| Title: | R emulator |
|---|---|
| Description: | A collection of R tools for fitting model results. |
| Authors: | David Klein [aut, cre] |
| Maintainer: | David Klein <[email protected]> |
| License: | LGPL-3 | file LICENSE |
| Version: | 1.22.0 |
| Built: | 2024-10-23 05:16:04 UTC |
| Source: | https://github.com/pik-piam/remulator |
Use bisection to find x so that myform(param, x) is close to approx_this
bisect(param, myform, approx_this, lower, upper, eps)bisect(param, myform, approx_this, lower, upper, eps)
param |
Parameters applied in |
myform |
User defined function used in approximation |
approx_this |
y-value for which x-value should be approximated |
lower |
Lower limit of interval to search in |
upper |
Upper limit of interval to search in |
eps |
Maximal distance of x to approx_this |
x-value that is within the eps distance to approx_this
David Klein
This function uses the raw data on which you performed the fit (calculate_fit) and the resulting
fit coefficients to calculate a couple of points on the fitted curve that can be used to plot the curve (plot_curve).
calc_supplycurve(data_in, fitcoef, myform, ylimit = "common")calc_supplycurve(data_in, fitcoef, myform, ylimit = "common")
data_in |
MAgPIE object containing the same data that was used to calculate the fitcoefficients. |
fitcoef |
MAgPIE object containing the fitcoefficients (output of |
myform |
Function that was fitted and is used here to calculate curve |
ylimit |
Choose the method to calculate the upper limit for the y values. Options: "individual", the maximal value up to which the y values of the supplycurve are calculated is done individualy for each reagion and year. "common" (default), the upper limit of the y values of the supplycurve for all regions and years is the same and is the maximum of the raw data. This is useful for plotting, because it expands "short" supplycurves beyond the maximal demand of the respective region and year and makes them better comparable. |
MAgPIE object containing the points on the curve.
David Klein
This is an internal function of the remulator package. It fits a curve to given data. For each region and year it minimizes the function sum((y - (a + b * x ^d))^2
x and y are the data provided by the user, and a, b, and d are the coefficients to be found. So, the fit is y = a+b*x^d.
calculate_fit(data, initial_values = c(1, 1, 1), form, ...)calculate_fit(data, initial_values = c(1, 1, 1), form, ...)
data |
MAgPIE object with data to fit. |
initial_values |
Initial values for the parameters to be optimized over. |
form |
Fit function for which least squares will be calaculated using the |
... |
Arguments passed on to the |
MAgPIE object with fit coefficients a, b, and d
David Klein
Example dataset for a regional MAgPIE object
example data as read from MAgPIE report with reduced set of variables
David Klein
This function fits a function of the form y = a + b * x ^ d for the given data.
emulator( data, name_x, name_y, name_modelstat = NULL, treat_as_feasible = c(2, 7), userfun = function(param, x) return(param[[1]] + param[[2]] * x^param[[3]]), initial_values = c(0, 0, 1), outlier_range = 1.5, n_suff = 1, fill = FALSE, output_path = "emulator", fitname = "linear", create_pdf = TRUE, ... )emulator( data, name_x, name_y, name_modelstat = NULL, treat_as_feasible = c(2, 7), userfun = function(param, x) return(param[[1]] + param[[2]] * x^param[[3]]), initial_values = c(0, 0, 1), outlier_range = 1.5, n_suff = 1, fill = FALSE, output_path = "emulator", fitname = "linear", create_pdf = TRUE, ... )
data |
MAgPIE object containing at least two variables and the modelstatus |
name_x |
Name of the variable in |
name_y |
Name of the variable in |
name_modelstat |
Name of the variable that contains the modelstatus |
treat_as_feasible |
GAMS model status codes that will be regarded feasible. See https://www.gams.com/24.8/docs/userguides/mccarl/modelstat_tmodstat.htm |
userfun |
Function to fit. User can provide a functional form using the following
syntax: |
initial_values |
Vector with initial values of the fit coefficients. |
outlier_range |
Before the actual fit a linear pre-fit is performed. Based on their distance to this
pre-fit the data points are allocated to quartiles. A data point is considered an outlier if it is more
than |
n_suff |
Minial number (default=1) of data points in a specific year and region that will be regarded as sufficient to perform a fit. If the number of available data points is less no fit will be generated for this year and region. |
fill |
Logical (default=FALSE) indicating whether data will be copied from subsequent year if in the current year not enough data points are avaialbe. |
output_path |
Path to save the output to |
fitname |
Name that describes the fit (default: linear) and will be used for naming the output folders. |
create_pdf |
Logical indicating whether a pdf should be produced that compiles all figures. |
... |
Arguments passed on to the |
MAgPIE object containning fit coefficients
David Klein
Checks whether set of given runs is complete.
