rSALMO: Simulation of ecological lake models

Simulation of ecological lake models. The current version of the package contains the C implementation of the lake model SALMO-II and an additional macrophyte module that can be run in 0D (1 box), 0.5 D (2 box) and vertically resolved in 1D.

AuthorThomas Petzoldt, Susanne Rolinski and Rene Sachse
Date of publication2015-02-15 23:39:28
MaintainerThomas Petzoldt <thomas.petzoldt@tu-dresden.de>
LicenseGPL (>= 2)
Version0.3-0
http://rlimnolab.r-forge.r-project.org/

View on R-Forge

Man pages

aggregate_daily: Calculate Daily Sums or Averages

approxTime: Linear Interpolation with Complete Matrices or Data Frames

areaFunction: Hypsographic Functions for Conical Lake Geometry

calczmix: Calculate Mixing Depth

call_salmodll: Call SALMO Shared Library

check_salmo_parms: Check SALMO Model Parameters

data_bautzen_1997: Input data set data_bautzen_1997

extract_phys: Extract Physical Structure from Input Data

get_salmo_parms: Get SALMO Parameters

hypso_bautzen: Data set hypso_bautzen

hypso_cone: Hypsographic Table of a Conic Lake

hypso_functions: Hypsographic Functions from Tabular Interpolation

init_salmo_integers: Initialize Index Values of Parameter List

irad: Irradiation Data Set

layers2vector: Convert Layer Structure to Vector

layers_long2wide: Reformat Layer Strcuture from Long Format to Wide Format

makeInputVector: Make Input Vector from List of Input Data

o2sat: Oxygen Saturation in Fresh Water

parms_mac_ctrl: parms_mac_ctrl data set

parms_mac_other: parms_mac_other data set

parms_mac_plants: parms_mac_plants data set

parms_salmo_ctrl: parms_salmo_ctrl data set

parms_salmo_other: parms_salmo_other data set

parms_salmo_phyto: parms_salmo_phyto data set

plot_inputs: Plot Inputs of a 1D Model

rSALMO-package: Ecological Simulation of Lakes

salmo_1d: Derivatives of SALMO

salmo_box: Derivatives of SALMO

salmo_mac_1d: Derivatives of SALMO with macrophytes

salmo_mac_box: Derivatives of SALMO with macrophytes

salmo_state_names: Column Names of SALMO State and Input Variables

sedimentation_matrix: Create Sedimentation and Migration Matrix for SALMO-1D

setparms: Set Model Parameters

transport: Calulate Vertical Transport for a 1D Lake Model

turbulence: Turbulence Data Set

Functions

aggregate_daily Man page
approxTime Man page
approxTime1 Man page
approxTimeEq Man page
approxTimeEq1 Man page
areaFunction Man page
arrangeLayerWise Man page
arrangeStateWise Man page
calczmix Man page
call_salmodll Man page
check_salmo_parms Man page
data_bautzen_1997 Man page
extract_phys Man page
findIndexEq Man page
get_salmo_parms Man page
hypso_bautzen Man page
hypso_cone Man page
hypso_functions Man page
init_salmo_integers Man page
irad Man page
layers2vector Man page
layers_long2wide Man page
makeInputVector Man page
o2sat Man page
parms_mac_ctrl Man page
parms_mac_other Man page
parms_mac_plants Man page
parms_salmo_ctrl Man page
parms_salmo_other Man page
parms_salmo_phyto Man page
plot_inputs Man page
rSALMO Man page
rSALMO-package Man page
salmo_1box Man page
salmo_1d Man page
salmo_2box Man page
salmo_input_names Man page
salmo_mac_1box Man page
salmo_mac_1d Man page
salmo_state_names Man page
sedimentation_matrix Man page
setparms Man page
transport Man page
turbulence Man page
vol2level Man page
volumeFunction Man page

