Package 'magclass'

Title: Data Class and Tools for Handling Spatial-Temporal Data
Description: Data class for increased interoperability working with spatial-temporal data together with corresponding functions and methods (conversions, basic calculations and basic data manipulation). The class distinguishes between spatial, temporal and other dimensions to facilitate the development and interoperability of tools build for it. Additional features are name-based addressing of data and internal consistency checks (e.g. checking for the right data order in calculations).
Authors: Jan Philipp Dietrich [aut, cre] (Potsdam Institute for Climate Impact Research, <https://orcid.org/0000-0002-4309-6431>), Benjamin Leon Bodirsky [aut] (Potsdam Institute for Climate Impact Research), Markus Bonsch [aut], Florian Humpenoeder [aut] (Potsdam Institute for Climate Impact Research), Stephen Bi [aut], Kristine Karstens [aut] (Potsdam Institute for Climate Impact Research), Debbora Leip [aut] (Potsdam Institute for Climate Impact Research), Pascal Sauer [aut] (Potsdam Institute for Climate Impact Research), Lavinia Baumstark [ctb] (Potsdam Institute for Climate Impact Research), Christoph Bertram [ctb], Anastasis Giannousakis [ctb], David Klein [ctb] (Potsdam Institute for Climate Impact Research), Ina Neher [ctb], Michaja Pehl [ctb] (Potsdam Institute for Climate Impact Research), Anselm Schultes [ctb], Miodrag Stevanovic [ctb] (Potsdam Institute for Climate Impact Research), Xiaoxi Wang [ctb], Felicitas Beier [ctb] (Potsdam Institute for Climate Impact Research), Mika Pflüger [ctb], Oliver Richters [ctb] (Potsdam Institute for Climate Impact Research)
Maintainer: Jan Philipp Dietrich <[email protected]>
License: LGPL-3 | file LICENSE
Version: 6.17.1
Built: 2024-10-30 05:17:18 UTC
Source: https://github.com/pik-piam/magclass

Help Index


Data Class and Tools for Handling Spatial-Temporal Data

Description

Data class for increased interoperability working with spatial-temporal data together with corresponding functions and methods (conversions, basic calculations and basic data manipulation). The class distinguishes between spatial, temporal and other dimensions to facilitate the development and interoperability of tools build for it. Additional features are name-based addressing of data and internal consistency checks (e.g. checking for the right data order in calculations).

Author(s)

Maintainer: Jan Philipp Dietrich <[email protected]>

See Also

Useful links:


add_columns

Description

Function adds new columns to the existing magpie object.

Usage

add_columns(x, addnm = "new", dim = 3.1, fill = NA)

Arguments

x

MAgPIE object which should be extended.

addnm

The new elements that should be added to the (sub)dimension

dim

The (sub)dimension to be filled either identified via name or dimension code (see dimCode for more information)

fill

fill value of length 1 for the newly added columns (NA by default)

Value

The extended MAgPIE object

Author(s)

Jan Philipp Dietrich, Benjamin Bodirsky

See Also

add_dimension,dimCode

Examples

a <- maxample("animal")
a2 <- add_columns(a, addnm = c("horse", "magpie"), dim = "species", fill = 42)
getItems(a2, dim = 3)
getItems(a2, dim = 3, split = TRUE)
head(a2[, , "magpie"])

add_dimension

Description

Function adds a name dimension as dimension number "dim" with the name "add" with an empty data column with the name "nm".

Usage

add_dimension(x, dim = 3.1, add = NULL, nm = "dummy")

Arguments

x

MAgPIE object which should be extended.

dim

The dimension number of the new dimension (e.g. 3.1)

add

The name of the new dimension

nm

The name of the first entry in dimension "add".

Value

The extended MAgPIE object

Author(s)

Jan Philipp Dietrich, Benjamin Bodirsky

See Also

add_columns,mbind

Examples

a <- maxample("animal")
str(add_dimension(a, dim = 3.2))
str(add_dimension(a, dim = 2.3, nm = paste0("d", 1:3)))

magpie method for tibble::as_tibble

Description

magpie method for tibble::as_tibble

Usage

## S3 method for class 'magpie'
as_tibble(
  x,
  ...,
  .rows = NULL,
  .name_repair = c("check_unique", "unique", "universal", "minimal"),
  rownames = pkgconfig::get_config("tibble::rownames", NULL)
)

Arguments

x

A magpie object

...

Unused, for extensibility.

.rows

The number of rows, useful to create a 0-column tibble or just as an additional check.

.name_repair

Treatment of problematic column names:

  • "minimal": No name repair or checks, beyond basic existence,

  • "unique": Make sure names are unique and not empty,

  • "check_unique": (default value), no name repair, but check they are unique,

  • "universal": Make the names unique and syntactic

  • a function: apply custom name repair (e.g., .name_repair = make.names for names in the style of base R).

  • A purrr-style anonymous function, see rlang::as_function()

This argument is passed on as repair to vctrs::vec_as_names(). See there for more details on these terms and the strategies used to enforce them.

rownames

How to treat existing row names of a data frame or matrix:

  • NULL: remove row names. This is the default.

  • NA: keep row names.

  • A string: the name of a new column. Existing rownames are transferred into this column and the row.names attribute is deleted. No name repair is applied to the new column name, even if x already contains a column of that name. Use as_tibble(rownames_to_column(...)) to safeguard against this case.

Read more in rownames.

Value

A tibble object


~~ Methods for Function as.array ~~

Description

~~ Methods for function as.array ~~

Usage

## S4 method for signature 'magpie'
as.array(x)

Arguments

x

object which should be converted to an array

Methods

list("signature(x = \"ANY\")")

standard as.array-method

list("signature(x = \"magpie\")")

Conversion takes place just by removing MAgPIE-object specific elements


~~ Methods for Function as.data.frame ~~

Description

~~ Methods for function as.data.frame ~~

Usage

## S4 method for signature 'magpie'
as.data.frame(x, rev = 1, raw = FALSE)

Arguments

x

A MAgPIE-object

rev

The revision of the algorithm that should be used for conversion. rev=1 creates columns with the predefined names Cell, Region, Year, Data1, Data2,... and Value, rev=2 uses the set names of the MAgPIE object for naming and adds an attribute "dimtype" to the data.frame which contains information about the types of the different columns (spatial, temporal, data or value), rev=3 is identical to rev=2 except that characters are not being converted to factors (stringsAsFactors = FALSE).

raw

Logical to control whether years beginning with "y" should be converted to integers (without "y") and coordinates should be converted to numerics. If set to raw columns are returned as they are in the initial object.

Methods

list("signature(x = \"magpie\")")

Conversion creates columns for Cell, Region, Year, Data1, Data2,... and Value

Examples

pop <- maxample("pop")
head(as.data.frame(pop))
head(as.data.frame(pop, rev = 2))

a <- maxample("animal")
head(as.data.frame(a, rev = 3))
head(as.data.frame(a, rev = 3, raw = TRUE))
attr(as.data.frame(a, rev = 3), "dimtype")

as.RasterBrick

Description

Convert magclass object to a RasterBrick object

Usage

as.RasterBrick(x, res = NULL)

Arguments

x

MAgPIE object

res

spatial data resolution. If not provided it will be guessed.

Value

A RasterBrick object

Author(s)

Jan Philipp Dietrich

See Also

getCoords

Examples

## Not run: 
if (requireNamespace("raster", quietly = TRUE)) {
   r <- raster::brick(ncols = 36, nrows = 18, nl = 4)
   r[14:18, 25:28] <- (1:20 %*% t(1:4))
   names(r) <- c("y2000..bla", "y2001..bla", "y2000..blub", "y2001..blub")
   m <- as.magpie(r)
   r2 <- as.RasterBrick(m)
}

## End(Not run)

as.SpatRaster

Description

Convert magclass object to a SpatRaster object. Requires the terra package.

Usage

as.SpatRaster(x, res = NULL)

Arguments

x

MAgPIE object

res

spatial data resolution. If not provided it will be guessed.

Value

A SpatRaster object

Author(s)

Jan Philipp Dietrich

See Also

getCoords

Examples

if (requireNamespace("terra", quietly = TRUE)) {
   r <- terra::rast(ncols = 360, nrows = 180, nl = 4)
   r[85:89, 176:179] <- (1:20 %*% t(1:4))
   r[15:19, 76:79] <-   (10 + 1:20 %*% t(1:4))
   names(r) <- c("y2000..bla", "y2001..bla", "y2000..blub", "y2001..blub")
   m <- as.magpie(r)
   r2 <- as.SpatRaster(m)
}

as.SpatRasterDataset

Description

Convert magclass object to a SpatRasterDataset object. Requires the terra package.

Usage

as.SpatRasterDataset(...)

Arguments

...

arguments passed to as.SpatRaster

Details

Calls as.SpatRaster and then spatRasterToDataset.

Value

A SpatRasterDataset object

Author(s)

Pascal Sauer


as.SpatVector

Description

Convert magclass object to a SpatVector object. Requires the terra package and requires the magclass object to provide the geometry of the spatial entities as "geometry" attribute in "WKT" format. (see object "m" in example).

