRAE: 0.1703357
+#> 
+#> In-channel retention ratio: -2.220446e-16
 #> 
 
-#> NSE:   0.9617705
-#> mNSE:  0.8097989
-#> KGE:   0.9692383
-#> RMSE:  2.087082
-#> PBIAS: 0.1
-#> RSR:   0.1596444
-#> RCV:   0.9760469
-#> GMRAE: 0.1689422
-#> MdRAE: 0.2053648
-#> 
-#> In-channel retention ratio: 0.00141047
+#> NSE:   0.9751637
+#> mNSE:  0.8381407
+#> KGE:   0.9229651
+#> RMSE:  1.682224
+#> PBIAS: 1.3
+#> RSR:   0.1286761
+#> RCV:   0.9248341
+#> GMRAE: 0.1722736
+#> MdRAE: 0.1733189
+#> 
+#> In-channel retention ratio: 0.0005124075
 #> 
 
-#> NSE:   0.962066
-#> mNSE:  0.8106337
-#> KGE:   0.969484
-#> RMSE:  2.079
-#> PBIAS: 0.2
-#> RSR:   0.1590262
-#> RCV:   0.9762867
-#> GMRAE: 0.1683249
-#> MdRAE: 0.2021909
+#> NSE:   0.9752522
+#> mNSE:  0.8384166
+#> KGE:   0.9230168
+#> RMSE:  1.679224
+#> PBIAS: 1.3
+#> RSR:   0.1284466
+#> RCV:   0.924948
+#> GMRAE: 0.1720404
+#> MdRAE: 0.1721504
 #> 
 #> In-channel retention ratio: 1.110223e-16
 #> 
 
-#> NSE:   0.962068
-#> mNSE:  0.8108216
-#> KGE:   0.969421
-#> RMSE:  2.078945
-#> PBIAS: 0.2
-#> RSR:   0.159022
-#> RCV:   0.9762746
-#> GMRAE: 0.1678508
-#> MdRAE: 0.2002773
+#> NSE:   0.9736669
+#> mNSE:  0.8376379
+#> KGE:   0.925005
+#> RMSE:  1.732172
+#> PBIAS: -0.4
+#> RSR:   0.1324967
+#> RCV:   0.9259289
+#> GMRAE: 0.1657955
+#> MdRAE: 0.211108
 #> 
-#> In-channel retention ratio: 0
+#> In-channel retention ratio: -2.220446e-16
 #> 
 
-#> NSE:   0.9620666
-#> mNSE:  0.8106619
-#> KGE:   0.9694761
-#> RMSE:  2.078983
-#> PBIAS: 0.2
-#> RSR:   0.1590249
-#> RCV:   0.9762849
-#> GMRAE: 0.1682543
-#> MdRAE: 0.2019038
+#> NSE:   0.9735493
+#> mNSE:  0.8376018
+#> KGE:   0.9249994
+#> RMSE:  1.736038
+#> PBIAS: -0.5
+#> RSR:   0.1327924
+#> RCV:   0.9259728
+#> GMRAE: 0.1653983
+#> MdRAE: 0.2128719
 #> 
-#> In-channel retention ratio: 7.771561e-16
+#> In-channel retention ratio: 5.551115e-16
 #> 
 
-#> NSE:   0.9620659
-#> mNSE:  0.8109816
-#> KGE:   0.969349
-#> RMSE:  2.079003
-#> PBIAS: 0.3
-#> RSR:   0.1590264
-#> RCV:   0.9762642
-#> GMRAE: 0.1674407
-#> MdRAE: 0.1986489
+#> NSE:   0.9737807
+#> mNSE:  0.8376739
+#> KGE:   0.9250022
+#> RMSE:  1.728424
+#> PBIAS: -0.3
+#> RSR:   0.1322101
+#> RCV:   0.925885
+#> GMRAE: 0.1661836
+#> MdRAE: 0.209342
 #> 
-#> In-channel retention ratio: 7.771561e-16
+#> In-channel retention ratio: -4.440892e-16
 #> 
 
-#> NSE:   0.9617783
-#> mNSE:  0.809986
-#> KGE:   0.9692028
-#> RMSE:  2.08687
-#> PBIAS: 0.1
-#> RSR:   0.1596282
-#> RCV:   0.9760347
-#> GMRAE: 0.1684769
-#> MdRAE: 0.2034539
-#> 
-#> In-channel retention ratio: 0.001410442
+#> NSE:   0.9735343
+#> mNSE:  0.8373667
+#> KGE:   0.9248663
+#> RMSE:  1.736529
+#> PBIAS: -0.5
+#> RSR:   0.13283
+#> RCV:   0.9258156
+#> GMRAE: 0.1659181
+#> MdRAE: 0.2122566
+#> 
+#> In-channel retention ratio: 0.0005124726
 #> 
 
-#> NSE:   0.962068
-#> mNSE:  0.8108216
-#> KGE:   0.969421
-#> RMSE:  2.078945
-#> PBIAS: 0.2
-#> RSR:   0.159022
-#> RCV:   0.9762746
-#> GMRAE: 0.1678508
-#> MdRAE: 0.2002773
+#> NSE:   0.9736669
+#> mNSE:  0.8376379
+#> KGE:   0.925005
+#> RMSE:  1.732172
+#> PBIAS: -0.4
+#> RSR:   0.1324967
+#> RCV:   0.9259289
+#> GMRAE: 0.1657955
+#> MdRAE: 0.211108
 #> 
-#> In-channel retention ratio: 0
+#> In-channel retention ratio: -2.220446e-16
 #> 
 
