updating soil query code
This commit is contained in:
Zoltan BARCZA
parent
57cf5db372
commit
a19c14a6b8
@ -10,11 +10,9 @@ colorText <- function(text,color){
|
|||||||
RMuso_version <- 7
|
RMuso_version <- 7
|
||||||
cat(sprintf('This is RBBGCMuso version 1.0\nDefault Biome-BGCMuSo version: %d\n',
|
cat(sprintf('This is RBBGCMuso version 1.0\nDefault Biome-BGCMuSo version: %d\n',
|
||||||
RMuso_version))
|
RMuso_version))
|
||||||
|
cat(sprintf('For quick tutorial visit %s\n', colorText('https://github.com/hollorol/RBBGCMuso',104)))
|
||||||
cat('Thanks for using RBBGCMuso!\n')
|
|
||||||
cat('For quick tutorial visit https://github.com/hollorol/RBBGCMuso\n')
|
|
||||||
cat(sprintf('For help, issue the command: %s\n',colorText('help(package="RBBGCMuso")',104)))
|
cat(sprintf('For help, issue the command: %s\n',colorText('help(package="RBBGCMuso")',104)))
|
||||||
cat('In order to get a sample simulation package use the copyMusoExample() command\n')
|
cat(sprintf('In order to get a sample simulation package use the %s command\n',colorText('copyMusoExample()',104)))
|
||||||
RMuso_constMatrix <- list(epc=NULL,soil=NULL)
|
RMuso_constMatrix <- list(epc=NULL,soil=NULL)
|
||||||
RMuso_varTable <- list()
|
RMuso_varTable <- list()
|
||||||
#___________________________
|
#___________________________
|
||||||
|
|||||||
@ -1,63 +0,0 @@
|
|||||||
SOILPROP FILE - lat: 60, lon: 50, created in: Mon Apr 20 10:44:56 2020
|
|
||||||
----------------------------------------------------------------------------------------
|
|
||||||
NITROGEN AND DECOMPOSITION PARAMETERS
|
|
||||||
0.1 (prop.) denitrification rate per g of CO2 respiration of SOM
|
|
||||||
0.2 (prop.) nitrification coefficient 1
|
|
||||||
0.07 (prop.) nitrification coefficient 2
|
|
||||||
0.02 (prop.) coefficient of N2O emission of nitrification
|
|
||||||
0.1 (prop.) NH4 mobilen proportion
|
|
||||||
1.0 (prop.) NO3 mobilen proportion
|
|
||||||
10 (m) e-folding depth of decomposition rate's depth scalar
|
|
||||||
0.002 (prop.) fraction of dissolved part of SOIL1 organic matter
|
|
||||||
0.002 (prop.) fraction of dissolved part of SOIL2 organic matter
|
|
||||||
0.002 (prop.) fraction of dissolved part of SOIL3 organic matter
|
|
||||||
0.002 (prop.) fraction of dissolved part of SOIL4 organic matter
|
|
||||||
0.1 (prop.) minimum WFPS for scalar of nitrification calculation
|
|
||||||
0.45 (prop.) lower optimum WFPS for scalar of nitrification calculation
|
|
||||||
0.55 (prop.) higher optimum WFPS for scalar of nitrification calculation
|
|
||||||
0.2 (prop.) minimum value for saturated WFPS scalar of nitrification calculation
|
|
||||||
10 (ppm) critical value of dissolved N and C in bottom (inactive layer)
|
|
||||||
----------------------------------------------------------------------------------------
|
|
||||||
RATE SCALARS
|
|
||||||
0.35 (prop) respiration fractions for fluxes between compartments (l1s1)
|
|
||||||
0.50 (prop) respiration fractions for fluxes between compartments (l2s2)
|
|
||||||
0.26 (prop) respiration fractions for fluxes between compartments (l4s3)
|
|
||||||
0.25 (prop) respiration fractions for fluxes between compartments (s1s2)
|
|
||||||
0.41 (prop) respiration fractions for fluxes between compartments (s2s3)
|
|
||||||
0.50 (prop) respiration fractions for fluxes between compartments (s3s4)