Usage

as.SpatVector(x)

Arguments

x

MAgPIE object

Value

A SpatVector object

Author(s)

Jan Philipp Dietrich

See Also

as.SpatRaster

Examples

if (requireNamespace("terra", quietly = TRUE)) {
   r <- terra::rast(ncols = 360, nrows = 180, nl = 4)
   r[85:89, 176:179] <- (1:20 %*% t(1:4))
   r[15:19, 76:79] <-   (10 + 1:20 %*% t(1:4))
   names(r) <- c("y2000..bla", "y2001..bla", "y2000..blub", "y2001..blub")
   v <- terra::as.polygons(r)
   m <- as.magpie(v)
   attr(m, "geometry")
   attr(m, "crs")
   v2 <- as.SpatVector(m)
}

MAgPIE-Clean

Description

Function cleans MAgPIE objects so that they follow some extended magpie object rules (currently it makes sure that the dimnames have names and removes cell numbers if it is purely regional data)

Usage

clean_magpie(x, what = "all", maindim = 1:3)

Arguments

x

MAgPIE object which should be cleaned.

what

term defining what type of cleaning should be performed. Current modes are "cells" (removes cell numbers if the data seems to be regional - this should be used carefully as it might remove cell numbers in some cases in which they should not be removed), "sets" (making sure that all dimensions have names), "items" (replace empty elements with single spaces " ") and "all" (performing all available cleaning methods)

maindim

main dimension(s) the cleaning should get applied to.

Value

The eventually corrected MAgPIE object

Author(s)

Jan Philipp Dietrich

See Also

"magpie"

Examples

pop <- maxample("pop")
a <- clean_magpie(pop)

Collapse dataset dimensions

Description

This function will remove names in the data dimension which are the same for each element (meaning that this data dimension contains exactly one element) or, if forced, remove any other subdimension. It is a generalized version of the function collapseNames

Usage

collapseDim(x, dim = NULL, keepdim = NULL)

Arguments

x

MAgPIE object

dim

Either NULL, dimension code or name of dimension or a vector of these. If set to NULL all single entry subdimensions will be removed as they are irrelevant to uniquely identfy a data element. If specified, only the specified subdimensions will be removed (See dimCode for more details how to specify a subdimension). CAUTION: The function also allows to specify subdimensions which are otherwise needed to clearly identify an entry. By removing these subdimensions duplicates in the data will be created potentially causing problems in the further use of the data set. Be careful in removing subdimensions.

keepdim

(only considered if dim is not specified) Can be used to converse single element subdimension which otherwise would get deleted. If dim is specified this setting will not have any effect.

Value

The provided MAgPIE object with collapsed dimensions

Note

This function has some similarities to dimReduce, but serves a different purpose. While collapseDim only removes dimensions which contain only a single element or which it is specifically told to remove, dimReduce looks whether the entries of a multi-entry dimension are all the same and removes dimensions for which this is the case. In some cases both will lead to the same result but in many other cases the results will differ.

Author(s)

Jan Philipp Dietrich

See Also

getItems "magpie"

Examples

x <- new.magpie(c("GLO.1", "GLO.2"), 2000, c("bla.a", "bla.b"))
collapseDim(x)
collapseDim(x, keepdim = 1:2)
collapseDim(x, dim = 1.1)
collapseDim(x, dim = 3.2)

Collapse dataset names

Description

This function has been superseded by collapseDim which is a more generalized version of this function. Please use this one instead!

Usage

collapseNames(x, collapsedim = NULL, preservedim = NULL)

Arguments

x

MAgPIE object

collapsedim

If you want to remove the names of particular dimensions provide the dimensions here. Since the function only works in the third dimension, you have to count from there on (e.g. dim = 3.2 refers to collapsedim = 2). Alternatively, you can also specify the name of the dimension. Default: NULL. CAUTION with parameter collapsedim! You could also force him to remove dimnames, which are NOT the same for each element and so create duplicates in dimnames.

preservedim

If you want to remove the name of particular dimensions except some, you can specify the dimension(s) to preserve here. See collapsedim for naming convention. Note that preservedim will be ignored in the case, of a specified collapsedim

Details

This function will remove names in the data dimension which are the same for each element (meaning that this data dimension contains exactly one element)

Value

The provided MAgPIE object with collapsed names

Author(s)

Jan Philipp Dietrich, David Klein, Xiaoxi Wang

See Also

collapseDim, getItems, "magpie"


~~ Methods for Function colSums and colMeans ~~

Description

~~ Methods for function colSums and colMeans ~~

Usage

## S4 method for signature 'magpie'
colSums(x, na.rm = FALSE, dims = 1, ...)

Arguments

x

object on which calculation should be performed

na.rm

logical. Should missing values (including NaN) be omitted from the calculations?

dims

integer: Which dimensions are regarded as "rows" or "columns" to sum over. For row*, the sum or mean is over dimensions dims+1, ...; for col* it is over dimensions 1:dims.

...

further arguments passed to other colSums/colMeans methods

Methods

list("signature(x = \"ANY\")")

normal colSums and colMeans method

list("signature(x = \"magpie\")")

classical method prepared to handle MAgPIE objects


complete_magpie

Description

MAgPIE objects can be incomplete to reduce memory. This function blows up a magpie object to its real dimensions, so you can apply unwrap.

Usage

complete_magpie(x, fill = NA, dim = 3)

Arguments

x

MAgPIE object which should be completed.

fill

Value that shall be written into the missing entries

dim

dimensions in which the completion should take place (1, 2 and/or 3). For full completion use 1:3

Value

The completed MAgPIE object

Author(s)

Jan Philipp Dietrich, Benjamin Bodirsky

See Also

add_dimension,clean_magpie

Examples

pop <- maxample("pop")
complete_magpie(pop)

ani <- maxample("animal")
complete_magpie(ani)

convergence

Description

Cross-Fades the values of one MAGPIE object into the values of another over a certain time

Usage

convergence(
  origin,
  aim,
  start_year = NULL,
  end_year = NULL,
  direction = NULL,
  type = "smooth",
  par = 1.5
)

Arguments

origin

an object with one name-column

aim

Can be twofold: An magpie object or a numeric value.

start_year

year in which the convergence from origin to aim starts. If set to NULL the the first year of aim is used as start_year

end_year

year in which the convergence from origin to aim shall be (nearly) reached. If set to NULL the the last year of aim is used as end_year.

direction

NULL, "up" or "down". NULL means normal convergence in both directions, "up" is only a convergence if origin<aim, "down" means only a convergence if origin>aim

type

"smooth", "s", "linear" or "decay". Describes the function used for convergence (x starts at 0 and ends at 1): "linear" means linear interpolation. "s" is an s-curve which starts from origin in start_year and reaches aim precisely in end_year. After 50% of the convergence time, it reaches about the middle of the two values. It's using the function x^4/(0.07+x^4)*1.07). "smooth" is a conversion based on the function x^3/(0.1+x^3). With "smooth" only 90% of convergence will be reached in the end year, full convergence is approached as x approaches infinity. "decay" is a conversion based on the function x / (par + x) * (par + 1).

par

parameter value for convergence function; currently only used for type="decay"

Value

returns a time-series with the same timesteps as origin, which lineary fades into the values of the aim object

Author(s)

Benjamin Bodirsky, Jan Philipp Dietrich

Examples

pop <- maxample("pop")
population <- add_columns(pop, "MIX")
population[, , "MIX"] <- convergence(population[, , "A2"], population[, , "B1"])

Copy Attributes

Description

This function copies attributes from one object and assigns them to another.

Usage

copy.attributes(
  from,
  to,
  delete = c("names", "row.names", "class", "dim", "dimnames"),
  delete2 = NULL
)

copy.attributes(
  to,
  delete = c("names", "row.names", "class", "dim", "dimnames"),
  delete2 = NULL
) <- value

Arguments

from

object from which the attributes should be taken

to

object to which the attributes should be written

delete

attributes which should not be copied. By default this are class specific attributes which might cause problems if copied to another object. But you can add or remove attributes from the vector.

delete2

Identical to delete and just added for convenience for the case that you want to delete additional attributes but do not want to repeat the vector given in delete. In the function both vectors, delete and delete2, are just merged to one deletion vector.

value

Same as "from" (object from which the attributes should be taken)

Functions

  • copy.attributes( to, delete = c("names", "row.names", "class", "dim", "dimnames"), delete2 = NULL ) <- value: assign attributes from object "value"

Author(s)

Jan Philipp Dietrich

Examples

from <- array(12)
attr(from,"blablub") <- "I am an attribute!"
attr(from,"blablub2") <- "I am another attribute!"

print(attributes(from))

to <- as.magpie(0)
print(attributes(to))

copy.attributes(to) <- from
print(attributes(to))

Copy MAgPIE-files

Description

This function copies MAgPIE-files from one location to another. During the copying it is also possible to change the file type (e.g. from 'mz' to 'csv')

Usage

copy.magpie(input_file, output_file, round = NULL)

Arguments

input_file

file, that should be copied

output_file

copy destination

round

number of digits the values should be rounded. NULL means no rounding

Author(s)

Jan Philipp Dietrich

See Also

read.magpie,write.magpie

Examples

# copy.magpie("bla.csv","blub.mz")

dimCode

Description

Function converts a dimension name or number to a dimension Code used for MAgPIE objects

Usage

dimCode(dim, x, missing = 0, strict = FALSE, sep = ".")