Files

DESCRIPTION
NAMESPACE
R
R/aaa_data.R R/aggregate_daily.R R/approxTime.R R/areaFunction.R R/calczmix.R R/call_salmodll.R R/checkparms.R R/extract_phys.R R/get_salmo_parms.R R/hypso_functions.R R/hyso_cone.R R/init_salmo_integers.R R/irad.R R/layers2vector.R R/layers_long2wide.R R/macrophytedll.R R/makeInputVector.R R/o2sat.R R/plot_inputs.R R/rSALMO-internal.R R/rSALMO-package.R R/salmo_1d.R R/salmo_box.R R/salmo_mac_1d.R R/salmo_mac_box.R R/salmo_state_names.R R/sedimentation_matrix.R R/setparms.R R/setparms_util.R R/transport.R R/turbulence.R
build
build/vignette.rds
data
data/data_bautzen_1997.txt.xz
data/datalist
data/hypso_bautzen.txt.gz
data/hypso_cone.rda
data/irad.rda
data/parms_mac_ctrl.txt.gz
data/parms_mac_other.txt.gz
data/parms_mac_plants.txt.gz
data/parms_salmo_ctrl.txt.gz
data/parms_salmo_other.txt.gz
data/parms_salmo_phyto.txt.gz
data/turbulence.rda
demo
demo/00Index
demo/demo_salmo_1box.R demo/demo_salmo_1d.R demo/demo_salmo_2box.R demo/demo_salmo_mac_1d.R
inst
inst/doc
inst/doc/salmo-equations.Rnw
inst/doc/salmo-equations.pdf
man
man/aggregate_daily.Rd man/approxTime.Rd man/areaFunction.Rd man/calczmix.Rd man/call_salmodll.Rd man/check_salmo_parms.Rd man/data_bautzen_1997.Rd man/extract_phys.Rd man/get_salmo_parms.Rd man/hypso_bautzen.Rd man/hypso_cone.Rd man/hypso_functions.Rd man/init_salmo_integers.Rd man/irad.Rd man/layers2vector.Rd man/layers_long2wide.Rd man/makeInputVector.Rd man/o2sat.Rd man/parms_mac_ctrl.Rd man/parms_mac_other.Rd man/parms_mac_plants.Rd man/parms_salmo_ctrl.Rd man/parms_salmo_other.Rd man/parms_salmo_phyto.Rd man/plot_inputs.Rd man/rSALMO-package.Rd man/salmo_1d.Rd man/salmo_box.Rd man/salmo_mac_1d.Rd man/salmo_mac_box.Rd man/salmo_state_names.Rd man/sedimentation_matrix.Rd man/setparms.Rd man/transport.Rd man/turbulence.Rd
src
src/MacrophyteSalmoInteraction.cpp
src/MacrophytesCore.cpp
src/MacrophytesCore.h
src/MacrophytesSalmoInterface.cpp
src/SalmoKern.cpp
src/salmo_constants.h
src/salmo_headers.h
src/salmo_macros.h
vignettes
vignettes/rsalmo.pdf
vignettes/salmo-2.png
vignettes/salmo-equations.Rnw
vignettes/salmo-equations.bbl
vignettes/salmo-equations.tex
vignettes/salmo.bib
work
work/Area3.R
work/Bautzen
work/Bautzen/create_data.R
work/Bautzen/struc_u1997
work/Bautzen/struc_uref-1997
work/Bautzen/tsb_hypso.dat
work/Bautzen/u1997
work/Bautzen/uref-1997
work/ToDo.txt
work/call_salmodll_macrophytes.R
work/cc.dat
work/cc.txt
work/createSalmoForcings.R
work/doc_snippets.txt
work/hypsographic_functions.R work/make_parvec.R work/roxygen_snippets.R work/run_salmo.R work/salmo_2box_Bautzen.R work/salmo_mac_1box.R work/test-1D-forcings.R work/test-1D-inputs.R work/test_approxTime.R work/test_layerwise.R work/test_salmo_ma.R
work/utest.txt
work/vector_names.R

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