+#> NSE:   0.9736871
+#> mNSE:  0.8376442
+#> KGE:   0.9250051
+#> RMSE:  1.731508
+#> PBIAS: -0.4
+#> RSR:   0.1324459
+#> RCV:   0.9259213
+#> GMRAE: 0.1658641
+#> MdRAE: 0.2107992
+#> 
+#> In-channel retention ratio: 5.551115e-16
+#> 
+
+#> NSE:   0.9735701
+#> mNSE:  0.8376081
+#> KGE:   0.925001
+#> RMSE:  1.735353
+#> PBIAS: -0.5
+#> RSR:   0.13274
+#> RCV:   0.9259651
+#> GMRAE: 0.1654684
+#> MdRAE: 0.2125634
+#> 
+#> In-channel retention ratio: 0
+#> 
+
+#> NSE:   0.9738003
+#> mNSE:  0.8376803
+#> KGE:   0.9250008
+#> RMSE:  1.727781
+#> PBIAS: -0.3
+#> RSR:   0.1321608
+#> RCV:   0.9258773
+#> GMRAE: 0.1662506
+#> MdRAE: 0.2090327
+#> 
+#> In-channel retention ratio: -2.220446e-16
+#> 
+
+#> NSE:   0.9735548
+#> mNSE:  0.8373729
+#> KGE:   0.9248671
+#> RMSE:  1.735855
+#> PBIAS: -0.4
+#> RSR:   0.1327784
+#> RCV:   0.9258079
+#> GMRAE: 0.1659875
+#> MdRAE: 0.2119479
+#> 
+#> In-channel retention ratio: 0.0005124721
+#> 
+
+#> NSE:   0.9736871
+#> mNSE:  0.8376442
+#> KGE:   0.9250051
+#> RMSE:  1.731508
+#> PBIAS: -0.4
+#> RSR:   0.1324459
+#> RCV:   0.9259213
+#> GMRAE: 0.1658641
+#> MdRAE: 0.2107992
+#> 
+#> In-channel retention ratio: 5.551115e-16
+#> 
+
 #> $par
-#> [1] 0.001523864 0.000000000
+#> [1] 0.001462119 0.000000000
 #> 
 #> $value
-#> [1] 0.962068
+#> [1] 0.9250051
 #> 
 #> $counts
 #> function gradient 
-#>        6        6 
+#>        7        7 
 #> 
 #> $convergence
 #> [1] 0
@@ -609,15 +674,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.9.
    
+  
    Site built with pkgdown 2.1.1.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/dev/reference/autoCalibrate2.html b/dev/reference/autoCalibrate2.html
new file mode 100644
index 0000000..429fa3e
--- /dev/null
+++ b/dev/reference/autoCalibrate2.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/dev/reference/calibrationQuality-RPhosFate-method-1.png b/dev/reference/calibrationQuality-RPhosFate-method-1.png
index fdfc601..8e2c86d 100644
Binary files a/dev/reference/calibrationQuality-RPhosFate-method-1.png and b/dev/reference/calibrationQuality-RPhosFate-method-1.png differ
diff --git a/dev/reference/calibrationQuality-RPhosFate-method.html b/dev/reference/calibrationQuality-RPhosFate-method.html
index b681052..c90ecdb 100644
--- a/dev/reference/calibrationQuality-RPhosFate-method.html
+++ b/dev/reference/calibrationQuality-RPhosFate-method.html
@@ -19,7 +19,7 @@
 
 
 
-    
+
 
     
    
       
    
 
@@ -41,7 +41,7 @@
    - +

    Calibration quality

    - Source: R/interface.R + Source: R/interface.R
    @@ -117,30 +117,30 @@

    Calibration quality

    - 
    # S4 method for RPhosFate
+    
    # S4 method for class 'RPhosFate'
 calibrationQuality(x, substance, col)

    Arguments

    -
    x
    + + +
    x

    An S4 RPhosFate river catchment object.

    -
    substance
    +
    substance

    A character string specifying the substance to calculate.

    -
    col
    +
    col

    A character string specifying the calibration data column with the respective substance river loads.

    Value

    - - -

    A named numeric vector containing the assessed metrics along with the +

    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).