Arguments

dim

A vector of dimension numbers or dimension names which should be translated

x

MAgPIE object in which the dimensions should be searched for.

missing

Either a value to which a dimension should be set in case that it is not found (default is 0), or "stop" indicating that the function should throw an error in these cases.

strict

if set to TRUE also properly set dimension names which refer to non-existing subdimensions will be treated as missing, otherwise these dimension codes will be returned, even if the subdimension does not exist

sep

A character separating joined dimension names

Value

A dimension code identifying the dimension. Either a integer which represents the main dimensions (1=spatial, 2=temporal, 3=data) or a numeric, representing the subdimensions of a dimension (e.g. 3.2 for the second data dimension).

Author(s)

Jan Philipp Dietrich, Kristine Karstens

See Also

mselect, getDim

Examples

pop <- maxample("pop")
dimCode(c("t", "scenario", "blablub"), pop)

dimExists

Description

Function checks whether a dimension exsist in a MAgPIE objects

Usage

dimExists(dim, x, sep = ".")

Arguments

dim

A vector of dimension numbers or dimension names which should be checked for

x

MAgPIE object in which the dimensions should be searched for.

sep

A character separating joined dimension names

Value

Boolean indicating whether dimension exists or not

Author(s)

Jan Philipp Dietrich

See Also

dimCode

Examples

pop <- maxample("pop")
dimExists(c("t","scenario","blablub"),pop)

dimOrder

Description

Changes the order of the sub-dimension in a magpie object similar to unwrapping and applying the aperm command, but more efficient.

Usage

dimOrder(x, perm, dim = 3)

Arguments

x

magpie object

perm

vector with the new order of the sub-dimension. Missing sub-dimensions will added automatically at the end

dim

main dimension in which the order of sub-dimensions should be changed (1, 2 or 3)

Value

magpie object

Author(s)

Jan Philipp Dietrich, Benjamin Leon Bodirsky

Examples

a <- maxample("animal")
head(a)
head(dimOrder(a, perm = 3:1, dim = 1))
head(dimOrder(a, perm = c(2,1,3), dim = 3))

dimReduce

Description

Remove dimensions which contain identical data for all elements in it

Usage

dimReduce(x, dim_exclude = NULL)

Arguments

x

MAgPIE object which should be reduced

dim_exclude

Vector with names of dimensions which must not be reduced

Value

The reduced MAgPIE object

Note

This function has some similarities to collapseDim, but serves a different purpose. While collapseDim only removes dimensions which contain only a single element or which it is specifically told to remove, dimReduce looks whether the entries of a multi-entry dimension are all the same and removes dimensions for which this is the case. In some cases both will lead to the same result but in many other cases the results will differ.

Author(s)

Jan Philipp Dietrich

See Also

add_dimension

Examples

# create data with 5 identical scenarios
p <- add_dimension(maxample("pop")[1:3, 1:3, ], nm = paste0("scen", 1:2))
str(p)
str(dimReduce(p))

# set years to same value
p[, , ] <- setYears(p[, 1, ], NULL)
str(p)
str(dimReduce(p))

# set regions to same value
p[, , ] <- setCells(p[1, , ], "GLO")
str(p)
str(dimReduce(p))

Summation over dimensions

Description

This function sums over any (sub-)dimension of a magpie object

Usage

dimSums(x, dim = 3, na.rm = FALSE)

Arguments

x

A MAgPIE-object

dim

The dimensions(s) to sum over. A vector of dimension codes or dimension names. See dimCode for more information

na.rm

logical. Should missing values (including NaN) be omitted from the calculations?

Value

A MAgPIE object with values summed over the specified dimensions

Author(s)

Jan Philipp Dietrich

See Also

rowSums, getItems, dimCode

Examples

a <- maxample("animal")
dimSums(a, dim = c(1, 2, 3.2))
dimSums(a, dim = c("x", "y", "cell", "month"))

escapeRegex

Description

Escapes all symbols in a string which have a special meaning in regular expressions.

Usage

escapeRegex(x)

Arguments

x

String or vector of strings that should be escaped.

Value

The escaped strings.

Author(s)

Jan Philipp Dietrich

See Also

grep


extend

Description

Extend a magpie object to a dense grid based on the given xRange, yRange and resolution. This is e.g. required when writing netCDF files. Extending a sparse magpie object to a dense grid requires much more memory, so use with caution.

Usage

extend(x, gridDefinition = NULL, crop = FALSE)

Arguments

x

A magpie object

gridDefinition

A vector of 5 numeric values: c(xMin, xMax, yMin, yMax, resolution). Use c(-179.75, 179.75, -89.75, 89.75, 0.5) to extend to a standard 0.5-degree-resolution lon/lat grid. If NULL, use min/max of coordinates in x and guessResolution.

crop

If TRUE, discard cells from x which are not in the gridDefinition grid. If FALSE, throw an error if the coordinates of x are not a subset of the extended coordinates.

Value

Magpie object x with dense grid according to gridDefinition, gaps filled with NA.

Author(s)

Pascal Sauer


Reconstructs full dimensionality of MAgPIE objects

Description

If a MAgPIE object is created from a source with more than one data dimension, these data dimensions are combined to a single dimension. fulldim reconstructs the original dimensionality and reports it.

Usage

fulldim(x, sep = ".")

Arguments

x

A MAgPIE-object

sep

A character separating joined dimension names

Value

A list containing in the first element the dim output and in the second element the dimnames output of the reconstructed array.

Author(s)

Jan Philipp Dietrich

See Also

as.magpie,unwrap,wrap


Get Cells

Description

Extracts cell names of a MAgPIE-object

Usage

getCells(x)

getCells(x) <- value

setCells(object, nm = "GLO")

Arguments

x, object

MAgPIE object

value, nm

cell names the data should be set to.

Details

setCells is a shortcut to use a MAgPIE object with manipulated cell names. setCells uses the variable names "object" and "nm" in order to be consistent to the already existing function setNames.

Value

getCells returns cell names of the MAgPIE-object, whereas setCells returns the MAgPIE object with the manipulated cell names.

Functions

  • getCells(x) <- value: set cell names

  • setCells(): set cell names

Author(s)

Jan Philipp Dietrich

See Also

getRegions, getNames, setNames, getCPR, read.magpie, write.magpie, "magpie"

Examples

a <- as.magpie(1)
 getCells(a)
 setCells(a, "AFR")

getComment

Description

Extracts the comment from a MAgPIE-object

Usage

getComment(x)

getComment(x) <- value

setComment(object, nm = NULL)

Arguments

x, object

MAgPIE object

value, nm

A vector containing the comment.

Value

getComment returns the comment attached to a MAgPIE-object, NULL if no comment is present. setComment returns the magpie object with the modified comment.

Functions

  • getComment(x) <- value: set comment

  • setComment(): set comment

Author(s)

Markus Bonsch

See Also

getRegions, getNames, getYears, getCPR, read.magpie, write.magpie, "magpie"

Examples

a <- as.magpie(1)
 #returns NULL
 getComment(a)
 #set the comment
 getComment(a)<-c("bla","blubb")
 getComment(a)

Get Coordinates

Description

Extracts spatial coordinates of a MAgPIE-object

Usage

getCoords(x, xlab = "x", ylab = "y")

getCoords(x, xlab = "x", ylab = "y") <- value

Arguments

x

MAgPIE object

xlab

label of x-dimension

ylab

label of y-dimension

value

coordinates as two column data.frame the data should be set to (first column = x, second column = y).

Value

coordinates of the MAgPIE-object

Functions

  • getCoords(x, xlab = "x", ylab = "y") <- value: set coordinates

Author(s)

Jan Philipp Dietrich

See Also

as.RasterBrick, getItems, "magpie"

Examples

a <- maxample("animal")
getCoords(a)

Get cells per region

Description

Counts how often each element of the provided subdimension exists in the given data set. Originally created to count the number of cells in a region (this is also where its name originates from) it can now be used to count elements of any subdimension via the dim argument.

Usage

getCPR(x, dim = 1.1)

Arguments

x

MAgPIE object or a resolution written as numeric (currently only data for 0.5 degree resolution is available).

dim

Dimension for which the items should be returned. Either number or name of dimension or a vector of these (in case of a vector all subimensions must belong to the same main dimension!). See dimCode for more details.

Value

cells per region

Author(s)

Jan Philipp Dietrich

See Also

getRegions, read.magpie, write.magpie

Examples

getCPR(0.5)
a <- maxample("animal")
getCPR(a, dim = "color")
getCPR(a, dim = 3.2)
getCPR(a, dim = "country")
getCPR(a, dim = c("color", "species"))

getDim

Description

Function which tries to detect the dimension to which the given elems belong

Usage

getDim(elems, x, fullmatch = FALSE, dimCode = TRUE)

Arguments

elems

A vector of characters containing the elements that should be found in the MAgPIE object

x

MAgPIE object in which elems should be searched for.

fullmatch

If enabled, only dimensions which match exactly the elements provided will be returned. Otherwise, it is sufficient if elems contains a subset of the dimension.

dimCode

If enabled, the dimCode will be returned, otherwise the name of the dimension.

Value

The name or dimCode of the dimensions in which elems were found.