|
|
||||||
0.7 (1/day) rate constant scalar of labile litter pool
|
|
||||||
0.07 (1/day) rate constant scalar of cellulose litter pool
|
|
||||||
0.014 (1/day) rate constant scalar of lignin litter pool
|
|
||||||
0.07 (1/day) rate constant scalar of fast microbial recycling pool
|
|
||||||
0.014 (1/day) rate constant scalar of medium microbial recycling pool
|
|
||||||
0.0014 (1/day) rate constant scalar of slow microbial recycling pool
|
|
||||||
0.0001 (1/day) rate constant scalar of recalcitrant SOM (humus) pool
|
|
||||||
0.001 (1/day) rate constant scalar of physical fragmentation of coarse woody debris
|
|
||||||
----------------------------------------------------------------------------------------
|
|
||||||
CH4 PARAMETERS
|
|
||||||
212.5 (DIM) soil CH4 emission bulk density dependence parameter1
|
|
||||||
1.81 (DIM) soil CH4 emission bulk density dependence parameter2
|
|
||||||
-1.353 (DIM) soil CH4 emission soil water content dependence parameter1
|
|
||||||
0.2 (DIM) soil CH4 emission soil water content dependence parameter2
|
|
||||||
2 (DIM) soil CH4 emission soil water content dependence parameter3
|
|
||||||
6.786 (DIM) soil CH4 emission soil water content dependence parameter4
|
|
||||||
0.010 (DIM) soil CH4 emission soil temperature dependence parameter1
|
|
||||||
----------------------------------------------------------------------------------------
|
|
||||||
SOIL PARAMETERS
|
|
||||||
2 (m) depth of soil
|
|
||||||
6 (mm)42 42 43 47 48 49 49 49 51 51 limit of first stage evaporation
|
|
||||||
20.00 (mm) maximum height of pond water
|
|
||||||
1 (dimless) curvature of soil stress function
|
|
||||||
-9999 (dimless) measured runoff curve number (-9999: no measured data, model estimation)
|
|
||||||
----------------------------------------------------------------------------------------
|
|
||||||
SOIL COMPOSITION AND CHARACTERISTIC VALUES (-9999: no measured data)
|
|
||||||
30.0 30.0 30.0 30.0 30.0 30.0 30.0 30.0 30.0 30.0 (%) sand percentage by volume in rock-free soil
|
|
||||||
50.0 50.0 50.0 50.0 50.0 50.0 50.0 50.0 50.0 50.0 (%) silt percentage by volume in rock-free soil
|
|
||||||
7.0 7.0 7.0 7.0 7.0 7.0 7.0 7.0 7.0 7.0 (dimless) soil pH (dimless) measured runoff curve number
|
|
||||||
-9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 (g/cm3) bulk density
|
|
||||||
-9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 (m3/m3) SWC at saturation
|
|
||||||
-9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 (m3/m3) SWC at field capacity
|
|
||||||
-9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 (m3/m3) SWC at wilting point
|
|
||||||
-9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 (m3/m3) SWC at hygroscopic water content
|
|
||||||
-9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 (dimless) drainage coefficient
|
|
||||||
-9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 -9999 (cm/day) hydraulic condictivity at saturation
|
|
||||||
@ -9,7 +9,7 @@
|
|||||||
|
|
||||||
getSoilDataFull <- function(lat, lon, apiURL) {
|
getSoilDataFull <- function(lat, lon, apiURL) {
|
||||||
if(missing(apiURL)){
|
if(missing(apiURL)){
|
||||||
apiURL <- "https://81.169.232.36"
|
apiURL <- "https://rest.isric.org/soilgrids/v2.0/properties"
|
||||||
}
|
}
|