    @@ -181,27 +181,19 @@

    Examples

    x <- snapGauges(x) calibrationQuality(x, "SS", "SS_load")# } -#> NSE: 0.7191828 -#> mNSE: 0.5345233 -#> KGE: 0.7323813 -#> RMSE: 5.656556 -#> PBIAS: -26.6 -#> RSR: 0.4326794 -#> RCV: 0.9761362 -#> GMRAE: 0.3842057 -#> MdRAE: 0.8072484 +#> NSE: 0.6071161 +#> mNSE: 0.4420663 +#> KGE: 0.6753664 +#> RMSE: 6.690713 +#> PBIAS: -31.9 +#> RSR: 0.5117838 +#> RCV: 0.9389487 +#> GMRAE: 0.3970503 +#> MdRAE: 0.9200186 #> -#> In-channel retention ratio: -4.440892e-16 +#> In-channel retention ratio: -2.220446e-16 #> -#> NSE mNSE KGE -#> 7.191828e-01 5.345233e-01 7.323813e-01 -#> RMSE PBIAS RSR -#> 5.656556e+00 -2.660000e+01 4.326794e-01 -#> RCV GMRAE MdRAE -#> 9.761362e-01 3.842057e-01 8.072484e-01 -#> inChannelRetentionRatio -#> -4.440892e-16
    @@ -217,15 +209,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/dev/reference/calibrationQuality.html b/dev/reference/calibrationQuality.html new file mode 100644 index 0000000..92aa1e0 --- /dev/null +++ b/dev/reference/calibrationQuality.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/dev/reference/catchment.html b/dev/reference/catchment.html index f1eb7fe..eeb9b54 100644 --- a/dev/reference/catchment.html +++ b/dev/reference/catchment.html @@ -12,7 +12,7 @@ - +
    @@ -34,7 +34,7 @@
    - +

    Initialise project

    - Source: R/interface.R + Source: R/interface.R
    @@ -110,34 +110,35 @@

    Initialise project

    Arguments

    -
    ...
    + + +
    ...

    Arguments used to initialise the project. See argument sections for further information.

    Value

    - - -

    An S4 RPhosFate river catchment object.

    +

    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 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).

      • +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: D8 flow directions required for transportPrerequisites and -substance transport.

        • +

      • 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).

        • @@ -149,23 +150,22 @@

        Input subdirectory

        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.

        • +

      • 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.

      • -

    • rhy: Hydraulic radii in m.

    • 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 @@ -185,7 +185,7 @@

      Result subdirectory

    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).

      • @@ -205,10 +205,10 @@

      Data management and processing arguments

    Model parameter arguments

    - +

    • ns_slp_min: A numeric scalar specifying the minimum bounding slope in % -(defaults to 0.001).

      • +(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 @@ -239,8 +239,6 @@

      Model parameter arguments

      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).

      • @@ -253,7 +251,7 @@

      Model parameter arguments

    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 @@ -316,15 +314,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/dev/reference/demoProject.html b/dev/reference/demoProject.html index f7459ca..5ab0fb3 100644 --- a/dev/reference/demoProject.html +++ b/dev/reference/demoProject.html @@ -12,7 +12,7 @@ - +
    @@ -34,7 +34,7 @@
    - +

    Demonstration project

    - Source: R/input.R + Source: R/input.R
    @@ -108,15 +108,15 @@

    Demonstration project

    Arguments

    -
    cs_dir
    + + +
    cs_dir

    An optional character string specifying an existing directory.

    Value

    - - -

    A character string containing the demonstration project root +

    A character string containing the demonstration project root directory.

    @@ -129,7 +129,7 @@

    Examples

    
 demoProject()
 #> Warning: A folder called "demoProject" already exists and is left as is.
-#> [1] "/tmp/Rtmp8JVKT3/demoProject"
+#> [1] "/tmp/Rtmp39m2Ag/demoProject"
    @@ -145,15 +145,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/dev/reference/emission-RPhosFate-method.html b/dev/reference/emission-RPhosFate-method.html index b150bfc..65193ba 100644 --- a/dev/reference/emission-RPhosFate-method.html +++ b/dev/reference/emission-RPhosFate-method.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    Emission

    - Source: R/RPhosFate.R + Source: R/RPhosFate.R
    @@ -88,25 +88,25 @@

    Emission

    - 
    # S4 method for RPhosFate
+    
    # S4 method for class 'RPhosFate'
 emission(x, substance = "PP")

    Arguments

    -
    x
    + + +
    x

    An S4 RPhosFate river catchment object.

    -
    substance
    +
    substance

    A character string specifying the substance to calculate.

    Value

    - - -

    An S4 RPhosFate river catchment object and side effects in +

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

    @@ -145,15 +145,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/dev/reference/emission.html b/dev/reference/emission.html new file mode 100644 index 0000000..25edbe7 --- /dev/null +++ b/dev/reference/emission.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/dev/reference/erosion-RPhosFate-method.html b/dev/reference/erosion-RPhosFate-method.html index f169f0c..9c3a8bf 100644 --- a/dev/reference/erosion-RPhosFate-method.html +++ b/dev/reference/erosion-RPhosFate-method.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    Erosion

    - Source: R/RPhosFate.R + Source: R/RPhosFate.R
    @@ -88,21 +88,21 @@

    Erosion

    - 
    # S4 method for RPhosFate
+    
    # S4 method for class 'RPhosFate'
 erosion(x)

    Arguments

    -
    x
    + + +
    x

    An S4 RPhosFate river catchment object.