Author(s)

Jan Philipp Dietrich

See Also

mcalc,dimCode

Examples

pop <- maxample("pop")
 getDim(c("AFR","CPA"),pop)
 getDim(c("AFR","CPA"),pop,fullmatch=TRUE)
 getDim(c("AFR","CPA"),pop,dimCode=FALSE)

Get Items

Description

Extract items of a given (sub-)dimension of a MAgPIE-object

Usage

getItems(x, dim = NULL, split = FALSE, full = FALSE)

getItems(x, dim, full = NULL, maindim = NULL, raw = FALSE) <- value

Arguments

x

MAgPIE object

dim

Dimension for which the items should be returned. Either number or name of dimension or a vector of these. See dimCode for more details.

split

Boolean which determines whether a main dimension should be split in subdimensions. Only applicable to main dimensions (1,2,3) and ignored for all other.

full

if TRUE dimension names are returned as they are (including repetitions), if FALSE only the dimension elements (unique list of entries) are returned.

maindim

main dimension the data should be added to (does not need to be set if dim exists in the data. Should be set if dim might not exist, or if dim might potentially exist in a different main dimension than the one anticipated).

raw

if set to FALSE inputs will be corrected (e.g. dots replaced by the letter "p") if necessary. If TRUE data will be written as is (risking the creation of inconsistent objects).

value

a vector with the length of the main dimension the dimnames should be replaced in / added to. If set to NULL the corresponding dimension will be removed.

Value

items of the requested dimension in the MAgPIE-object. If split=TRUE and applied to a main dimension (1,2,3) a list of items for each sub-dimension.

Functions

  • getItems(x, dim, full = NULL, maindim = NULL, raw = FALSE) <- value: set dimension names

Author(s)

Jan Philipp Dietrich

See Also

dimCode

Examples

x <- maxample("pop")
getItems(x, "scenario")
getItems(x, 3.1)
getItems(x, "i") <- paste0("REG", seq_len(ncells(x)))
getItems(x, "i")
y <- x[, 1, ]
getItems(y, "t") <- NULL

Get dataset names

Description

Extracts dataset names of a MAgPIE-object

Usage

getNames(x, fulldim = FALSE, dim = NULL)

getNames(x, dim = NULL) <- value

Arguments

x

MAgPIE object

fulldim

specifies, how the object is treated. In case of FALSE, it is assumed that x is 3 dimensional and dimnames(x)[[3]] is returned. In case of TRUE, the dimnames of the real third dimension namesare returned

dim

Argument to choose a specific data dimension either by name of the dimension or by number of the data dimension.

value

a vector of names current names should be replaced with. If only one data element exists you can also set the name to NULL.

Details

setNames is a shortcut to use a MAgPIE object with manipulated data names. The setNames method uses the variable names "object" and "nm" in order to be consistent to the already existing function setNames.

Value

getNames returns data names of the MAgPIE-object, whereas setNames returns the MAgPIE object with the manipulated data names.

Functions

  • getNames(x, dim = NULL) <- value: set names

Author(s)

Jan Philipp Dietrich

See Also

setNames-methods, getRegions, getYears, getCPR, read.magpie, write.magpie,ndata, "magpie"

Examples

a <- as.magpie(1)
getNames(a)
setNames(a, "bla")

x <- new.magpie("GLO", 2000, c("a.o1", "b.o1", "a.o2"))
getNames(x, dim = 2)

getSets(x, fulldim = FALSE)[3] <- "bla.blub"
getNames(x, dim = "bla")

getSets(x)[4] <- "ble"
getNames(x, dim = "ble") <- c("Hi", "Bye")
x

Get a list of celluare region-belongings

Description

Extracts a vector containing the region of each cell of a MAgPIE-object

Usage

getRegionList(x)

getRegionList(x) <- value

Arguments

x

MAgPIE object

value

A vector with ncell elements containing the regions of each cell.

Value

A vector with ncell elements containing the region of each cell.

Functions

  • getRegionList(x) <- value: set region names

Author(s)

Jan Philipp Dietrich

See Also

getRegions,getYears, getNames, getCPR, read.magpie, write.magpie, "magpie"

Examples

# a <- read.magpie("example.mz")
# getRegionList(a)

Get regions

Description

Extracts regions of a MAgPIE-object

Usage

getRegions(x)

getRegions(x) <- value

Arguments

x

MAgPIE object

value

Vector containing the new region names of the MAgPIE objects. If you also want to change the mapping of regions to cell please use getRegionList instead.

Value

Regions of the MAgPIE-object

Functions

  • getRegions(x) <- value: overwrite region names

Author(s)

Jan Philipp Dietrich

See Also

getYears, getNames, getCPR, read.magpie, write.magpie, "magpie"

Examples

# a <- read.magpie("example.mz")
# getRegions(a)

Get sets

Description

Extracts sets of a MAgPIE-object if available

Usage

getSets(x, fulldim = TRUE, sep = ".")

getSets(x, fulldim = TRUE, sep = ".") <- value

Arguments

x

MAgPIE object

fulldim

bool: Consider dimension 3 as a possible aggregate of more dimensions (TRUE) or stick to it as one dimension (FALSE)

sep

A character separating joined dimension names

value

A vector with set names you want to replace the current set names of the object with.

Value

Sets of the MAgPIE-object. If no information about contained sets is available NULL

Functions

  • getSets(x, fulldim = TRUE, sep = ".") <- value: replace set names

Author(s)

Markus Bonsch, Jan Philipp Dietrich

See Also

getRegions, getNames,getYears, getCPR, read.magpie, write.magpie, "magpie"

Examples

a <- new.magpie("GLO.1", 2000, c("a.o1", "b.o1", "a.o2"))
 getSets(a) <- c("reg", "cell", "t", "bla", "blub")
 getSets(a)

 getSets(a)["d3.1"] <- "BLA"
 getSets(a, fulldim = FALSE)
 getSets(a)

Get years

Description

Extracts years of a MAgPIE-object

Usage

getYears(x, as.integer = FALSE)

getYears(x) <- value

setYears(object, nm = NULL)

Arguments

x, object

MAgPIE object

as.integer

Switch to decide, if output should be the used year-name (e.g. "y1995") or the year as integer value (e.g. 1995)

value, nm

Years the data should be set to. Either supplied as a vector of integers or a vector of characters in the predefined year format ("y0000"). If only 1 year exist you can also set the name of the year to NULL.

Details

setYears is a shortcut to use a MAgPIE object with manipulated year names. setYears uses the variable names "object" and "nm" in order to be consistent to the already existing function setNames.

Value

getYears returns years of the MAgPIE-object, whereas setYears returns the MAgPIE object with the manipulated years.

Functions

  • getYears(x) <- value: rename years

  • setYears(): set years

Author(s)

Jan Philipp Dietrich

See Also

getRegions, getNames, setNames, getCPR, read.magpie, write.magpie, "magpie"

Examples

a <- as.magpie(1)
 getYears(a)
 setYears(a,1995)

guessResolution

Description

Guess the resolution of the given magpie object/coordinates by looking at the minimum difference between unique sorted values. Fall back to 0.5 if guess is infinite.

Usage

guessResolution(x)

Arguments

x

A magpie object or the coordinates of a magpie object (the result of getCoords)

Value

The guessed resolution of the data

Author(s)

Jan Philipp Dietrich, Pascal Sauer


Has Coordinates

Description

Checks, whether object contains coordinates.

Usage

hasCoords(x, xlab = "x", ylab = "y")

Arguments

x

MAgPIE object

xlab

label of x-dimension

ylab

label of y-dimension

Value

Boolean indicating whether coordinates were found or not

Author(s)

Jan Philipp Dietrich

See Also

getCoords

Examples

hasCoords(maxample("pop"))
hasCoords(maxample("animal"))

Has Sets

Description

Checks, whether set names have been set

Usage

hasSets(x)

Arguments

x

MAgPIE object

Value

Boolean indicating whether coordinates were found or not

Author(s)

Jan Philipp Dietrich

See Also

getCoords

Examples

hasSets(maxample("pop"))
hasSets(maxample("animal"))

head/tail

Description

head and tail methods for MAgPIE objects to extract the head or tail of an object

Usage

## S3 method for class 'magpie'
head(x, n1 = 3L, n2 = 6L, n3 = 2L, ...)

Arguments

x

MAgPIE object

n1, n2, n3

number of lines in first, second and third dimension that should be returned. If the given number is higher than the length of the dimension all entries in this dimension will be returned.

...

arguments to be passed to or from other methods.

Value

head returns the first n1 x n2 x n3 entries, tail returns the last n1 x n2 x n3 entries.

Author(s)

Jan Philipp Dietrich

See Also

head, tail

Examples

pop <- maxample("pop")
 head(pop)
 tail(pop,2,4,1)

is.temporal, is.spatial

Description

Functions to find out whether a vector consists of strings consistent with the definition for auto-detection of temporal or spatial data.

Usage

is.temporal(x)

Arguments

x

A vector

Value

Returns TRUE or FALSE

Author(s)

Jan Philipp Dietrich

Examples

is.temporal(1991:1993)
is.spatial(c("GLO","AFR"))

isYear

Description

Function to find out whether a vector consists of strings in the format "yXXXX" or "XXXX" with X being a number

Usage

isYear(x, with_y = TRUE)

Arguments

x

A vector

with_y

indicates which dataformat years have to have (4-digit without y (e.g.1984) or 5digit including y (y1984))

Value

Returns a vector of the length of x with TRUE and FALSE

Author(s)

Benjamin Bodirsky

Examples

x <- c("1955", "y1853", "12a4")
isYear(x, with_y = TRUE)
isYear(x, with_y = FALSE)

log-method for MAgPIE objects

Description

log-method for MAgPIE-objects respectively. Works exactly as for arrays.

