diff --git a/RBBGCMuso/R/atStart.R b/RBBGCMuso/R/atStart.R index 2deb775..d63f2b8 100644 --- a/RBBGCMuso/R/atStart.R +++ b/RBBGCMuso/R/atStart.R @@ -10,11 +10,9 @@ colorText <- function(text,color){ RMuso_version <- 7 cat(sprintf('This is RBBGCMuso version 1.0\nDefault Biome-BGCMuSo version: %d\n', RMuso_version)) - - cat('Thanks for using RBBGCMuso!\n') - cat('For quick tutorial visit https://github.com/hollorol/RBBGCMuso\n') + cat(sprintf('For quick tutorial visit %s\n', colorText('https://github.com/hollorol/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_varTable <- list() #___________________________ diff --git a/RBBGCMuso/R/recent.soi b/RBBGCMuso/R/recent.soi deleted file mode 100644 index f69f1ce..0000000 --- a/RBBGCMuso/R/recent.soi +++ /dev/null @@ -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 diff --git a/RBBGCMuso/R/soilQuery.R b/RBBGCMuso/R/soilQuery.R index 6c4e189..02476fe 100644 --- a/RBBGCMuso/R/soilQuery.R +++ b/RBBGCMuso/R/soilQuery.R @@ -9,7 +9,7 @@ getSoilDataFull <- function(lat, lon, 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}") soilREST <- #with_config(config(ssl_verifypeer=0L, ssl_verifyhost=0L), @@ -31,9 +31,9 @@ getSoilDataFull <- function(lat, lon, apiURL) { createSoilFile <- function(lat,lon, outputFile="recent.soi", 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)){ - apiURL <- "https://rest.soilgrids.org/soilgrids/v2.0/properties" + apiURL <- "https://rest.isric.org/soilgrids/v2.0/properties" } outFile <- suppressWarnings(readLines(template)) 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")}) - 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")) - 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")) - outFile[57] <- sprintf("%s (dimless) soil PH", + outFile[92] <- sprintf("%s (dimless) soil PH", paste(createMusoLayers(getMeanSoil(rest,"phh2o")/10), collapse="\t")) # outFile[58] <- sprintf("%s (%%) bulk density",paste(createMusoLayers(soilDepth),collapse="\t")) writeLines(outFile,outputFile) diff --git a/RBBGCMuso/R/tuner.R b/RBBGCMuso/R/tuner.R index 62336bb..8ce54c2 100644 --- a/RBBGCMuso/R/tuner.R +++ b/RBBGCMuso/R/tuner.R @@ -1,6 +1,6 @@ #' 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 #' @importFrom plotly plotlyOutput