bugfixes

NAMESPACE

@@ -1,172 +1,102 @@
 # Generated by roxygen2: do not edit by hand
 
 export(calc1stBioenergyPast)
-export(calcBioenergyCombined)
 export(calcBodyHeight)
 export(calcDemography)
-export(calcEATLancetDiets)
-export(calcEATLancetWaste)
-export(calcEnergyFactor)
 export(calcFAOForestRelocate)
-export(calcFAOForestryDemand)
-export(calcFAO_fishery)
-export(calcFishCCimpacts)
 export(calcForestArea)
-export(calcForestAreaInitialization)
-export(calcForestHarvestCosts)
-export(calcForestProductionInitialization)
-export(calcForestryProductionRatio)
 export(calcIntake)
-export(calcIntake2)
-export(calcIntakeByGroup)
-export(calcManagementFactor)
 export(calcPhysicalInactivity)
 export(calcTimberDemand)
-export(calcTimberDemandExt)
-export(calcTimberShare)
-export(convertFAO_fishery)
 export(convertMAgPIE)
-export(correctCheung2016)
-export(correctCheung2018)
-export(readBijl2017)
-export(readCheung2016)
-export(readCheung2018)
 export(readFAO_FRA2015)
-export(readFAO_fishery)
 export(readFeedEfficiencyReg)
 export(readFeedShareReg)
-export(readPYieldCoeff)
-export(spatial_header)
-export(toolBiomassSupplyAggregate)
 export(toolCalcIEAfromStructureMappingPEFE)
 export(toolCell2isoCell)
-export(toolCubicFunctionAggregate)
-export(toolCubicFunctionDisaggregate)
 export(toolFAOcombine)
 export(toolHarmonize2Baseline)
 export(toolHoldConstantBeyondEnd)
 export(toolIntake)
-export(toolIntake2)
 export(toolIso2CellCountries)
-export(toolIsocode2Country)
-export(toolNUTSaggregate)
 export(toolPregnant)
-export(toolPregnant2)
-export(toolSolarFunctionAggregate)
-import(countrycode)
-import(dplyr)
 import(madrat)
 import(magclass)
 import(ncdf4)
 import(nleqslv)
-import(readxl)
 import(rhdf5)
-importClassesFrom(data.table,data.table)
-importFrom(R.utils,isZero)
 importFrom(SPEI,thornthwaite)
 importFrom(WDI,WDI)
 importFrom(WDI,WDIcache)
 importFrom(WDI,WDIsearch)
 importFrom(abind,abind)
-importFrom(alabama,auglag)
 importFrom(assertr,assert)
 importFrom(assertr,not_na)
-importFrom(assertthat,assert_that)
 importFrom(compiler,cmpfun)
 importFrom(countrycode,countrycode)
-importFrom(data.table,":=")
 importFrom(data.table,CJ)
-importFrom(data.table,as.data.table)
 importFrom(data.table,data.table)
-importFrom(data.table,dcast)
 importFrom(data.table,fread)
-importFrom(data.table,melt.data.table)
-importFrom(data.table,rbindlist)
-importFrom(data.table,setcolorder)
 importFrom(data.table,setkey)
 importFrom(data.table,setnames)
 importFrom(data.table,tstrsplit)
-importFrom(demystas,vectorEnum)
 importFrom(doParallel,registerDoParallel)
 importFrom(dplyr,"%>%")
-importFrom(dplyr,add_row)
 importFrom(dplyr,anti_join)
-importFrom(dplyr,arrange)
 importFrom(dplyr,arrange_)
 importFrom(dplyr,as_tibble)
 importFrom(dplyr,between)
-importFrom(dplyr,bind_cols)
-importFrom(dplyr,bind_rows)
-importFrom(dplyr,desc)
-importFrom(dplyr,filter)
 importFrom(dplyr,filter_)
 importFrom(dplyr,first)
 importFrom(dplyr,full_join)
 importFrom(dplyr,group_by)
 importFrom(dplyr,group_by_)
 importFrom(dplyr,inner_join)
-importFrom(dplyr,lag)
 importFrom(dplyr,last)
 importFrom(dplyr,left_join)
 importFrom(dplyr,matches)
 importFrom(dplyr,min_rank)
 importFrom(dplyr,mutate)
 importFrom(dplyr,mutate_)
-importFrom(dplyr,mutate_at)
-importFrom(dplyr,recode)
 importFrom(dplyr,rename)
 importFrom(dplyr,rename_)
 importFrom(dplyr,select)
 importFrom(dplyr,select_)
 importFrom(dplyr,summarise)
-importFrom(dplyr,summarise_)
 importFrom(dplyr,sym)
 importFrom(dplyr,tbl_df)
 importFrom(dplyr,tibble)
 importFrom(dplyr,tribble)
-importFrom(dplyr,ungroup)
 importFrom(foreach,"%:%")
 importFrom(foreach,"%dopar%")
 importFrom(foreach,foreach)
-importFrom(gdata,duplicated2)
-importFrom(grDevices,boxplot.stats)
 importFrom(graphics,plot)
 importFrom(lazyeval,interp)
 importFrom(lpjclass,as.lpj)
 importFrom(lpjclass,read.LPJ_input)
 importFrom(lpjclass,readLPJ)
 importFrom(lucode,path)
-importFrom(luscale,getAggregationMatrix)
 importFrom(luscale,groupAggregate)
 importFrom(luscale,rename_dimnames)
 importFrom(luscale,speed_aggregate)
-importFrom(luscale,superAggregate)
 importFrom(luscale,weighted_mean.groupAggregate)
 importFrom(madrat,calcOutput)
 importFrom(madrat,madlapply)
 importFrom(madrat,readSource)
 importFrom(madrat,regionscode)
 importFrom(madrat,toolAggregate)
 importFrom(madrat,toolCountry2isocode)
-importFrom(madrat,toolCountryFill)