Usage

## S4 method for signature 'magpie'
log(x, base = exp(1))

Arguments

x

a magpie object

base

ia positive or complex number: the base with respect to which logarithms are computed. Defaults to e=exp(1).

Methods

x = "magpie"

works as log(x) for arrays.


Lowpass Filter

Description

Filters high frequencies out of a time series. The filter has the structure x'(n) = (x(n-1)+2*x(n)+x(n+1))/4

Usage

lowpass(x, i = 1, fix = NULL, altFilter = NULL, warn = TRUE)

Arguments

x

Vector of data points, that should be filtered or MAgPIE object

i

number of iterations the filter should be applied to the data

fix

Fixes the starting and/or ending data point. Default value is NULL which doesn't fix any point. Available options are: "start" for fixing the starting point, "end" for fixing the ending point and "both" for fixing both ends of the data.

altFilter

set special filter rule to indexes defined in this parameter. The special filter has the structure x'(n) = (2*x(n)+x(n+1))/3

warn

boolean deciding whether lowpass issues a warning for critical parameter choices or not

Value

The filtered data vector or MAgPIE object

Author(s)

Jan Philipp Dietrich, Misko Stevanovic

Examples

lowpass(c(1, 2, 11, 3, 4))
# to fix the starting point
lowpass(c(0, 9, 1, 5, 14, 20, 6, 11, 0), i = 2, fix = "start")

magclassdata

Description

General magclass-dataset

Details

Please do not directly access that data. It should be only used by library functions.

Author(s)

Jan Philipp Dietrich


magpie_expand

Description

Expands a MAgPIE object based on a reference

Usage

magpie_expand(x, ref)

Arguments

x

MAgPIE object that should be expanded

ref

MAgPIE object that serves as a reference

Details

Expansion means here that the dimensions of x are expanded accordingly to ref. Please note that this is really only about expansion. In the case that one dimension of ref is smaller than of x nothing happens with this dimension. At the moment magpie_expand is only internally available in the magclass library

You can influence the verbosity of this function by setting the option "magclass.verbosity". By default verbosity is set to 1 which means that only warnings are returned. Setting verbosity to 2 means that warnings as well as additional notes are returned. This is done by options(verbosity.level=2)

With version 5 of the package magpie_expand has been updated to a newer version (currently 2.1) and since version 6 this is the only currently supported version. To switch to the old setup you have to install magclass in a version < 6 and set options(magclass_expand_version=1).

By default expansion is based on the elements in a dimension ignoring the set name of the dimension. To expand based on set names instead of contents (recommended) you can switch options(magclass_setMatching=TRUE). Please be careful with this setting as it alters the behavior of magclass objects quite significantly! For more information have a look at vignette("magclass-expansion").

Value

An expanded version of x.

Author(s)

Jan Philipp Dietrich

See Also

as.magpie, options

Examples

a <- new.magpie(c("AFR", "CPA"), "y1995", c("m", "n"))
b <- new.magpie("GLO", "y1995", c("bla", "blub"))
magpie_expand(b, a)
options(magclass.verbosity = 2)
magpie_expand(b, a)

magpie_expand_dim

Description

Expands a single MAgPIE object dimension

Usage

magpie_expand_dim(x, ref, dim = 1)

Arguments

x

MAgPIE object that should be expanded

ref

MAgPIE object that serves as a reference

dim

dimension that should be expanded

Details

Expansion means here that the dimensions of x are expanded acordingly to ref. Please note that this is really only about expansion. In the case that one dimension of ref is smaller than of x nothing happens with this dimension. At the moment magpie_expand is only internally available in the magclass library

In contrast to magpie_expand this function is expanding only a single dimension. It is meant as a support function for magpie_expand itself.

Value

An expanded version of x.

Author(s)

Jan Philipp Dietrich

See Also

as.magpie, options

Examples

d <- new.magpie(c("AFR.BLUB.1", "AFR.BLUB.2", "EUR.BLUB.1",
                    "AFR.BLA.1", "AFR.BLA.2", "EUR.BLA.1"), fill = 1)
 getSets(d)[1:3] <- c("reg", "b", "i")
 e <- new.magpie(c("BLA.AFR.A", "BLA.EUR.A", "BLUB.AFR.A", "BLUB.EUR.A",
                    "BLA.AFR.B", "BLA.EUR.B", "BLUB.AFR.B", "BLUB.EUR.B"), fill = 2)
 getSets(e)[1:3] <- c("b", "reg", "a")
 magclass:::magpie_expand_dim(d, e, dim = 1)

Class "magpie" ~~~

Description

The MAgPIE class is a data format for cellular MAgPIE data with a close relationship to the array data format. is.magpie tests if x is an MAgPIE-object, as.magpie transforms x to an MAgPIE-object (if possible).

Arguments

x

An object that should be either tested or transformed as/to an MAgPIE-object.

...

additional arguments supplied for the conversion to a MAgPIE object. Allowed arguments for arrays and dataframes are spatial and temporal both expecting a vector of dimension or column numbers which contain the spatial or temporal information. By default both arguments are set to NULL which means that the as.magpie will try to detect automatically the temporal and spatial dimensions. The arguments will just overwrite the automatic detection. If you want to specify that the data does not contain a spatial or temporal dimension you can set the corresponding argument to 0. In addition as.magpie for data.frames is also expecting an argument called datacol which expects a number stating which is the first column containing data. This argument should be used if the dimensions are not detected corretly, e.g. if the last dimension column contains years which are then detected as values and therefore interpreted as first data column. In addition an argument tidy=TRUE can be used to indicate that the data.frame structure is following the rules of tidy data (last column is the data column all other columns contain dimension information). This information will help the conversion. sep defines the dimension separator (default is ".") and replacement defines how the separator as a reserved character should be converted in order to not mess up with the object (default "_"). Another available argument for conversions of data.frames and quitte objects to magpie is filter if set to TRUE (default) "." (separator) will be replaced withe the replacement character and empty entries will be replaced with a single space. If set to FALSE no filter will be applied to the data.

Objects from the Class

Objects can be created by calls of the form new("magpie", data, dim, dimnames, ...). MAgPIE objects have three dimensions (cells,years,datatype) and the dimensionnames of the first dimension have the structure "REGION.cellnumber". MAgPIE-objects behave the same like array-objects with 2 exceptions:
1.Dimensions of the object will not collapse (e.g. x[1,1,1] will remain 3D instead of becoming 1D)
2.It is possible to extract full regions just by typing x["REGIONNAME",,].

Please mind following standards:
Header must not contain any purely numeric entries, but combinations of characters and numbers are allowed (e.g. "bla","12" is forbidden, wheras "bla","b12" is allowed)
Years always have the structure "y" + 4-digit number, e.g. "y1995"
Regions always have the structure 3 capital letters, e.g. "AFR" or "GLO"

This standards are necessary to allow the scripts to detect headers, years and regions properly and to have a distinction to other data.

Author(s)

Jan Philipp Dietrich

See Also

read.magpie, write.magpie, getRegions, getYears, getNames, getCPR, ncells, nyears, ndata

Examples

showClass("magpie")

pop <- maxample("pop")

# returning PAO and PAS for 2025
pop["PA", 2025, , pmatch = "left"]

# returning CPA for 2025
pop["PA", 2025, , pmatch = "right"]

# returning CPA PAO and PAS for 2025
pop["PA", 2025, , pmatch = TRUE]

# returning PAS and 2025
pop["PAS", 2025, ]

# return all entries for year 2025
pop[2025, dim = 2]

# returning everything but values for PAS or values for 2025
pop["PAS", 2025, , invert = TRUE]

# accessing subdimension via set name

a <- maxample("animal")
a[list(country = "NLD", y = "53p25"), , list(species = c("rabbit", "dog"))]

# please note that the list elements act as filter. For instance, the
# following example will not contain any dogs as the data set does
# not contain any dogs which are black.
a[list(country = "NLD", y = "53p25"), , list(species = c("rabbit", "dog"), color = "black")]

# it is also possible to extract given combinations of subdimensions
# via a data-frame
df <- data.frame(getItems(a, 3, split = TRUE, full = TRUE))[c(1, 3, 4), ][3:2]
getItems(a[df], 3)

# Unknown dimensions to be added in output!
df$blub <- paste0("bl", 1:dim(df)[1])
getItems(a[df], 3)

MAgPIE-Sort

Description

Brings the spatial and temporal structure of MAgPIE objects in the right order. This function is especially useful when you create new MAgPIE objects as the order typically should be correct for MAgPIE objects.

Usage

magpiesort(x)

Arguments

x

MAgPIE object which might not be in the right order.

Value

The eventually corrected MAgPIE object (right order in spatial in temporal dimension)

Author(s)

Jan Philipp Dietrich

See Also

"magpie"

Examples

pop <- maxample("pop")
a <- magpiesort(pop)

magpply

Description

apply command for magpieobjects. Very efficient for replacing loops.

Usage

magpply(X, FUN, MARGIN = NULL, DIM = NULL, ..., INTEGRATE = FALSE)

Arguments

X

magpie object

FUN

function that shall be applied X

MARGIN

dimension over which FUN shall be applied (like a loop over that dimension). This dimension will be preserved in the output object (see also DIM).

DIM

dimension in which FUN shall be applied. This dimension will be missing in the output. DIM and MARGIN are opposite ways of expressing the dimensions to be addressed and you must only use one of them with MARGIN excluding dimensions from the calculation and DIM including them.

