upload mdi files

HowToMakeRpackage_LPJmL-MDI.R

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+#--------------------------------------------
+# Building and installation of an R package:
+# Matthias Forkel, 2017-08-02
+#--------------------------------------------
+
+# package development is based on inlinedocs (for in-line documentation)
+library(inlinedocs)
+library(here)
+
+# name and directory of package
+pkg.name <- "LPJmLmdi"
+path <- paste(here::here(), sep="/")
+
+
+# BUILDING
+#---------
+
+# Building is only required if you further develop the package, i.e. if you want to newly 
+# create help files and perform tests. Continue with the next section if you just downloaded 
+# the package and you want to install it.
+
+# build package structure and Rd files
+setwd(path)
+package.skeleton.dx(pkg.name)
+
+# check package
+cmd <- sprintf(paste("%s CMD check --as-cran", pkg.name), file.path(R.home("bin"), "R"))
+system(cmd, intern=TRUE)
+
+# build package
+cmd <- sprintf(paste("%s CMD build --resave-data", pkg.name), file.path(R.home("bin"), "R"))
+system(cmd, intern=TRUE)
+
+
+# INSTALLATION
+#-------------
+
+# installation
+cmd <- paste("R CMD INSTALL --html", pkg.name, "--resave-data")
+tryCatch(system(cmd), finally=setwd(path))
+
+# load package
+library(pkg.name, character.only=TRUE)
+
+# check package help files:
+?OptimizeLPJgenoud
+
+

LPJmLmdi.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX

LPJmLmdi/.Rhistory

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+install.packages("bfast")
+install.packages("phenopix")
+here()
+setwd("~/shares/home/code/R/_gitlab/")
+pkgs <- c("RobinsonMaps")
+i <- 1
+setwd(pkgs[i])
+cmd <- paste("R CMD INSTALL --html ", pkgs[i], " --resave-data")
+tryCatch(system(cmd), finally=setwd(path))
+getwd()
+pkgs <- c("RobinsonMaps", "ModelDataComp")
+setwd("..")
+setwd(pkgs[i])
+cmd <- paste("R CMD INSTALL --html ", pkgs[i], " --resave-data")
+tryCatch(system(cmd))
+setwd("..")
+getwd()
+pkgs <- c("RobinsonMaps", "ModelDataComp")
+i <- 2
+setwd(pkgs[i])
+cmd <- paste("R CMD INSTALL --html ", pkgs[i], " --resave-data")
+tryCatch(system(cmd))
+setwd("..")
+install.packages("lhs")
+setwd("~/shares/home/code/R/_gitlab/")
+pkgs <- c("RobinsonMaps", "ModelDataComp")
+i <- 2
+setwd(pkgs[i])
+cmd <- paste("R CMD INSTALL --html ", pkgs[i], " --resave-data")
+tryCatch(system(cmd))
+setwd("..")
+install.packages("randomForest")
+i <- 2
+setwd(pkgs[i])
+cmd <- paste("R CMD INSTALL --html ", pkgs[i], " --resave-data")
+tryCatch(system(cmd))
+setwd("..")
+pkgs <- c("RobinsonMaps", "ModelDataComp", "Raster4ML")
+i <- 3
+setwd(pkgs[i])
+cmd <- paste("R CMD INSTALL --html ", pkgs[i], " --resave-data")
+tryCatch(system(cmd))
+setwd("..")
+install.packages("ICEbox")
+install.packages("ff")
+setwd("~/shares/home/code/R/greenbrown")
+cmd <- paste("R CMD INSTALL --html greenbrown --resave-data")
+tryCatch(system(cmd))
+setwd("~/shares/home/code/R/_gitlab/")
+pkgs <- c("RobinsonMaps", "ModelDataComp", "Raster4ML")
+i <- 3
+setwd(pkgs[i])
+cmd <- paste("R CMD INSTALL --html ", pkgs[i], " --resave-data")
+tryCatch(system(cmd))
+setwd("..")
+setwd("~/shares/home/code/R/_gitlab-pik/LPJmLmdi/")
+tryCatch(system("R CMD INSTALL --html LPJmLmdi --resave-data"))
+grep("o", letters)
+# package development is based on inlinedocs (for in-line documentation)
+library(inlinedocs)
+library(here)
+# name and directory of package
+pkg.name <- "LPJmLmdi"
+path <- paste(here::here(), sep="/")
+# Building is only required if you further develop the package, i.e. if you want to newly
+# create help files and perform tests. Continue with the next section if you just downloaded
+# the package and you want to install it.
+# build package structure and Rd files
+setwd(path)
+package.skeleton.dx(pkg.name)
+# check package
+cmd <- sprintf(paste("%s CMD check --as-cran", pkg.name), file.path(R.home("bin"), "R"))
+system(cmd, intern=TRUE)
+# check package
+cmd <- sprintf(paste("%s CMD check --as-cran", pkg.name), file.path(R.home("bin"), "R"))
+system(cmd, intern=TRUE)
+# build package
+cmd <- sprintf(paste("%s CMD build --resave-data", pkg.name), file.path(R.home("bin"), "R"))
+system(cmd, intern=TRUE)
+# installation
+setwd(here::here())
+cmd <- paste("R CMD INSTALL --html", pkg.name, "--resave-data")
+tryCatch(system(cmd), finally=setwd(path))
+# load package
+library(pkg.name, character.only=TRUE)
+?PlotParUnc

LPJmLmdi/DESCRIPTION

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+Package: LPJmLmdi
+Title: Model-Data Integration for the LPJmL Dynamic Global Vegetation Model
+Version: 1.3
+Date: 2019-01-22
+Author: Matthias Forkel <[email protected]> [aut, cre], Markus Drüke <[email protected]> [aut]
+Maintainer: Matthias Forkel <[email protected]>, Markus Drüke <[email protected]>
+Description: Model-data integration framework for the LPJmL dynamic global vegetation model. Specifically, the package provides functions 1) to optimize LPJmL model parameters using the GENOUD genetic optimization algorithm, 2) to read and write LPJmL input data, and 3) to read LPJmL output files.
+Depends: R (>= 2.15.3), raster, plyr, rgenoud, ncdf4, ModelDataComp
+Imports: dplyr, plotrix, fields, tidyr
+License: GPL-2
+URL: 
+LazyLoad: yes

LPJmLmdi/NAMESPACE

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+importFrom("plotrix", "color.legend")
+importFrom("tidyr", "separate", "unite", "gather")
+importFrom("RColorBrewer", "brewer.pal")
+exportPattern("^[[:alpha:]]+")
+