Merge pull request #88 from tscheypidi/master

adapated unit calculations to new version 0.7 of the units package

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '97942820'
+ValidationKey: '98024454'
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
 - 'Warning: namespace ''.*'' is not available and has been replaced'

.zenodo.json

@@ -1,6 +1,6 @@
 {
   "title": "magclass: Data Class and Tools for Handling Spatial-Temporal Data",
-  "version": "5.24.6",
+  "version": "5.24.7",
   "description": "<p>Data class for increased interoperability working with spatial-\n    temporal data together with corresponding functions and methods (conversions,\n    basic calculations and basic data manipulation). The class distinguishes\n    between spatial, temporal and other dimensions to facilitate the development\n    and interoperability of tools build for it. Additional features are name-based\n    addressing of data and internal consistency checks (e.g. checking for the right\n    data order in calculations).<\/p>",
   "creators": [
     {

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: magclass
 Type: Package
 Title: Data Class and Tools for Handling Spatial-Temporal Data
-Version: 5.24.6
-Date: 2021-02-12
+Version: 5.24.7
+Date: 2021-02-24
 Authors@R: c(person("Jan Philipp", "Dietrich", email = "dietrich@pik-potsdam.de", role = c("aut","cre")),
              person("Benjamin Leon", "Bodirsky", email = "bodirsky@pik-potsdam.de", role = "aut"),
              person("Markus", "Bonsch", role = "aut"),
@@ -44,7 +44,7 @@ Suggests:
     reshape2,
     data.tree,
     raster,
-    units,
+    units(>= 0.7.0),
     udunits2,
     ncdf4,
     covr

R/getMetadata.R

@@ -33,22 +33,24 @@
 #' \code{\link{getYears}}, \code{\link{getCPR}}, \code{\link{read.magpie}},
 #' \code{\link{write.magpie}}, \code{"\linkS4class{magpie}"}
 #' @examples
-#'  withMetadata(TRUE)
-#'  a <- as.magpie(1)
-#'  #returns NULL
-#'  getMetadata(a)
-#'  #set the unit field
-#'  getMetadata(a, "unit") <- "GtCO2eq"
-#'  getMetadata(a)
+#'  \dontrun{
+#'    withMetadata(TRUE)
+#'    a <- as.magpie(1)
+#'    #returns NULL
+#'    getMetadata(a)
+#'    #set the unit field
+#'    getMetadata(a, "unit") <- "GtCO2eq"
+#'    getMetadata(a)
 #'  
-#'  #set all Metadata fields
-#'  M <- list(unit='kg', source=list(author='John Doe', date='January 1, 2017', 
-#'  title='example', publication='BigJournal, Vol. 200, pp. 100-115', institution='IEA'), 
-#'  date=as.character(Sys.time()), user='my name', calcHistory=list('downloadSource','readSource'), 
-#'  description='nonsense data')
-#'  getMetadata(a) <- M
-#'  getMetadata(a)
-#'  withMetadata(FALSE)
+#'    #set all Metadata fields
+#'    M <- list(unit='kg', source=list(author='John Doe', date='January 1, 2017', 
+#'    title='example', publication='BigJournal, Vol. 200, pp. 100-115', institution='IEA'), 
+#'    date=as.character(Sys.time()), user='my name', calcHistory=list('downloadSource','readSource'), 
+#'    description='nonsense data')
+#'    getMetadata(a) <- M
+#'    getMetadata(a)
+#'    withMetadata(FALSE)
+#'  }
 #' @export
 
 getMetadata <- function(x, type=NULL) {

R/install_magpie_units.R

@@ -30,6 +30,9 @@
 #' 
 install_magpie_units <- function(x=NULL) {
   if (!withMetadata()) return(x)
+  if (!requireNamespace("units", versionCheck = list(name = "units", op = ">=", version = "0.7.0"), quietly = TRUE)) {
+    stop("units package in version >= 0.7 required")
+  }
   units::units_options(auto_convert_names_to_symbols=FALSE, allow_mixed=FALSE, negative_power=TRUE, set_units_mode="standard")
 