...

further parameters passed on to FUN

INTEGRATE

if TRUE, the output will be filled into an magpie object of the same dimensionality as X

Value

magpie object

Author(s)

Jan Philipp Dietrich, Benjamin Leon Bodirsky

Examples

pop <- maxample("pop")
magpply(pop, FUN = sum, MARGIN = 2)
fourdim <- pop * setNames(pop, c("jkk", "lk"))
magpply(fourdim, FUN = sum, MARGIN = c(1, 3.1))

Match dimensions of a magpie object to those of a reference object

Description

A helper that restricts and expands a magpie object x to the size of a magpie object ref. Dimension names not present in x are added and set to the value provided by fill. Dimension names not present in ref are cropped.

Usage

matchDim(x, ref, dim = 1:3, fill = NA)

Arguments

x

A magpie object to be modified.

ref

A magpie object used as a reference for the modification. Returns x if ref is NULL.

dim

Subset of dimensions for which the matching should be done. Can be either a number between 1 and 3 or a vector of these. Defaults to all dimensions (i.e. 1:3).

fill

Value to be set in new dimensions.

Value

The modified magpie object.

Author(s)

Falk Benke


maxample

Description

A collection of magclass example data sets

Usage

maxample(data)

Arguments

data

name of the example data set. Currently available are "pop" (regional population data, previously named "population_magpie"), "animal" (fictional, high-dimensional animal sighting data set) and "bilateral" (fictional, bilateral trade cost data set).

Value

the chosen example data set

Author(s)

Jan Philipp Dietrich

Examples

p <- maxample("pop")
str(p)

a <- maxample("animal")
str(a)
getItems(a, split = TRUE)

mbind

Description

Merges MAgPIE-objects with identical structure in two dimensions. If data differs in the temporal or spatial dimension each year or region/cell must appear only once!

Usage

mbind(...)

Arguments

...

MAgPIE objects or a list of MAgPIE objects that should be merged.

Value

The merged MAgPIE object

Author(s)

Jan Philipp Dietrich, Misko Stevanovic

See Also

"magpie"

Examples

m <- new.magpie(c("AFR", "CPA", "EUR"), c(1995, 2005), "Data1", fill = c(1, 2, 3, 4, 5, 6))
ms <- dimSums(m, dim = 3.1)
mbind(m, ms)
my <- new.magpie(getRegions(m), 2010, getNames(m), fill = c(6, 6, 4))
mbind(m, my)
md <- new.magpie(getRegions(m), getYears(m), "Data2", fill = c(7, 6, 5, 7, 8, 9))
mbind(m, md)

pop <- maxample("pop")
a <- mbind(pop, pop)
dim(pop)
dim(a)

mcalc

Description

Select values from a MAgPIE-object

Usage

mcalc(x, f, dim = NULL, append = FALSE)

Arguments

x

MAgPIE object

f

A formula describing the calculation that should be performed

dim

The dimension in which the manipulation should take place. If set to NULL function tries to detect the dimension automatically.

append

If set to TRUE the result will be appended to x, otherwise the result will be returned.

Details

This functions only work for MAgPIE objects with named dimensions as the dimension name (set_name) has to be used to indicate in which dimension the entries should be searched for!

Value

The calculated MAgPIE object in the case that append is set to FALSE. Otherwise nothing is returned (as x is appended in place)

Author(s)

Jan Philipp Dietrich

See Also

mselect

Examples

pop <- maxample("pop")
pop
mcalc(pop, X12 ~ A2 * B1, append = TRUE)
pop
mcalc(pop, `Nearly B1` ~ 0.5 * A2 + 99.5 * B1)

MSelect

Description

Select values from a MAgPIE-object

Usage

mselect(x, ..., collapseNames = FALSE)

mselect(x, ...) <- value

Arguments

x

MAgPIE object

...

entry selections of the form set_name=c(set_elem1,set_elem2). Alternatively a single list element containing these selections can be provided.

collapseNames

Boolean which decides whether names should be collapsed or not.

value

values on which the selected magpie entries should be set.

Details

This functions only work for MAgPIE objects with named dimensions as the dimension name (set_name) has to be used to indicate in which dimension the entries should be searched for!

Value

The reduced MAgPIE object containing only the selected entries or the full MAgPIE object in which a selection of entries was manipulated.

Functions

  • mselect(x, ...) <- value: replace values in magpie object

Author(s)

Jan Philipp Dietrich

See Also

collapseNames, "magpie"

Examples

pop <- maxample("pop")
mselect(pop, i = c("AFR", "EUR"), scenario = "A2", t = "y2035")

Count elements

Description

Functions to count the number of cells/years/datasets/regions of an MAgPIE-object

Usage

ncells(x)

ndata(x)

nregions(x)

nyears(x)

Arguments

x

A MAgPIE-object

Value

value

The number of cells/years/datasets/regions of x

Functions

  • ndata(): count datasets

  • nregions(): count regions

  • nyears(): count years

Author(s)

Jan Philipp Dietrich

Examples

a <- is.magpie(NULL)
ncells(a)
nyears(a)
ndata(a)
nregions(a)

Count sub-dimensions

Description

Functions to count the subdimensions of an MAgPIE-object

Usage

ndim(x, dim = NULL)

Arguments

x

A MAgPIE-object

dim

main dimension in which the sub-dimensions should be counted. If NULL the sum of all subdimensions is returned

Value

Number of subdimensions

Author(s)

Jan Philipp Dietrich

Examples

a <- maxample("animal")
  ndim(a)
  ndim(a,1)
  ndim(a,2)
  ndim(a,3)

new.magpie

Description

Creates a new MAgPIE object

Usage

new.magpie(
  cells_and_regions = "GLO",
  years = NULL,
  names = NULL,
  fill = NA,
  sort = FALSE,
  sets = NULL,
  unit = NULL
)

Arguments

cells_and_regions

Either the region names (e.g. "AFR"), or the cells (e.g. 1:10), or both in combination (e.g. "AFR.1"). NULL means no spatial element.

years

dimnames for years in the format "yXXXX" or as integers. NULL means one year which is not further specified

names

dimnames for names. NULL means one data element which is not further specified

fill

Default value for the MAgPIE object

sort

Bolean. Decides, wheher output should be sorted or not.

sets

A vector of dimension names. See getSets for more information.

unit

deprecated

Value

an empty magpie object filled with fill, with the given dimnames

Author(s)

Benjamin Bodirsky, Jan Philipp Dietrich

See Also

as.magpie

Examples

a <- new.magpie(1:10, 1995:2000)
b <- new.magpie(c("AFR", "CPA"), "y1995", c("bla", "blub"), sets = c("i", "t", "value"))
c <- new.magpie()

population_magpie

Description

Example dataset for a regional MAgPIE object

Value

A2 and B1 population scenario from SRES

Author(s)

Benjamin Bodirsky


print

Description

print method for MAgPIE objects for conventient display of magpie data.

Usage

## S3 method for class 'magpie'
print(x, drop = TRUE, reshape = FALSE, ...)

Arguments

x

MAgPIE object

drop

argument which controls whether empty dimensions should be skipped or not.

reshape

argument that controls tabular representation of nested data dimension cross tables, FALSE will reproduce standard print behavior any pair of two dimension numbers will create a table for these two dims, and loop over the other dimensions

...

arguments to be passed to or from other methods.

Value

Invisibly, the MAgPIE object x.

Author(s)

Jan Philipp Dietrich, Kristine Karstens, Felicitas Beier

See Also

print

Examples

pop <- maxample("pop")
print(pop)
print(pop[, 1, ], drop = FALSE)
print(pop[, 1, ])

Read MAgPIE-object from file

Description

Reads a MAgPIE-file and converts it to a 3D array of the structure (cells,years,datacolumn)

Usage

read.magpie(
  file_name,
  file_folder = "",
  file_type = NULL,
  as.array = FALSE,
  comment.char = "*",
  check.names = FALSE,
  ...
)

Arguments

file_name

file name including file ending (wildcards are supported). Optionally also the full path can be specified here (instead of splitting it to file_name and file_folder)

file_folder

folder the file is located in (alternatively you can also specify the full path in file_name - wildcards are supported)

file_type

format the data is stored in. If file_type=NULL the file ending of the file_name is used as format. If format is different to the formats mentioned standard MAgPIE format is assumed. See write.magpie for a list of supported file formats.

as.array

Should the input be transformed to an array? This can be useful for regional or global inputs, but all advantages of the magpie-class are lost.

comment.char

character: a character vector of length one containing a single character or an empty string. Use "" to turn off the interpretation of comments altogether. If a comment is found it will be stored in attr(,"comment"). In text files the comment has to be at the beginning of the file in order to be recognized by read.magpie.

check.names

logical. If TRUE then the names of the variables in the data frame are checked to ensure that they are syntactically valid variable names. Same functionality as in read.table.

...

additional arguments passed to specific read functions (e.g. varname for specifying the variable to be read in from a multi-variable NCDF file.)

Details

See write.magpie for a list of supported file formats.

Value

x

MAgPIE-object

Note

See write.magpie for the detailed structure of binary MAgPIE formats .m and .mz.

Author(s)

Jan Philipp Dietrich, Stephen Bi, Florian Humpenoeder, Pascal Sauer

See Also

"magpie", write.magpie


Read file in report format

Description

This function reads the content of a reporting file (a file in the model intercomparison file format *.mif) into a list of MAgPIE objects or a single MAgPIE object.

