replace speed_aggregate

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '27903624'
+ValidationKey: '27948800'
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
 - 'Warning: namespace ''.*'' is not available and has been replaced'

.pre-commit-config.yaml

@@ -3,7 +3,7 @@
 exclude: '^tests/testthat/_snaps/.*$'
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: 2c9f875913ee60ca25ce70243dc24d5b6415598c  # frozen: v4.6.0
     hooks:
     -   id: check-case-conflict
     -   id: check-json
@@ -15,7 +15,7 @@ repos:
     -   id: mixed-line-ending
 
 -   repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.4.0
+    rev: 7910e0323d7213f34275a7a562b9ef0fde8ce1b9  # frozen: v0.4.2
     hooks:
     -   id: parsable-R
     -   id: deps-in-desc

CITATION.cff

@@ -2,8 +2,8 @@ cff-version: 1.2.0
 message: If you use this software, please cite it using the metadata from this file.
 type: software
 title: 'mrcommons: MadRat commons Input Data Library'
-version: 1.40.7
-date-released: '2024-04-19'
+version: 1.40.8
+date-released: '2024-05-07'
 abstract: Provides useful functions and a common structure to all the input data required
   to run models like MAgPIE and REMIND of model input data.
 authors:

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: mrcommons
 Type: Package
 Title: MadRat commons Input Data Library
-Version: 1.40.7
-Date: 2024-04-19
+Version: 1.40.8
+Date: 2024-05-07
 Authors@R: c(person("Benjamin Leon", "Bodirsky", email = "[email protected]", role = "aut"),
              person("Kristine", "Karstens", role = "aut"),
              person("Lavinia", "Baumstark", role = "aut"),

NAMESPACE

@@ -93,7 +93,6 @@ importFrom(lpjmlkit,read_io)
 importFrom(luscale,getAggregationMatrix)
 importFrom(luscale,groupAggregate)
 importFrom(luscale,rename_dimnames)
-importFrom(luscale,speed_aggregate)
 importFrom(madrat,calcOutput)
 importFrom(madrat,getISOlist)
 importFrom(madrat,metadataGFZ)

R/calcBodyHeight.R

@@ -8,8 +8,6 @@
 #' Also,the year 1965 is extrapolatedusing the worldbank population
 #' data and sex, age, and education structure of 1970.
 #' @export
-#' @importFrom luscale speed_aggregate
-
 calcBodyHeight <- function(convert = TRUE) {
 
   demo <- calcOutput("Demography", education = FALSE, aggregate = FALSE)

R/calcDemography.R

@@ -16,8 +16,8 @@ calcDemography <- function(convert = TRUE, education = TRUE) {
   lutz <- readSource("Lutz2014", convert = convert)
 
   mapping2 <- toolGetMapping(type = "sectoral", name = "lutz2hic2.csv",
-                              where = "mappingfolder")
-  demo <- luscale::speed_aggregate(x = lutz, rel = mapping2, from = "lutz", to = "hic", dim = 3.2)
+                             where = "mappingfolder")
+  demo <- toolAggregate(x = lutz, rel = mapping2, from = "lutz", to = "hic", dim = 3.2)
 
   demo <- demo[, , "B", invert = TRUE]
   demo <- demo[, , "All", invert = TRUE]
@@ -39,8 +39,7 @@ calcDemography <- function(convert = TRUE, education = TRUE) {
                              naming = "scenario",
                              years = magpiesets::findset("time"),
                              aggregate = FALSE)
-    diff <- dimSums(demo, dim = c("sex", "age", "education")) - population[,  getYears(demo),
-                                                                              getNames(demo, dim = 1)]
+    diff <- dimSums(demo, dim = c("sex", "age", "education")) - population[, getYears(demo), getNames(demo, dim = 1)]
     diff[] <- abs(diff)
     if (sum(diff) > 100) {
       vcat(2, paste0(
@@ -59,13 +58,13 @@ calcDemography <- function(convert = TRUE, education = TRUE) {
     }
 
     # recalibration to SSP population scenarios
-     # create SSP2EU and SDP scenarios columns based on SSP2 and SSP1
-      if (any(c("SDP", "SDP_EI", "SDP_MC", "SDP_RC", "SSP2EU") %in% getNames(population))) {
-         demo <- add_columns(demo, addnm = c("SDP", "SDP_EI", "SDP_MC", "SDP_RC", "SSP2EU"),
-                             dim = 3.1, fill = NA)
-         demo[, , "SSP2EU"] <- demo[, , "SSP2"]
-         demo[, , "SDP", pmatch = TRUE] <- demo[, , "SSP1"]
-      }
+    # create SSP2EU and SDP scenarios columns based on SSP2 and SSP1
+    if (any(c("SDP", "SDP_EI", "SDP_MC", "SDP_RC", "SSP2EU") %in% getNames(population))) {
+      demo <- add_columns(demo, addnm = c("SDP", "SDP_EI", "SDP_MC", "SDP_RC", "SSP2EU"),
+                          dim = 3.1, fill = NA)
+      demo[, , "SSP2EU"] <- demo[, , "SSP2"]
+      demo[, , "SDP", pmatch = TRUE] <- demo[, , "SSP1"]
+    }
 
     demoShr <- demo / dimSums(demo, dim = c("sex", "age", "education"))
     vcat(verbosity = 2, paste0("Year 1965 in demography data missing. Used values of 1970 instead"))