    Value

    - - -

    An S4 RPhosFate river catchment object and side effects in +

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

    @@ -150,15 +150,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/dev/reference/erosion.html b/dev/reference/erosion.html new file mode 100644 index 0000000..c88dbef --- /dev/null +++ b/dev/reference/erosion.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/dev/reference/erosionPrerequisites-RPhosFate-method.html b/dev/reference/erosionPrerequisites-RPhosFate-method.html index df33571..ffb3c90 100644 --- a/dev/reference/erosionPrerequisites-RPhosFate-method.html +++ b/dev/reference/erosionPrerequisites-RPhosFate-method.html @@ -1,12 +1,10 @@ Erosion prerequisites — erosionPrerequisites,RPhosFate-method • RPhosFate - +
    @@ -28,7 +26,7 @@
    - +

    Erosion prerequisites

    - Source: R/RPhosFate.R + Source: R/RPhosFate.R

    Calculates and writes capped slopes, L- and RUSLE S-factors (equations for -summer conditions and slopes \(\geq\) 15 ft) to disk. Weighted flow -accumulations less than one are set to one for the calculation of the -L-factors.

    +summer conditions and slopes \(\geq\) 15 ft) to disk.

    - 
    # S4 method for RPhosFate
+    
    # S4 method for class 'RPhosFate'
 erosionPrerequisites(x)

    Arguments

    -
    x
    + + +
    x

    An S4 RPhosFate river catchment object.

    Value

    - - -

    An S4 RPhosFate river catchment object and side effects in +

    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., +

    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.

    @@ -151,15 +150,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/dev/reference/erosionPrerequisites.html b/dev/reference/erosionPrerequisites.html new file mode 100644 index 0000000..c1f02ff --- /dev/null +++ b/dev/reference/erosionPrerequisites.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/dev/reference/firstRun-RPhosFate-method.html b/dev/reference/firstRun-RPhosFate-method.html index 3b84806..c3256fe 100644 --- a/dev/reference/firstRun-RPhosFate-method.html +++ b/dev/reference/firstRun-RPhosFate-method.html @@ -1,13 +1,12 @@ First run — firstRun,RPhosFate-method • RPhosFate - +
    @@ -29,7 +28,7 @@
    - +

    First run

    - Source: R/interface.R + Source: R/interface.R

    Calls erosionPrerequisites, erosion, emission, -transportPrerequisites, transportCalcOrder 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.

    +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.

    - 
    # S4 method for RPhosFate
+    
    # S4 method for class 'RPhosFate'
 firstRun(x, substance = "PP")

    Arguments

    -
    x
    + + +
    x

    An S4 RPhosFate river catchment object.

    -
    substance
    +
    substance

    A character string specifying the substance to calculate.

    Value

    - - -

    An S4 RPhosFate river catchment object and side effects in +

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

    @@ -150,15 +148,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/dev/reference/firstRun.html b/dev/reference/firstRun.html new file mode 100644 index 0000000..65924d3 --- /dev/null +++ b/dev/reference/firstRun.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/dev/reference/getLayer-RPhosFate-method.html b/dev/reference/getLayer-RPhosFate-method.html index 5b286b2..5d76a47 100644 --- a/dev/reference/getLayer-RPhosFate-method.html +++ b/dev/reference/getLayer-RPhosFate-method.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    Get layer

    - Source: R/gettersSetters.R + Source: R/gettersSetters.R
    @@ -88,20 +88,22 @@

    Get layer

    - 
    # S4 method for RPhosFate
-getLayer(x, i, j = NULL)
-
-# S4 method for RPhosFate,ANY,ANY
-[(x, i, j)
    + 
    # S4 method for class 'RPhosFate'
+getLayer(x, i, j = NULL)
+
+# S4 method for class 'RPhosFate,ANY,ANY'
+x[i, j]

    Arguments

    -
    x
    + + +
    x

    An S4 RPhosFate river catchment object.

    -
    i
    +
    i

    A character string specifying a layer name. Substance related layers whose names start with xx are treated differently. They have to be queried by their name (not filename), for example, "xxc" in combination @@ -110,33 +112,32 @@

    Arguments

    information.

    -
    j
    +
    j

    A character string specifying a substance if applicable.

    Value

    - - -

    A terra::SpatRaster object.

    +

    A terra::SpatRaster object.

    Input subdirectory

    - +

    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).

      • +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: D8 flow directions required for transportPrerequisites and -substance transport.

        • +

      • 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).

        • @@ -148,23 +149,22 @@

        Input subdirectory

        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.

        • +

      • 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.

      • -

    • rhy: Hydraulic radii in m.

    • 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 @@ -197,16 +197,16 @@

      Examples

      # presupposed method call x <- firstRun(x, "SS") -getLayer(x, "dir") +getLayer(x, "dir_inf") #> class : SpatRaster #> dimensions : 92, 155, 1 (nrow, ncol, nlyr) #> resolution : 10, 10 (x, y) #> extent : 4702990, 4704540, 2795190, 2796110 (xmin, xmax, ymin, ymax) #> coord. ref. : +proj=laea +lat_0=52 +lon_0=10 +x_0=4321000 +y_0=3210000 +ellps=GRS80 +units=m +no_defs -#> source : dir.tif -#> name : dir -#> min value : 1 -#> max value : 128 +#> source : dir_inf.tif +#> name : dir_inf +#> min value : 0.2138069 +#> max value : 360.0000000 getLayer(x, "xxt", "SS") #> class : SpatRaster #> dimensions : 92, 155, 1 (nrow, ncol, nlyr) @@ -214,9 +214,9 @@