Usage

read.report(file, as.list = TRUE, showSeparatorWarning = TRUE)

Arguments

file

file name the object should be read from.

as.list

if TRUE a list is returned (default), if FALSE it is tried to merge all information in one MAgPIE object (still under development and works currently only if the entries for the different models and scenarios have exactly the same regions and years).

showSeparatorWarning

Boolean (default value TRUE) that decides whether the warning about the replacement of dots in variable names is displayed (default value) or not.

Details

The Model Intercomparison File Format (MIF) is the default file format for data produced by Integrated Assessment Models. It is based on the common format used for Model Intercomparison Projects such as EMF and SSP with some slight changes/clarifications in its definition. For interactions between models this format should be used. For everything else it is at least recommended to use this format, too.

Aim of this standardization is to achieve a more flexible and smooth communication between models and to facilitate the creation of aggregated outputs from integrated assessment scenario runs which then can easily be uploaded to external databases such as the EMF or SSP database. By using this standard most of the required decisions for a working input output interface between models have already been specified which significantly reduces the required work to get a new interaction running.

Definition

The format is characterized by the following features:

  • The file ending is ".mif"

  • The file is written in ASCII format

  • Entries are separated with ";", every line ends with a ";"

  • The file always contains a header

  • The format of the header is: Model;Scenario;Region;Variable;Unit;<ADDITIONAL_COLUMNS>;<YEARS>;

The first 5 entries always have to exist, <ADDITIONAL_COLUMNS> is additional information which can be added optionally (e.g. "Description") and <YEARS> are the years for which data is delivered. <YEARS> are always written as 4 digit numbers. In the (very unlikely) case that a year before 1000 is used the number has to start with a 0, e.g. 0950. <ADDITIONAL_COLUMNS> can be anything, there are no further rules at the moment what it can contain. However, there are strict rules for naming these columns. Allowed are single names starting with a capital letter without special characters in it except "_" which is allowed. Examples: "Description" allowed, "More Description" not allowed, "More_Description" allowed, "123Description" not allowed, "Description123" allowed. Scripts using this format must be able to ignore additional columns. For years there are no specific limitations/requirements which years should be reported. Scripts dealing with this data must be able to work with different temporal resolutions. For variables basically everything can be reported here. Missing values have to be marked with "N/A".

Author(s)

Jan Philipp Dietrich

See Also

write.report

Examples

## Not run: 
read.report("report.csv")

## End(Not run)

Replace Non-Finite Data

Description

Replaces all instances of non-finite data (NA, NaN, Inf, and -Inf).

Usage

replace_non_finite(x, replace = 0)

Arguments

x

A vector or magpie object.

replace

A value to replace non-finite data with.

Value

A vector or magpie object, same as x.

Author(s)

Michaja Pehl

Examples

part  <- new.magpie(letters[1:3], years = 'y1995', names = 'foo')
total <- new.magpie(letters[1:3], years = 'y1995', names = 'foo')

part[,,]  <- c(0, 1, 2)
total[,,] <- c(0, 10, 10)

part / total

replace_non_finite(part / total)

Round-method for MAgPIE objects

Description

Round-method for MAgPIE-objects respectively. Works exactly as for arrays.

Usage

## S4 method for signature 'magpie'
round(x, digits = 0)

Arguments

x

a magpie object

digits

integer indicating the number of decimal places (round) or significant digits (signif) to be used. Negative values are allowed.

Methods

x = "magpie"

works as round(x) for arrays.


~~ Methods for Function rowSums and rowMeans ~~

Description

~~ Methods for function rowSums and rowMeans~~

Usage

## S4 method for signature 'magpie'
rowSums(x, na.rm = FALSE, dims = 1, ...)

Arguments

x

object on which calculation should be performed

na.rm

logical. Should missing values (including NaN) be omitted from the calculations?

dims

integer: Which dimensions are regarded as "rows" or "columns" to sum over. For row*, the sum or mean is over dimensions dims+1, ...; for col* it is over dimensions 1:dims.

...

further arguments passed to other colSums/colMeans methods

Methods

list("signature(x = \"ANY\")")

normal rowSums and rowMeans method

list("signature(x = \"magpie\")")

classical method prepared to handle MAgPIE objects


Set Items

Description

Set items of a given (sub-)dimension of a MAgPIE-object

Usage

setItems(x, dim, value, maindim = NULL, raw = FALSE)

Arguments

x

MAgPIE object

dim

Dimension for which the items should be returned. Either number or name of dimension or a vector of these. See dimCode for more details.

value

a vector with the length of the main dimension the dimnames should be replaced in / added to. If set to NULL the corresponding dimension will be removed.

maindim

main dimension the data should be added to (does not need to be set if dim exists in the data. Should be set if dim might not exist, or if dim might potentially exist in a different main dimension than the one anticipated).

raw

if set to FALSE inputs will be corrected (e.g. dots replaced by the letter "p") if necessary. If TRUE data will be written as is (risking the creation of inconsistent objects).

Value

the manipulated MAgPIE object

Author(s)

Jan Philipp Dietrich

See Also

getItems

Examples

x <- maxample("pop")
setItems(x, "i", paste0("REG", 1:ncells(x)))

Get dataset names

Description

Extracts dataset names of a MAgPIE-object

Usage

## S4 method for signature 'magpie'
setNames(object = nm, nm)

Arguments

object

MAgPIE object

nm

a vector of names current names should be replaced with. If only one data element exists you can also set the name to NULL.

Details

setNames is a shortcut to use a MAgPIE object with manipulated data names. The setNames method uses the variable names "object" and "nm" in order to be consistent to the already existing function setNames.

Methods

list("signature(object = \"ANY\")")

normal setNames method

list("signature(object = \"magpie\")")

setNames for MAgPIE objects

See Also

getNames,


~~ Method for function show ~~

Description

Show a magpie object by calling the default show method, print, or str, depending on options("magclass_show_func").

Usage

## S4 method for signature 'magpie'
show(object)

Arguments

object

A MAgPIE-object

Author(s)

Pascal Sauer


sizeCheck

Description

Calculates expected magclass object length and checks that it stays below the limit defined with magclass_sizeLimit (default = 10^9). This is useful to prevent out of memory errors in case of unwanted object expansions Ignored if getOption("magclass_sizeLimit") is negative.

Usage

sizeCheck(dim)

Arguments

dim

dimensions of the current object as returned by function dim

Author(s)

Jan Philipp Dietrich

Examples

pop <- maxample("pop")
magclass:::sizeCheck(dim(pop))

## Not run: 
magclass:::sizeCheck(c(6765L, 10946L, 17711L))

## End(Not run)

spatRasterToDataset

Description

Convert a SpatRaster to a SpatRasterDataset.

Usage

spatRasterToDataset(x)

Arguments

x

SpatRaster with names of the form "y[0-9]+..[varname]"

Value

SpatRasterDataset

Author(s)

Pascal Sauer


str

Description

str method for MAgPIE objects for conventient display of the structure of a magpie object.

Usage

## S3 method for class 'magpie'
str(object, ...)

Arguments

object

MAgPIE object

...

arguments to be passed to or from other methods.

Details

In contrast to the default str this will not show the attributes of [email protected] as these contain only a duplicate of dimnames. Also, dim is not shown, because the information it provides is implicitly included in dimnames.

Author(s)

Pascal Sauer

See Also

str

Examples

str(maxample("pop"))

suppressSpecificWarnings

Description

Like suppressWarnings, but instead of suppressing all warnings this only suppresses warnings if they match the given pattern.

Usage

suppressSpecificWarnings(expr, regularExpr, fixed = FALSE)

Arguments

expr

The expression/code to evaluate, can be a block of code inside curly braces.

regularExpr

Only warnings matching this regular expression are suppressed.

fixed

Match the literal string given by regularExpr instead of interpreting it as a regular expression. Passed to grepl.

Value

The result of evaluating expr.

Author(s)

Pascal Sauer

See Also

suppressWarnings


time_interpolate

Description

Function to extrapolate missing years in MAgPIE objects.

Usage

time_interpolate(
  dataset,
  interpolated_year,
  integrate_interpolated_years = FALSE,
  extrapolation_type = "linear"
)

Arguments

dataset

An MAgPIE object

interpolated_year

Vector of years, of which values are required. Can be in the formats 1999 or y1999.

integrate_interpolated_years

FALSE returns only the dataset of the interpolated year, TRUE returns the whole dataset, including all years of data and the itnerpolated year

extrapolation_type

Determines what happens if extrapolation is required, i.e. if a requested year lies outside the range of years in dataset. Specify "linear" for a linear extrapolation. "constant" uses the value from dataset closest in time to the requested year.

Value

Uses linear extrapolation to estimate the values of the interpolated year, using the values of the two surrounding years. If the value is before or after the years in data, the two closest neighbours are used for extrapolation.

Author(s)

Benjamin Bodirsky, Jan Philipp Dietrich

See Also

convergence

Examples

p <- maxample("pop")
time_interpolate(p, "y2000", integrate = TRUE)
time_interpolate(p, c("y1980", "y2000"), integrate = TRUE, extrapolation_type = "constant")

splits a data.frame or vector of strings with form 'variable (unit)' into a data.frame with variable and unit separated

Description

splits a data.frame or vector of strings with form 'variable (unit)' into a data.frame with variable and unit separated

Usage

unitsplit(x, col = "variable")

Arguments

x

data.frame or vector of strings

col

column name. Default: variable

Author(s)

Jan Philipp Dietrich, Mika Pflüger, Oliver Richters


Unwrap

Description

Creates a higher dimensional array by separating all subdimensions in the third dimension of a MAgPIE object and returning them as separate dimension.