R/calcIntakeBodyweight.R

@@ -37,8 +37,8 @@ calcIntakeBodyweight <- function(bodyweight, bodyheight = NULL, inactivity, tmea
     requirement <- readSource("HHS_USDA", convert = FALSE)
     weight <- requirement * 0 + 1
     mapping <- toolGetMapping(type = "sectoral", name = "HHS_USDA2hic.csv", where = "mappingfolder")
-    requirement <- speed_aggregate(x = requirement, rel = mapping, weight = weight,
-                                   from = "HHS_USDA", to = "hic", dim = 3.2)
+    requirement <- toolAggregate(x = requirement, rel = mapping, weight = weight,
+                                 from = "HHS_USDA", to = "hic", dim = 3.2)
 
     standardizedRequirement <- (collapseNames(requirement[, , "Sedentary"])
                                 * inactivity + collapseNames(requirement[, , "Active"]) * (1 - inactivity))

R/convertLutz2014.R

@@ -22,7 +22,7 @@ convertLutz2014 <- function(x) {
 
   x <- toolCountryFill(x, fill = NA, no_remove_warning = "ANT")
 
-  # BB: use of speed_aggregate with an external mapping could replace the following function and speed it up
+  # BB: use of toolAggregate with an external mapping could replace the following function and speed it up
   fillCountryByAverageOfRegion <- function(x, country, region) {
     vcat(2, paste0("interpolating country: ", country))
     values <- x[region, , ]

README.md

@@ -1,6 +1,6 @@
 # MadRat commons Input Data Library
 
-R package **mrcommons**, version **1.40.7**
+R package **mrcommons**, version **1.40.8**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/mrcommons)](https://cran.r-project.org/package=mrcommons) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3822009.svg)](https://doi.org/10.5281/zenodo.3822009) [![R build status](https://github.com/pik-piam/mrcommons/workflows/check/badge.svg)](https://github.com/pik-piam/mrcommons/actions) [![codecov](https://codecov.io/gh/pik-piam/mrcommons/branch/master/graph/badge.svg)](https://app.codecov.io/gh/pik-piam/mrcommons) [![r-universe](https://pik-piam.r-universe.dev/badges/mrcommons)](https://pik-piam.r-universe.dev/builds)
 
@@ -39,7 +39,7 @@ In case of questions / problems please contact Jan Philipp Dietrich <dietrich@pi
 
 To cite package **mrcommons** in publications use:
 
-Bodirsky B, Karstens K, Baumstark L, Weindl I, Wang X, Mishra A, Wirth S, Stevanovic M, Steinmetz N, Kreidenweis U, Rodrigues R, Popov R, Humpenoeder F, Giannousakis A, Levesque A, Klein D, Araujo E, Beier F, Oeser J, Pehl M, Leip D, Crawford M, Molina Bacca E, von Jeetze P, Martinelli E, Schreyer F, Soergel B, Sauer P, Hötten D, Hasse R, Abrahão G, Weigmann P, Dietrich J (2024). _mrcommons: MadRat commons Input Data Library_. doi: 10.5281/zenodo.3822009 (URL: https://doi.org/10.5281/zenodo.3822009), R package version 1.40.7, <URL: https://github.com/pik-piam/mrcommons>.
+Bodirsky B, Karstens K, Baumstark L, Weindl I, Wang X, Mishra A, Wirth S, Stevanovic M, Steinmetz N, Kreidenweis U, Rodrigues R, Popov R, Humpenoeder F, Giannousakis A, Levesque A, Klein D, Araujo E, Beier F, Oeser J, Pehl M, Leip D, Crawford M, Molina Bacca E, von Jeetze P, Martinelli E, Schreyer F, Soergel B, Sauer P, Hötten D, Hasse R, Abrahão G, Weigmann P, Dietrich J (2024). _mrcommons: MadRat commons Input Data Library_. doi:10.5281/zenodo.3822009 <https://doi.org/10.5281/zenodo.3822009>, R package version 1.40.8, <https://github.com/pik-piam/mrcommons>.
 
 A BibTeX entry for LaTeX users is
 
@@ -48,8 +48,8 @@ A BibTeX entry for LaTeX users is
   title = {mrcommons: MadRat commons Input Data Library},
   author = {Benjamin Leon Bodirsky and Kristine Karstens and Lavinia Baumstark and Isabelle Weindl and Xiaoxi Wang and Abhijeet Mishra and Stephen Wirth and Mishko Stevanovic and Nele Steinmetz and Ulrich Kreidenweis and Renato Rodrigues and Roman Popov and Florian Humpenoeder and Anastasis Giannousakis and Antoine Levesque and David Klein and Ewerton Araujo and Felicitas Beier and Julian Oeser and Michaja Pehl and Debbora Leip and Michael Crawford and Edna {Molina Bacca} and Patrick {von Jeetze} and Eleonora Martinelli and Felix Schreyer and Bjoern Soergel and Pascal Sauer and David Hötten and Robin Hasse and Gabriel Abrahão and Pascal Weigmann and Jan Philipp Dietrich},
   year = {2024},
-  note = {R package version 1.40.7},
-  doi = {10.5281/zenodo.3822009},
+  note = {R package version 1.40.8},
   url = {https://github.com/pik-piam/mrcommons},
+  doi = {10.5281/zenodo.3822009},
 }
 ```