      Examples

      #> extent : 4702990, 4704540, 2795190, 2796110 (xmin, xmax, ymin, ymax) #> coord. ref. : +proj=laea +lat_0=52 +lon_0=10 +x_0=4321000 +y_0=3210000 +ellps=GRS80 +units=m +no_defs #> source : sst.tif -#> name : sst -#> min value : 0.00000 -#> max value : 18.83847 +#> name : sst +#> min value : 3.027626e-06 +#> max value : 1.754717e+01 getLayer(x, "xxe", "PP")# } #> class : SpatRaster #> dimensions : 92, 155, 1 (nrow, ncol, nlyr) @@ -225,8 +225,8 @@

      Examples

      #> coord. ref. : +proj=laea +lat_0=52 +lon_0=10 +x_0=4321000 +y_0=3210000 +ellps=GRS80 +units=m +no_defs #> source : ppe.tif #> name : ppe -#> min value : 1.387505e-05 -#> max value : 1.202173e+00 +#> min value : 5.648591e-05 +#> max value : 9.866220e-01
    @@ -242,15 +242,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/dev/reference/getLayer.html b/dev/reference/getLayer.html new file mode 100644 index 0000000..c9b9653 --- /dev/null +++ b/dev/reference/getLayer.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/dev/reference/getParameter-RPhosFate-method.html b/dev/reference/getParameter-RPhosFate-method.html index 7192f27..598e15e 100644 --- a/dev/reference/getParameter-RPhosFate-method.html +++ b/dev/reference/getParameter-RPhosFate-method.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    Get parameter(s)

    - Source: R/gettersSetters.R + Source: R/gettersSetters.R
    @@ -88,17 +88,19 @@

    Get parameter(s)

    - 
    # S4 method for RPhosFate
+    
    # S4 method for class 'RPhosFate'
 getParameter(x, parameter = NULL)

    Arguments

    -
    x
    + + +
    x

    An S4 RPhosFate river catchment object.

    -
    parameter
    +
    parameter

    A character string specifying a parameter name or NULL for a list of all parameters. See model parameter arguments section for further information.

    @@ -106,17 +108,15 @@

    Arguments

    Value

    - - -

    Depends on the queried parameter or a list in case of all +

    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 0.001).

      • +(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 @@ -147,8 +147,6 @@

      Model parameter arguments

      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).

      • @@ -178,7 +176,7 @@

      Examples

      getParameter(x) #> $ns_slp_min -#> [1] 0.001 +#> [1] 1 #> #> $ns_slp_max #> [1] 999 @@ -212,9 +210,6 @@

      Examples

      #> PP #> 2 #> -#> $iv_fDo -#> [1] 32 16 8 64 0 4 128 1 2 -#> #> $nm_olc #> [,1] [,2] #> [1,] 4704255 2795195 @@ -242,15 +237,15 @@

      Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/dev/reference/getParameter.html b/dev/reference/getParameter.html new file mode 100644 index 0000000..d6bd50d --- /dev/null +++ b/dev/reference/getParameter.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/dev/reference/img2tif.html b/dev/reference/img2tif.html index c5e4f10..f8b458a 100644 --- a/dev/reference/img2tif.html +++ b/dev/reference/img2tif.html @@ -4,7 +4,7 @@ - +
    @@ -26,7 +26,7 @@
    - +

    Convert ERDAS IMAGINE to GeoTIFF raster files

    - Source: R/input.R + Source: R/input.R
    @@ -95,11 +95,13 @@

    Convert ERDAS IMAGINE to GeoTIFF raster files

    Arguments

    -
    cs_dir
    + + +
    cs_dir

    A character string specifying an existing directory.

    -
    cs_crs
    +
    cs_crs

    An optional character string used to set the coordinate reference system of all output raster files. See terra::crs for further information.

    @@ -107,9 +109,7 @@

    Arguments

    Value

    - - -

    A character vector containing the paths to the processed ERDAS +

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

    @@ -125,15 +125,15 @@

    Value

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/dev/reference/index.html b/dev/reference/index.html index 2346518..6f85461 100644 --- a/dev/reference/index.html +++ b/dev/reference/index.html @@ -1,9 +1,9 @@ -Function reference • RPhosFatePackage index • RPhosFate - +
    @@ -25,7 +25,7 @@
    - +
    @@ -173,10 +173,6 @@

    Low-level interface transportPrerequisites(<RPhosFate>)

    Transport prerequisites

    - -

    transportCalcOrder(<RPhosFate>)

    - -

    Transport calculation order

    transport(<RPhosFate>)

    @@ -202,15 +198,15 @@

    Class description
    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/dev/reference/saveState-RPhosFate-method.html b/dev/reference/saveState-RPhosFate-method.html index 7c6f1fb..3320093 100644 --- a/dev/reference/saveState-RPhosFate-method.html +++ b/dev/reference/saveState-RPhosFate-method.html @@ -1,10 +1,9 @@ -Save state — saveState,RPhosFate-method • RPhosFateSave state — saveState,RPhosFate-method • RPhosFate - +
    @@ -26,7 +25,7 @@
    - +

    Save state

    - Source: R/interface.R + Source: R/interface.R
    -

    Saves parameters (parameters.yaml) and transport calculation order -(order.rds) to disk.

    +

    Saves parameters (parameters.yaml) to disk.