||||||
apiString <- glue("{apiURL}/query?lon={lon}&lat={lat}")
|
apiString <- glue("{apiURL}/query?lon={lon}&lat={lat}")
|
||||||
soilREST <- #with_config(config(ssl_verifypeer=0L, ssl_verifyhost=0L),
|
soilREST <- #with_config(config(ssl_verifypeer=0L, ssl_verifyhost=0L),
|
||||||
@ -31,9 +31,9 @@ getSoilDataFull <- function(lat, lon, apiURL) {
|
|||||||
createSoilFile <- function(lat,lon,
|
createSoilFile <- function(lat,lon,
|
||||||
outputFile="recent.soi",
|
outputFile="recent.soi",
|
||||||
method="constant",apiURL,
|
method="constant",apiURL,
|
||||||
template=system.file("examples/hhs/hhs.soi",package="RBBGCMuso")) {
|
template=system.file("examples/hhs/hhs_MuSo7.soi",package="RBBGCMuso")) {
|
||||||
if(missing(apiURL)){
|
if(missing(apiURL)){
|
||||||
apiURL <- "https://rest.soilgrids.org/soilgrids/v2.0/properties"
|
apiURL <- "https://rest.isric.org/soilgrids/v2.0/properties"
|
||||||
}
|
}
|
||||||
outFile <- suppressWarnings(readLines(template))
|
outFile <- suppressWarnings(readLines(template))
|
||||||
outFile[1] <- sprintf("SOILPROP FILE - lat: %s, lon: %s, created in: %s",lat,lon,date())
|
outFile[1] <- sprintf("SOILPROP FILE - lat: %s, lon: %s, created in: %s",lat,lon,date())
|
||||||
@ -50,11 +50,11 @@ createSoilFile <- function(lat,lon,
|
|||||||
}
|
}
|
||||||
|
|
||||||
soilDepth <- tryCatch(getMeanSoil(rest,"bdod")/100,error=function(e){stop("There is no data for the given coordinates")})
|
soilDepth <- tryCatch(getMeanSoil(rest,"bdod")/100,error=function(e){stop("There is no data for the given coordinates")})
|
||||||
outFile[55] <- sprintf("%s (%%) percentage of sand by volume in rock free soil",
|
outFile[90] <- sprintf("%s (%%) percentage of sand by volume in rock free soil",
|
||||||
paste(createMusoLayers(getMeanSoil(rest,"sand")/10), collapse="\t"))
|
paste(createMusoLayers(getMeanSoil(rest,"sand")/10), collapse="\t"))
|
||||||
outFile[56] <- sprintf("%s (%%) percentage of silt by volume in rock free soil",
|
outFile[91] <- sprintf("%s (%%) percentage of silt by volume in rock free soil",
|
||||||
paste(createMusoLayers(getMeanSoil(rest,"silt")/10), collapse="\t"))
|
paste(createMusoLayers(getMeanSoil(rest,"silt")/10), collapse="\t"))
|
||||||
outFile[57] <- sprintf("%s (dimless) soil PH",
|
outFile[92] <- sprintf("%s (dimless) soil PH",
|
||||||
paste(createMusoLayers(getMeanSoil(rest,"phh2o")/10), collapse="\t"))
|
paste(createMusoLayers(getMeanSoil(rest,"phh2o")/10), collapse="\t"))
|
||||||
# outFile[58] <- sprintf("%s (%%) bulk density",paste(createMusoLayers(soilDepth),collapse="\t"))
|
# outFile[58] <- sprintf("%s (%%) bulk density",paste(createMusoLayers(soilDepth),collapse="\t"))
|
||||||
writeLines(outFile,outputFile)
|
writeLines(outFile,outputFile)
|
||||||
|
|||||||
@ -1,6 +1,6 @@
|
|||||||
#' tuneMusoUI
|
#' tuneMusoUI
|
||||||
#'
|
#'
|
||||||
#' This is a simple parameter tuner function which works great in a flat directory systemj
|
#' This is a simple parameter tuner function which works great in a flat directory system
|
||||||
#'
|
#'
|
||||||
#' @param parameterFile optional, the parameter csv file
|
#' @param parameterFile optional, the parameter csv file
|
||||||
#' @importFrom plotly plotlyOutput
|
#' @importFrom plotly plotlyOutput
|
||||||
|
|||||||
Loading…
Reference in New Issue
Block a user