Usage

unwrap(x, sep = NULL)

Arguments

x

A MAgPIE object

sep

deprecated, please do not use anymore

Value

An array with the full dimensionality of the original data

Author(s)

Jan Philipp Dietrich

See Also

wrap,fulldim

Examples

a <- as.magpie(array(1:6, c(3, 2), list(c("bla", "blub", "ble"), c("up", "down"))))
unwrap(a)

where

Description

Analysis function for magpie objects

Usage

where(x, plot = NULL)

Arguments

x

A logical statement with a magpie object

plot

deprecated. Use the function whereplot in package luplot.

Value

A list of analysis parameters

Author(s)

Benjamin Leon Bodirsky, Jan Philipp Dietrich

See Also

whereplot in package luplot

Examples

p <- maxample("pop")
where(p > 500)

Wrap

Description

Reshape an array or a matrix by permuting and/or joining dimensions.

Usage

wrap(x, map = list(NA), sep = ".")

Arguments

x

An array

map

A list of length equal to the number of dimensions in the reshaped array. Each element should be an integer vectors specifying the dimensions to be joined in corresponding new dimension. One element may equal NA to indicate that that dimension should be a join of all non-specified (remaining) dimensions. Default is to wrap everything into a vector.

sep

A character separating joined dimension names

Note

This function is extracted from the R.utils library which is licensed under LGPL>=2.1 and written by Henrik Bengtsson.

Author(s)

Henrik Bengtsson, Jan Philipp Dietrich

See Also

unwrap,fulldim


Write MAgPIE-object to file

Description

Writes a magpie object to a file. The file type is determined by the filename extension. The written file can be read again using read.magpie.

Usage

write.magpie(
  x,
  file_name,
  file_folder = "",
  file_type = NULL,
  append = FALSE,
  comment = NULL,
  comment.char = "*",
  mode = NULL,
  zname = "time",
  ...
)

Arguments

x

a magclass object. An exception is that formats written via the raster package (currently "asc", "grd" and "tif") also accept RasterBrick objects which have been previously created from a magclass object via as.RasterBrick)

file_name

file name including file ending (wildcards are supported). Optionally also the full path can be specified here (instead of splitting it to file_name and file_folder)

file_folder

folder the file should be written to (alternatively you can also specify the full path in file_name - wildcards are supported)

file_type

Format the data should be stored as. If file_type=NULL the file ending of the file_name is used as format. See detailed description for a list of available file types. Please be aware that the file_name is independent of the file_type you choose here, so no additional file ending will be added!

append

Decides whether an existing file should be overwritten (FALSE) or the data should be added to it (TRUE). Append = TRUE only works if the existing data can be combined with the new data using the mbind function

comment

Vector of strings: Optional comment giving additional information about the data. If different to NULL this will overwrite the content of attr(x,"comment"). For nc files the unit can be passed with e.g. 'comment = "unit: kg"'.

comment.char

character: a character vector of length one containing a single character or an empty string. Use "" to turn off the interpretation of comments altogether.

mode

File permissions the file should be written with as 3-digit number (e.g. "777" means full access for user, group and all, "750" means full access for user, read access for group and no acess for anybody else). Set to NULL system defaults will be used. Access codes are identical to the codes used in unix function chmod.

zname

name of the time variable for raster files like nc, asc, grd and tif

...

additional arguments passed to specific write functions. Check ?magclass::writeNC for available arguments when writing nc files.

Details

This function supports writing the following file types:

  • "cs2" is the new standard format for cellular data with or without header and the first columns (year,regiospatial) or only (regiospatial)

  • "cs2b" is identical to "cs2" except that it will suppress the data name if it has only 1 element in the data dimension.

  • "csv" is the standard format for regional data with or without header and the first columns (year,region,cellnumber) or only (region,cellnumber)

  • "cs3" is another csv format which is specifically designed for multidimensional data for usage in GAMS.

  • "cs4" alternative multidimensional format compatible to GAMS, in contrast to cs3 it can also handle sparse data

  • "csvr", "cs2r", "cs3r", "cs4r" which are the same formats as the ones previously explained with the only difference that they have a REMIND compatible format

  • "cs5" a more generalized version of cs4

  • "rds" is an R-default format for storing R objects

  • "m" (magpie) and "mz" (magpie zipped) are new formats developed to allow a less storage intensive management of MAgPIE-data. The only difference between both formats is that .mz is gzipped whereas .m is not compressed. So .mz needs less memory, whereas .m might have a higher compatibility to other languages

  • "asc" is the ASCII grid format. It can only be applied for gridded data and writes one file per year per data column. In the case that more than one year and data column is supplied several files are written with the structure filename_year_datacolumn.asc

  • "tif" is the GEOtiff format for gridded data.

  • "grd" is the native raster format for gridded data.

  • "nc" is the netCDF format for gridded data. Check ?magclass::writeNC for more details on how nc files are written.

Note

The binary MAgPIE formats .m and .mz have the following content/structure (you only have to care for that if you want to implement read.magpie/write.magpie functions in other languages):

[ FileFormatVersion | Current file format version number (currently 6) | integer | 2 Byte ]
[ nchar_comment | Number of character bytes of the file comment | integer | 4 Byte ]
[ nbyte_metadata | Number of bytes of the serialized metadata (currently = 0) | integer | 4 Byte ]
[ nchar_sets | Number of characters bytes of all regionnames + 2 delimiter | integer | 2 Byte]
[ nyears | Number of years | integer | 2 Byte ]
[ yearList | All years of the dataset (0, if year is not present) | integer | 2*nyears Byte ]
[ ncells | Number of cells | integer | 4 Byte ]
[ nchar_cell | Number of characters bytes of all regionnames + (nreg-1) for delimiters | integer | 4 Byte ]
[ cells | Cell names saved as cell1\cell2 (\n is the delimiter) | character | 1*nchar_cell Byte ]
[ nelem | Total number of data elements | integer | 4 Byte ]
[ nchar_data | Number of char. bytes of all datanames + (ndata - 1) for delimiters | integer | 4 Byte ]
[ datanames | Names saved in the format data1\ndata2 (\n as del.) | character | 1*nchar_data Byte ]
[ data | Data of the MAgPIE array in vectorized form | numeric | 4*nelem Byte ]
[ comment | Comment with additional information about the data | character | 1*nchar_comment Byte ]
[ sets | Set names with \n as delimiter | character | 1*nchar_sets Byte]
[ metadata | serialized metadata information (currently not in use) | bytes | 1*nbyte_metadata Byte]

Author(s)

Jan Philipp Dietrich, Stephen Bi, Florian Humpenoeder, Pascal Sauer

See Also

"magpie", read.magpie,mbind

Examples

pop <- maxample("pop")
path <- tempfile(fileext = ".mz")
write.magpie(pop, path)
pop2 <- read.magpie(path)

Write file in report format

Description

This function writes the content of a MAgPIE object into a file or returns it directly using the reporting format as it is used for many model inter-comparisons.

Usage

write.report(
  x,
  file = NULL,
  model = NULL,
  scenario = NULL,
  unit = NULL,
  ndigit = 4,
  append = FALSE,
  skipempty = TRUE,
  extracols = NULL
)

Arguments

x

MAgPIE object or a list of lists with MAgPIE objects as created by read.report. In the latter case settings for model and scenario are overwritten by the information given in the list.

file

file name the object should be written to. If NULL the formatted content is returned

model

Name of the model which calculated the results

scenario

The scenario which was used to get that results.

unit

Unit of the data. Only relevant if unit is not already supplied in Dimnames (format "name (unit)"). Can be either a single string or a vector of strings with a length equal to the number of different data elements in the MAgPIE object

ndigit

Number of digits the output should have

append

Logical which decides whether data should be added to an existing file or an existing file should be overwritten

skipempty

Determines whether empty entries (all data NA) should be written to file or not.

extracols

names of dimensions which should appear in the output as additional columns

Author(s)

Jan Philipp Dietrich

See Also

read.report

Examples

write.report(maxample("pop"))

Write file in report format

Description

This function is deprecated, please use write.report instead.

Usage

write.report2(...)

Arguments

...

arguments are forwarded to write.report

Author(s)

Jan Philipp Dietrich

See Also

write.report


Write a magpie object to a netCDF file

Description

Write a magpie object to a netCDF file

Usage

writeNC(
  x,
  filename,
  unit,
  ...,
  compression = 2,
  missval = NA,
  gridDefinition = NULL,
  zname = "time",
  progress = FALSE
)

Arguments

x

A magpie object

filename

Name of the netCDF file to write

unit

Unit of the data, to omit pass "" (empty string)

...

For future expansion

compression

Level of compression to use (1-9), NA for no compression

missval

The value that encodes NA in the resulting netCDF file

gridDefinition

A vector of 5 numeric values: c(xMin, xMax, yMin, yMax, resolution). Use c(-179.75, 179.75, -89.75, 89.75, 0.5) to write a standard 0.5-degree-resolution lon/lat grid. If NULL, use min/max of coordinates in x and guessResolution

zname

Name of the z dimension in the netCDF file

progress

If TRUE, print progress messages

Author(s)

Pascal Sauer