    - 
    # S4 method for RPhosFate
+    
    # S4 method for class 'RPhosFate'
 saveState(x)

    Arguments

    -
    x
    + + +
    x

    An S4 RPhosFate river catchment object.

    Value

    - - -

    NULL invisibly and side effects in the form of files.

    +

    NULL invisibly and side effects in the form of files.

    See also

    @@ -139,15 +137,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/dev/reference/saveState.html b/dev/reference/saveState.html new file mode 100644 index 0000000..62f45f0 --- /dev/null +++ b/dev/reference/saveState.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/dev/reference/setParameter-RPhosFate-method.html b/dev/reference/setParameter-RPhosFate-method.html index 7f71953..5650abb 100644 --- a/dev/reference/setParameter-RPhosFate-method.html +++ b/dev/reference/setParameter-RPhosFate-method.html @@ -3,7 +3,7 @@ - +
    @@ -25,7 +25,7 @@
    - +

    Set parameter(s)

    - Source: R/gettersSetters.R + Source: R/gettersSetters.R
    @@ -88,33 +88,33 @@

    Set parameter(s)

    - 
    # S4 method for RPhosFate
+    
    # S4 method for class 'RPhosFate'
 setParameter(x, ...)

    Arguments

    -
    x
    + + +
    x

    An S4 RPhosFate river catchment object.

    -
    ...
    +
    ...

    Names and values of the parameters to set. See model parameter arguments section for further information.

    Value

    - - -

    An S4 RPhosFate river catchment object.

    +

    An S4 RPhosFate river catchment object.

    Model parameter arguments

    - +

    • ns_slp_min: A numeric scalar specifying the minimum bounding slope in % -(defaults to 0.001).

      • +(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 @@ -145,8 +145,6 @@

      Model parameter arguments

      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).

      • @@ -173,6 +171,7 @@

      Examples

      cv_dir = cv_dir, ls_ini = TRUE ) +#> Warning: Omitted parameter "iv_fDo", as it is no longer required. It will definitely be lost upon saving the project's state. x <- setParameter(x, ns_dep_ovl = 15e-4) x <- setParameter( @@ -195,15 +194,15 @@

      Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/dev/reference/setParameter.html b/dev/reference/setParameter.html new file mode 100644 index 0000000..e2b6064 --- /dev/null +++ b/dev/reference/setParameter.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/dev/reference/snapGauges-RPhosFate-method.html b/dev/reference/snapGauges-RPhosFate-method.html index 4f23bde..6e778ac 100644 --- a/dev/reference/snapGauges-RPhosFate-method.html +++ b/dev/reference/snapGauges-RPhosFate-method.html @@ -4,7 +4,7 @@ - +
    @@ -26,7 +26,7 @@
    - +

    Snap gauge(s)

    - Source: R/interface.R + Source: R/interface.R
    @@ -90,21 +90,21 @@

    Snap gauge(s)

    - 
    # S4 method for RPhosFate
+    
    # S4 method for class 'RPhosFate'
 snapGauges(x)

    Arguments

    -
    x
    + + +
    x

    An S4 RPhosFate river catchment object.

    Value

    - - -

    An S4 RPhosFate river catchment object.

    +

    An S4 RPhosFate river catchment object.

    See also

    @@ -122,6 +122,7 @@

    Examples

    cv_dir = cv_dir, ls_ini = TRUE ) +#> Warning: Omitted parameter "iv_fDo", as it is no longer required. It will definitely be lost upon saving the project's state. x <- snapGauges(x) @@ -139,15 +140,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/dev/reference/snapGauges.html b/dev/reference/snapGauges.html new file mode 100644 index 0000000..f5724a6 --- /dev/null +++ b/dev/reference/snapGauges.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/dev/reference/subsequentRun-RPhosFate-method.html b/dev/reference/subsequentRun-RPhosFate-method.html index 1c5ccd2..7f8d04d 100644 --- a/dev/reference/subsequentRun-RPhosFate-method.html +++ b/dev/reference/subsequentRun-RPhosFate-method.html @@ -1,11 +1,11 @@ Subsequent run — subsequentRun,RPhosFate-method • RPhosFate - +
    @@ -27,7 +27,7 @@
    - +

    Subsequent run

    - Source: R/interface.R + Source: R/interface.R

    Calls transport for the specified substance and optionally -erosionPrerequisites, erosion, emission, -transportPrerequisites and/or transportCalcOrder beforehand.

    +erosionPrerequisites, erosion, emission and +transportPrerequisites beforehand.

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

    Arguments

    -
    x
    + + +
    x

    An S4 RPhosFate river catchment object.

    -
    substance
    +
    substance

    A character string specifying the substance to calculate.

    -
    erosionPrerequisites
    +
    erosionPrerequisites

    A logical scalar specifying if erosionPrerequisites is called.

    -
    erosion
    +
    erosion

    A logical scalar specifying if erosion is called.

    -
    emission
    +
    emission

    A logical scalar specifying if emission is called. It is never called with substance = "SS" though.

    -
    transportPrerequisites
    +
    transportPrerequisites

    A logical scalar specifying if transportPrerequisites is called.

    - -
    transportCalcOrder
    -

    A logical scalar specifying if -transportCalcOrder is called.