   unit_syntax <- function(z) {
@@ -225,7 +228,7 @@ install_magpie_units <- function(x=NULL) {
         }else {
           base <- paste0("t_",base)
           base <- gsub("of_","",base)
-          units::install_conversion_constant(base,"tonne",1)
+          units::install_unit(base,"tonne",1)
         }
       }else if (grepl("square",pre[jj],ignore.case=TRUE)) {
         if (suff=="") {
@@ -255,7 +258,7 @@ install_magpie_units <- function(x=NULL) {
         base <- remove_spaces(base)
       }else {
         warning(base," has been successfully installed but is not a recognized unit. Standardize if possible.")
-        units::install_symbolic_unit(base,dimensionless=FALSE)
+        units::install_unit(base,"")
       }
     }
     return(units::as_units(multiplier,paste0(SI_prefix,base,suff)))
@@ -280,7 +283,7 @@ install_magpie_units <- function(x=NULL) {
           if (is_unit_installed(remove_spaces(b[[i]]))) {
             b[[i]] <- remove_spaces(b[[i]])
           }else {
-            units::install_symbolic_unit(b[[i]],dimensionless=FALSE)
+            units::install_unit(b[[i]],"")
           }
         }
       }
@@ -317,7 +320,7 @@ install_magpie_units <- function(x=NULL) {
             if (is_unit_installed(remove_spaces(w[[ii]]))) {
               w[[ii]] <- remove_spaces(w[[ii]])
             }else {
-              units::install_symbolic_unit(w[[ii]],dimensionless=FALSE)
+              units::install_unit(w[[ii]],"")
             }
           }
         }
@@ -351,32 +354,6 @@ install_magpie_units <- function(x=NULL) {
     }
     if (grepl(",",a,fixed=TRUE) | grepl(";",a,fixed=TRUE)) {
       return(units::as_units("unknown"))
-    #*****Mixed units handling in development*****  
-    #  a <- unlist(strsplit(a,","))
-    #  a <- unlist(strsplit(a,";"))
-    #  for (i in 1:length(a)) {
-    #    if (grepl("_for_",a[i]) | grepl("_in_",a[i])) {
-    #      warning("Unit entry \"",a[i],"\" should only include the unit and not the description.")
-    #    }
-    #    a[i] <- gsub("^_*","",gsub("_*$","",a[i]))
-    #    if (is_unit_installed(remove_spaces(a[i]))) {
-    #      a[i] <- remove_spaces(a[i])
-    #    }else {
-    #      a[i] <- split_denominator(a[i])
-    #      a[i] <- split_multiples(a[i])
-    #      if (!is_unit_installed(a[i])) {
-    #        a[i] <- unit_syntax(a[i])
-    #        if (!is_unit_installed(a[i])) {
-    #          if (!is_unit_installed(remove_spaces(a[i]))) {
-    #            units::install_symbolic_unit(a[i],dimensionless=FALSE)
-    #          }else {
-    #            a[i] <- remove_spaces(a[i])
-    #          }
-    #        }
-    #      }
-    #    }
-    #  }
-    #  return(units::mixed_units(1,a))
     }
     if (grepl("/",a,fixed=TRUE) | grepl("*",a,fixed=TRUE)) {
       a <- split_denominator(a)
@@ -386,7 +363,7 @@ install_magpie_units <- function(x=NULL) {
     }
     if (!is_unit_installed(a)) {
       if (!is_unit_installed(remove_spaces(a))) {
-        units::install_symbolic_unit(a,dimensionless=FALSE)
+        units::install_unit(a,"")
       }else {
         a <- remove_spaces(a)
       }
@@ -395,36 +372,9 @@ install_magpie_units <- function(x=NULL) {
   }
 