-importFrom(madrat,toolFillWithRegionAvg)
-importFrom(madrat,toolGetMapping)
 importFrom(madrat,toolISOhistorical)
 importFrom(madrat,toolMappingFile)
 importFrom(madrat,toolNAreplace)
 importFrom(madrat,toolSubtypeSelect)
 importFrom(madrat,toolXlargest)
-importFrom(madrat,vcat)
 importFrom(magclass,"getCells<-")
 importFrom(magclass,"getNames<-")
 importFrom(magclass,"getRegionList<-")
-importFrom(magclass,"getRegions<-")
-importFrom(magclass,"getSets<-")
 importFrom(magclass,"getYears<-")
-importFrom(magclass,"mselect<-")
 importFrom(magclass,add_columns)
 importFrom(magclass,add_dimension)
-importFrom(magclass,as.data.frame)
 importFrom(magclass,as.magpie)
 importFrom(magclass,calibrate_it)
 importFrom(magclass,clean_magpie)
@@ -184,99 +114,64 @@ importFrom(magclass,getRegions)
 importFrom(magclass,getSets)
 importFrom(magclass,getYears)
 importFrom(magclass,is.magpie)
-importFrom(magclass,lowpass)
 importFrom(magclass,magpie_expand)
 importFrom(magclass,magpiesort)
 importFrom(magclass,mbind)
 importFrom(magclass,mbind2)
-importFrom(magclass,mselect)
-importFrom(magclass,ncells)
 importFrom(magclass,ndata)
 importFrom(magclass,new.magpie)
 importFrom(magclass,nregions)
-importFrom(magclass,nyears)
 importFrom(magclass,place_x_in_y)
 importFrom(magclass,read.magpie)
 importFrom(magclass,read.report)
 importFrom(magclass,setCells)
 importFrom(magclass,setNames)
 importFrom(magclass,setYears)
-importFrom(magclass,time_interpolate)
 importFrom(magclass,unwrap)
 importFrom(magclass,where)
 importFrom(magclass,wrap)
-importFrom(magclass,write.magpie)
 importFrom(magpiesets,findset)
 importFrom(magpiesets,reporthelper)
 importFrom(magpiesets,reportingnames)
-importFrom(mgsub,mgsub)
 importFrom(mstools,toolFertilizerDistribution)
 importFrom(mstools,toolHoldConstant)
 importFrom(ncdf4,nc_close)
 importFrom(ncdf4,nc_open)
 importFrom(ncdf4,ncvar_get)
 importFrom(nleqslv,nleqslv)
-importFrom(nnls,nnls)
 importFrom(parallel,detectCores)
 importFrom(parallel,makeCluster)
 importFrom(parallel,stopCluster)
 importFrom(plyr,ddply)
-importFrom(plyr,round_any)
 importFrom(quitte,add_countrycode_)
 importFrom(quitte,as.quitte)
 importFrom(quitte,cartesian)
 importFrom(quitte,character.data.frame)
-importFrom(quitte,getVars)
-importFrom(quitte,inline.data.frame)
 importFrom(quitte,interpolate_missing_periods)
-importFrom(quitte,interpolate_missing_periods_)
 importFrom(quitte,overwrite)
-importFrom(quitte,removeColNa)
-importFrom(quitte,revalue.levels)
 importFrom(quitte,seq_range)
-importFrom(raster,"crs<-")
 importFrom(raster,"extent<-")
 importFrom(raster,aggregate)
-importFrom(raster,as.matrix)
 importFrom(raster,brick)
 importFrom(raster,extent)
 importFrom(raster,projectRaster)
 importFrom(raster,raster)
-importFrom(raster,rasterFromXYZ)
-importFrom(raster,res)
 importFrom(raster,subset)
-importFrom(raster,writeRaster)
 importFrom(readr,col_character)
 importFrom(readr,col_skip)
 importFrom(readr,cols)
-importFrom(readr,read_csv)
 importFrom(readr,read_csv2)
 importFrom(readr,read_delim)
 importFrom(readr,read_rds)
-importFrom(readxl,excel_sheets)
 importFrom(readxl,read_excel)
-importFrom(readxl,read_xlsx)
-importFrom(reshape,merge_recurse)
 importFrom(reshape2,acast)
 importFrom(reshape2,melt)
-importFrom(rhdf5,H5close)
-importFrom(rhdf5,h5read)
 importFrom(rlang,.data)
 importFrom(rlang,is_empty)
 importFrom(stats,approx)
-importFrom(stats,coef)
-importFrom(stats,complete.cases)
-importFrom(stats,lm)
-importFrom(stats,median)
-importFrom(stats,na.exclude)
 importFrom(stats,na.omit)
-importFrom(stats,predict)
-importFrom(stats,qnorm)
 importFrom(stats,quantile)
 importFrom(stats,reshape)
-importFrom(stats,uniroot)
-importFrom(stats,weighted.mean)
-importFrom(stringi,stri_trans_general)
 importFrom(stringr,str_sub)
 importFrom(tidyr,complete)
 importFrom(tidyr,crossing)
@@ -286,19 +181,15 @@ importFrom(tidyr,gather_)
 importFrom(tidyr,nesting)
 importFrom(tidyr,nesting_)
 importFrom(tidyr,replace_na)
-importFrom(tidyr,separate_)
 importFrom(tidyr,spread)
 importFrom(tidyr,unite)
 importFrom(tidyr,unite_)
 importFrom(tools,file_ext)
 importFrom(tools,file_path_sans_ext)
 importFrom(utils,data)
 importFrom(utils,download.file)
-importFrom(utils,head)
 importFrom(utils,read.csv)
 importFrom(utils,read.csv2)
 importFrom(utils,read.table)
 importFrom(utils,tail)
 importFrom(utils,unzip)
-importFrom(utils,write.csv2)
-importFrom(zoo,na.approx)