    -

    Value

    - - -

    An S4 RPhosFate river catchment object and side effects in +

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

    @@ -161,6 +155,7 @@

    Examples

    cv_dir = cv_dir, ls_ini = TRUE ) +#> Warning: Omitted parameter "iv_fDo", as it is no longer required. It will definitely be lost upon saving the project's state. # presupposed method call x <- firstRun(x, "SS") @@ -180,15 +175,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/dev/reference/subsequentRun.html b/dev/reference/subsequentRun.html new file mode 100644 index 0000000..a8faab0 --- /dev/null +++ b/dev/reference/subsequentRun.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/dev/reference/transport-RPhosFate-method.html b/dev/reference/transport-RPhosFate-method.html index 11dae20..d6651d9 100644 --- a/dev/reference/transport-RPhosFate-method.html +++ b/dev/reference/transport-RPhosFate-method.html @@ -4,7 +4,7 @@ - +
    @@ -26,7 +26,7 @@
    - +

    Transport

    - Source: R/RPhosFate.R + Source: R/RPhosFate.R
    @@ -90,31 +90,34 @@

    Transport

    - 
    # S4 method for RPhosFate
+    
    # S4 method for class 'RPhosFate'
 transport(x, substance = "PP")

    Arguments

    -
    x
    + + +
    x

    An S4 RPhosFate river catchment object.

    -
    substance
    +
    substance

    A character string specifying the substance to calculate.

    Value

    - - -

    An S4 RPhosFate river catchment object and side effects in +

    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

    @@ -132,12 +135,12 @@

    Examples

    cv_dir = cv_dir, ls_ini = TRUE ) +#> Warning: Omitted parameter "iv_fDo", as it is no longer required. It will definitely be lost upon saving the project's state. # presupposed method calls x <- erosionPrerequisites(x) x <- erosion(x) x <- emission(x, "PP") x <- transportPrerequisites(x) -x <- transportCalcOrder(x) x <- transport(x, "PP")# } @@ -155,15 +158,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/dev/reference/transport.html b/dev/reference/transport.html new file mode 100644 index 0000000..da987dd --- /dev/null +++ b/dev/reference/transport.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/dev/reference/transportCalcOrder-RPhosFate-method.html b/dev/reference/transportCalcOrder-RPhosFate-method.html deleted file mode 100644 index 4fb120b..0000000 --- a/dev/reference/transportCalcOrder-RPhosFate-method.html +++ /dev/null @@ -1,151 +0,0 @@ - -Transport calculation order — transportCalcOrder,RPhosFate-method • RPhosFate - - -
    -
    - - - -
    -
    -
    -

    Transport calculation order

    - Source: R/RPhosFate.R - -
    - -
    -

    Determines the cell transport calculation order.

    -
    - -
    - 
    # S4 method for RPhosFate
-transportCalcOrder(x)
    -
    - -
    -

    Arguments

    -
    x
    -

    An S4 RPhosFate river catchment object.

    - -
    -
    -

    Value

    - - -

    An S4 RPhosFate river catchment object.

    -
    -
    -

    See also

    -

    firstRun, subsequentRun

    -
    - -
    -

    Examples

    - 
    # \donttest{
-# temporary demonstration project copy
-cv_dir <- demoProject()
-#> Warning: A folder called "demoProject" already exists and is left as is.
-# load temporary demonstration project
-x <- RPhosFate(
-  cv_dir = cv_dir,
-  ls_ini = TRUE
-)
-
-x <- transportCalcOrder(x)# }
-
-
    -
    -
    - -
    - - -
    -

    Developed by Gerold Hepp.

    -
    - -
    -

    Site built with pkgdown 2.0.9.

    -
    - -
    - - - - - - - - diff --git a/dev/reference/transportPrerequisites-RPhosFate-method.html b/dev/reference/transportPrerequisites-RPhosFate-method.html index 7b475cf..900131c 100644 --- a/dev/reference/transportPrerequisites-RPhosFate-method.html +++ b/dev/reference/transportPrerequisites-RPhosFate-method.html @@ -1,10 +1,10 @@ -Transport prerequisites — transportPrerequisites,RPhosFate-method • RPhosFateTransport prerequisites — transportPrerequisites,RPhosFate-method • RPhosFate - +
    @@ -26,7 +26,7 @@
    - +

    Transport prerequisites

    - Source: R/RPhosFate.R + Source: R/RPhosFate.R
    -

    Calculates hydraulic radii and determines cells representing inlets as well -as riparian zones before writing them to disk.

    +

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

    - 
    # S4 method for RPhosFate
+    
    # S4 method for class 'RPhosFate'
 transportPrerequisites(x)

    Arguments

    -
    x
    + + +
    x

    An S4 RPhosFate river catchment object.

    Value

    - - -

    An S4 RPhosFate river catchment object and side effects in +

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

    -
    -
    -

    References

    -

    Molnár, P., Ramírez, J.A., 1998. Energy dissipation theories and -optimal channel characteristics of river networks. Water Resources Research -34, 1809–1818.