   #Initialize some commonly used units in MAGPIE and REMIND
-  if (!is_unit_installed("tDM") & !is_unit_installed("pkm") & !is_unit_installed("unknown")) {
-    units::install_conversion_constant("tDM","tonne",1)                      #tonnes of dry matter
-    units::install_conversion_constant("tWM","tonne",1)                      #tonnes of wet matter
-    units::install_conversion_constant("BTU","toe",2.5e-8)                   #tonnes of oil equivalent
-    units::install_symbolic_unit("people",dimensionless=FALSE)               #people
-    units::install_conversion_constant("people","person",1)                  #people interchangeable with person
-    units::install_conversion_constant("people","capita",1)                  #capita interchangeable with people
-    units::install_symbolic_unit("animal",dimensionless=FALSE)               #animals
-    units::install_symbolic_unit("tCO2eq",dimensionless=FALSE)               #tonnes of CO2 equivalent
-    units::install_conversion_constant("tCO2eq","tCO2_",1)                   #tonnes of CO2
-    units::install_conversion_constant("tC","tCO2_",44/12)                   #tonnes of carbon
-    units::install_conversion_constant("tN2O","tCO2eq",298)                  #tonnes of N2O
-    units::install_conversion_constant("tN","tN2O",44/28)                    #tonnes of nitrogen
-    units::install_conversion_constant("tN","tNO2_",46/14)                   #tonnes of NO2
-    units::install_conversion_constant("tN","tNO3_",62/14)                   #tonnes of NO3
-    units::install_conversion_constant("tN","tNH3_",17/14)                   #tonnes of NH3
-    units::install_conversion_constant("tCH4_","tCO2eq",36)                  #tonnes of methane
-    units::install_symbolic_unit("USD",dimensionless=FALSE)                  #US Dollars in 2018 currency value (InflationTool.com)
-    units::install_conversion_constant("USD05_","USD",1/1.33)                  #US Dollars in 2005 currency value (InflationTool.com)
-    units::install_conversion_constant("USD95_","USD05_",1/1.27)               #US Dollars in 1995 currency value (InflationTool.com)
-    units::install_conversion_constant("EUR","USD",1/1.13365)                  #Euros at exchange rate with USD on 11.12.2018 (XE.com)
-    units::install_conversion_constant("EUR05_","EUR",1/1.24)                  #Euros in 2005 currency value (InflationTool.com)
-    units::install_conversion_constant("EUR95_","EUR05_",1/1.22)               #Euros in 1995 currency value (InflationTool.com)
-    units::install_symbolic_unit("share",dimensionless=TRUE)                 #Share (dimension)
-    units::install_symbolic_unit("passenger",dimensionless=FALSE)            #passengers
-    units::install_conversion_constant("pkm","passenger*km",1)               #passenger-kilometer pkm
-    units::install_conversion_constant("Wh","W*h",1)                         #Watt-hours
-    units::install_conversion_constant("annum","year",1)                     #annum
-    units::install_conversion_constant("Wa","watt*annum",1)                  #Watts-annum
-    units::install_symbolic_unit("unknown")                                  #unknown units; placeholder for mixed units
+  if (!is_unit_installed("tDM") || !is_unit_installed("pkm") || !is_unit_installed("unknown")) {
+    units <- readRDS(system.file("extdata/metadata/units.rds", package = "magclass"))
+    for(i in 1:nrow(units)) units::install_unit(symbol = units$unit[i], def = units$def[i],  name= units$name[i])
   }
 
   if (is.null(x)) {

R/withMetadata.R

@@ -11,11 +11,13 @@
 #' @author Jan Philipp Dietrich
 #' @seealso \code{\link{getMetadata}}
 #' @examples
-#'  withMetadata()
-#'  withMetadata(TRUE)
-#'  a <- as.magpie(1)
-#'  getMetadata(a)
-#'  withMetadata(FALSE)
+#' \dontrun{
+#'    withMetadata()
+#'    withMetadata(TRUE)
+#'    a <- as.magpie(1)
+#'    getMetadata(a)
+#'    withMetadata(FALSE)
+#'  }
 #' @export
 
 withMetadata <- function(set=NULL,verbosity=NULL) {

README.md

@@ -1,6 +1,6 @@
 # Data Class and Tools for Handling Spatial-Temporal Data
 
-R package **magclass**, version **5.24.6**
+R package **magclass**, version **5.24.7**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/magclass)](https://cran.r-project.org/package=magclass) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1158580.svg)](https://doi.org/10.5281/zenodo.1158580)  [![R build status](https://github.com/pik-piam/magclass/workflows/check/badge.svg)](https://github.com/pik-piam/magclass/actions) [![codecov](https://codecov.io/gh/pik-piam/magclass/branch/master/graph/badge.svg)](https://codecov.io/gh/pik-piam/magclass)
 