R/calcAtmosphericDeposition.R

@@ -8,7 +8,6 @@
 #' @return List of magpie objects with results on country level, weight on country level, unit and description.
 #' @author Benjamin Leon Bodirsky
 #' @seealso
-#' \code{\link{calcAtmosphericDepositionRates}},
 #' \code{\link{calcNitrogenBudgetCropland}}
 #' @examples
 #' 

R/calcFEdemand.R

@@ -3,9 +3,10 @@
 #' Returns the Edge data at the Remind level
 #'
 #' @param subtype Final energy (FE) or Energy service (ES) or Useful/Final Energy items from EDGEv3 corresponding to REMIND FE items (UE_for_Eff,FE_for_Eff)
-#' @importFrom data.table data.table tstrsplit setnames CJ setkey
+#' @importFrom data.table data.table tstrsplit setnames CJ setkey as.data.table := 
 #' @importFrom stats approx
-#' @importFrom dplyr as_tibble tibble last sym between first tribble
+#' @importFrom dplyr as_tibble tibble last sym between first tribble bind_rows filter ungroup
+#' lag arrange
 #' @importFrom tidyr extract complete nesting replace_na crossing unite
 #' @importFrom readr read_delim
 #' @importFrom quitte seq_range interpolate_missing_periods character.data.frame

R/calcLivestockProductivity.R

@@ -9,8 +9,7 @@
 #' @return MAgPIE-FEED data for livestock-yields and corresonding weights as a
 #' list of two MAgPIE objects
 #' @author Isabelle Weindl, Lavinia Baumstark, Stephen Wirth
-#' @seealso \code{\link{calcOutput}}, \code{\link{calcRegressionFEED}},
-#' \code{\link{readSource}}
+#' @seealso \code{\link{calcOutput}}, \code{\link{readSource}}
 #' @examples
 #' 
 #' \dontrun{ 

R/calcMAgPIEReport.R

@@ -1,4 +1,4 @@
-
+#' @importFrom quitte inline.data.frame
 
 calcMAgPIEReport <- function(subtype){
 

R/convertGFED.R

@@ -4,7 +4,7 @@
 #' @param subtype emissions or emissionfactors
 #' @return magpie object of the GFED data in country level
 #' @author Lavinia Baumstark, Abhijeet Mishra
-#' @seealso \code{\link{readGFED}} {\link{extractGFED}}
+#' @seealso \code{\link{readGFED}}
 #' @examples
 #' 
 #' \dontrun{ x <- readGFED(subtype="emissions")