    See also

    @@ -129,6 +123,7 @@

    Examples

    cv_dir = cv_dir, ls_ini = TRUE ) +#> Warning: Omitted parameter "iv_fDo", as it is no longer required. It will definitely be lost upon saving the project's state. x <- transportPrerequisites(x)# } @@ -146,15 +141,15 @@

    Examples

    -

    Site built with pkgdown 2.0.9.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/dev/reference/transportPrerequisites.html b/dev/reference/transportPrerequisites.html new file mode 100644 index 0000000..cf71161 --- /dev/null +++ b/dev/reference/transportPrerequisites.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/dev/sitemap.xml b/dev/sitemap.xml index e46ee14..6c302ea 100644 --- a/dev/sitemap.xml +++ b/dev/sitemap.xml @@ -1,90 +1,31 @@ - - - - https://gisler.github.io/RPhosFate/CONTRIBUTING.html - - - https://gisler.github.io/RPhosFate/LICENSE.html - - - https://gisler.github.io/RPhosFate/articles/basicWorkflow.html - - - https://gisler.github.io/RPhosFate/articles/index.html - - - https://gisler.github.io/RPhosFate/authors.html - - - https://gisler.github.io/RPhosFate/index.html - - - https://gisler.github.io/RPhosFate/news/index.html - - - https://gisler.github.io/RPhosFate/reference/DEMrelatedInput.html - - - https://gisler.github.io/RPhosFate/reference/RPhosFate-class.html - - - https://gisler.github.io/RPhosFate/reference/autoCalibrate-RPhosFate-method.html - - - https://gisler.github.io/RPhosFate/reference/autoCalibrate2-RPhosFate-method.html - - - https://gisler.github.io/RPhosFate/reference/calibrationQuality-RPhosFate-method.html - - - https://gisler.github.io/RPhosFate/reference/catchment.html - - - https://gisler.github.io/RPhosFate/reference/demoProject.html - - - https://gisler.github.io/RPhosFate/reference/emission-RPhosFate-method.html - - - https://gisler.github.io/RPhosFate/reference/erosion-RPhosFate-method.html - - - https://gisler.github.io/RPhosFate/reference/erosionPrerequisites-RPhosFate-method.html - - - https://gisler.github.io/RPhosFate/reference/firstRun-RPhosFate-method.html - - - https://gisler.github.io/RPhosFate/reference/getLayer-RPhosFate-method.html - - - https://gisler.github.io/RPhosFate/reference/getParameter-RPhosFate-method.html - - - https://gisler.github.io/RPhosFate/reference/img2tif.html - - - https://gisler.github.io/RPhosFate/reference/index.html - - - https://gisler.github.io/RPhosFate/reference/saveState-RPhosFate-method.html - - - https://gisler.github.io/RPhosFate/reference/setParameter-RPhosFate-method.html - - - https://gisler.github.io/RPhosFate/reference/snapGauges-RPhosFate-method.html - - - https://gisler.github.io/RPhosFate/reference/subsequentRun-RPhosFate-method.html - - - https://gisler.github.io/RPhosFate/reference/transport-RPhosFate-method.html - - - https://gisler.github.io/RPhosFate/reference/transportCalcOrder-RPhosFate-method.html - - - https://gisler.github.io/RPhosFate/reference/transportPrerequisites-RPhosFate-method.html - + +https://gisler.github.io/RPhosFate/CONTRIBUTING.html +https://gisler.github.io/RPhosFate/LICENSE.html +https://gisler.github.io/RPhosFate/articles/basicWorkflow.html +https://gisler.github.io/RPhosFate/articles/index.html +https://gisler.github.io/RPhosFate/authors.html +https://gisler.github.io/RPhosFate/index.html +https://gisler.github.io/RPhosFate/news/index.html +https://gisler.github.io/RPhosFate/reference/DEMrelatedInput.html +https://gisler.github.io/RPhosFate/reference/RPhosFate-class.html +https://gisler.github.io/RPhosFate/reference/autoCalibrate-RPhosFate-method.html +https://gisler.github.io/RPhosFate/reference/autoCalibrate2-RPhosFate-method.html +https://gisler.github.io/RPhosFate/reference/calibrationQuality-RPhosFate-method.html +https://gisler.github.io/RPhosFate/reference/catchment.html +https://gisler.github.io/RPhosFate/reference/demoProject.html +https://gisler.github.io/RPhosFate/reference/emission-RPhosFate-method.html +https://gisler.github.io/RPhosFate/reference/erosion-RPhosFate-method.html +https://gisler.github.io/RPhosFate/reference/erosionPrerequisites-RPhosFate-method.html +https://gisler.github.io/RPhosFate/reference/firstRun-RPhosFate-method.html +https://gisler.github.io/RPhosFate/reference/getLayer-RPhosFate-method.html +https://gisler.github.io/RPhosFate/reference/getParameter-RPhosFate-method.html +https://gisler.github.io/RPhosFate/reference/img2tif.html +https://gisler.github.io/RPhosFate/reference/index.html +https://gisler.github.io/RPhosFate/reference/saveState-RPhosFate-method.html +https://gisler.github.io/RPhosFate/reference/setParameter-RPhosFate-method.html +https://gisler.github.io/RPhosFate/reference/snapGauges-RPhosFate-method.html +https://gisler.github.io/RPhosFate/reference/subsequentRun-RPhosFate-method.html +https://gisler.github.io/RPhosFate/reference/transport-RPhosFate-method.html +https://gisler.github.io/RPhosFate/reference/transportPrerequisites-RPhosFate-method.html +