@@ -54,11 +54,10 @@ In case of questions / problems please contact Jan Philipp Dietrich <dietrich@pi
 
 To cite package **magclass** in publications use:
 
-Dietrich J, Bodirsky B, Bonsch M, Humpenoeder F, Bi S, Karstens K, Leip
-D (2021). _magclass: Data Class and Tools for Handling Spatial-Temporal
-Data_. doi: 10.5281/zenodo.1158580 (URL:
-https://doi.org/10.5281/zenodo.1158580), R package version 5.24.6,
-<URL: https://github.com/pik-piam/magclass>.
+Dietrich J, Bodirsky B, Bonsch M, Humpenoeder F, Bi S, Karstens K, Leip D (2021). _magclass: Data Class
+and Tools for Handling Spatial-Temporal Data_. doi: 10.5281/zenodo.1158580 (URL:
+https://doi.org/10.5281/zenodo.1158580), R package version 5.24.7, <URL:
+https://github.com/pik-piam/magclass>.
 
 A BibTeX entry for LaTeX users is
 
@@ -67,7 +66,7 @@ A BibTeX entry for LaTeX users is
   title = {magclass: Data Class and Tools for Handling Spatial-Temporal Data},
   author = {Jan Philipp Dietrich and Benjamin Leon Bodirsky and Markus Bonsch and Florian Humpenoeder and Stephen Bi and Kristine Karstens and Debbora Leip},
   year = {2021},
-  note = {R package version 5.24.6},
+  note = {R package version 5.24.7},
   doi = {10.5281/zenodo.1158580},
   url = {https://github.com/pik-piam/magclass},
 }

cran-comments.md

@@ -1,4 +1,10 @@
-Bugfix update:
+FEATURES:
+- added coordinates support
+- added conversion functions raster <-> magclass
+- added collapseDim
 
-- added stringsAsFactor argument explicitly to functions where it was missing to prepare for upcoming updating in default settings
+NOTES:
+* checking dependencies in R code ... NOTE
+Missing or unexported object: 'units::install_unit'
 
+This note might occur if an older version of the "units" package is installed on the test system. The magclass package is already prepared for the changes which come with version 0.7.0 of package "units", but it also still works with older versions of the "units" package. 

tests/testthat/test-metadata.R

@@ -23,14 +23,15 @@ test_that("Read/write metadata works", {
 })
 
 test_that("Unit calculations work", {
+  skip_if_not_installed("units",minimum_version = "0.7.0")
   expect_identical(units(pop), install_magpie_units("1e+06 people"))
-  expect_identical(units(pop+pop), install_magpie_units("1e+06 people"))
-  expect_identical(units(pop*pop), install_magpie_units("1e+12 people^2"))
+  expect_identical(units(pop + pop), install_magpie_units("1e+06 people"))
+  expect_identical(units(pop * pop), install_magpie_units("1e+12 people^2"))
   pop2 <- pop
   units(pop2) <- "people"
   expect_identical(units(pop2), install_magpie_units("people"))
   expect_identical(as.vector(pop2[1,1,1]),as.vector(10^6*pop[1,1,1]))
-  expect_equivalent(pop2-pop,0*pop)
+  expect_equivalent(pop2 - pop, 0 * pop)
   expect_identical(units(animal), install_magpie_units("km^-2"))
   expect_identical(units(pop/animal), install_magpie_units("1e06 km^2*people"))
   expect_identical(units(pop/animal), install_magpie_units("1e06 people*km^2"))