emulator_runs_complete(list_of_directories, runnumbers = 1:73)emulator_runs_complete(list_of_directories, runnumbers = 1:73)
list_of_directories |
Vector of strings containing path names. Must have "-xy" at the end of each name, with xy beinga one or two digit number. |
runnumbers |
Vector of integers providing the number that have to be present in |
Logical. TRUE if set of numbers at the end of the path names is idential to runnumbers.
David Klein
Find fit coefficients for years where no fit could be calculated
fill_missing_years(fitcoef, nodata, method = 1)fill_missing_years(fitcoef, nodata, method = 1)
fitcoef |
MAgPIE object containing the fit coefficients |
nodata |
MAgPIE object of the same shape as |
method |
Choose method that finds fit coefficients for years with no fit. Currently there is only one method availalbe that in a first step takes the fit from the subsequent year. If all subsequent years have no fit it takes the fit from the preceding year. |
Magpie object with the updated fit coefficients. Has an attribute attached providing the years missing fits were taken from.
David Klein
This is an internal function of the remulator package. It fits a user defined function to data minimizing the sum of the error squares.
minimize_least_squares(dat, initial_values, userform, ...)minimize_least_squares(dat, initial_values, userform, ...)
dat |
Array with data points to fit containing one column with sample numbers, one column with x values, and one column with y values |
initial_values |
Initial values for the parameters to be optimized over. |
userform |
Fit function for which least squares will be calaculated using the |
... |
Arguments passed on to the |
list containing fit coefficients and messages
David Klein
This function sets duplicated samples (per region, year, model, scenario) to NA. This is useful to clean your data before fitting.
mute_duplicated(data)mute_duplicated(data)
data |
MAgPIE object containing the samples to remove the duplicates from. |
Magpie object with duplicated samples set to NA.
David Klein
This function sets data of infeasible years and all years after the first infeasible
year to NA because results after an infeasible year are not meaningful. The modelstatus
has to be provided as one of the variables in the data. This function will look for the
modelstatus variable with the name given in name. If return_infes is TRUE
this function return the matrix with infeasible years instead of the data.
mute_infes(data, name = "Modelstatus (-)", feasible = 2)mute_infes(data, name = "Modelstatus (-)", feasible = 2)
data |
MAgPIE object containing the results of a MAgPIE run and the modelstatus. |
name |
String providing the name of the variable that holds the modelstatus. |
feasible |
Integer vector defining which modelstatus will be treated as feasible. |
Magpie object with either filtered model data or the modelstatus.
David Klein
This function counts data points (per region, year, scenario) and sets them to NA if the count
is less than given in n_suff. This is useful to clean your data before fitting. No fit will
be calculated where no data is available.
mute_insufficient(data, n_suff)mute_insufficient(data, n_suff)
data |
MAgPIE object containing the samples to remove the duplicates from. |
n_suff |
Minial number (default=1) of data points that will be regarded as sufficient to perform a fit. |
Magpie object with duplicated samples set to NA.
David Klein
This function sets outlier samples (per region, year, model, scenario) to NA. This is useful to
clean your data before fitting. A data point is considered an outlier if it is more than range times
of the interquartile range away from the the upper or lower end of the interquartile range
http://colingorrie.github.io/outlier-detection.html
mute_outliers(data, range = 1.5)mute_outliers(data, range = 1.5)
data |
MAgPIE object containing the samples to remove the duplicates from. |
range |
Multiplied with the interquartile range this is the maximal distance a data point may have to not be considered an outlier. |
Magpie object with duplicated samples set to NA.
David Klein
This function calculates supplycurves of multiple scenarios and plots them into one figure to compare them.
plot_compare_supplycurves(folders, pdfname = NULL)plot_compare_supplycurves(folders, pdfname = NULL)
folders |
Vector giving the paths to the fitted data (usually within the 'output/emulator' folder) |
pdfname |
If you want the figures to be compiled in a pdf provide the name of the file here |
David Klein
This function produces plot showing the raw data and the fittet curves. It saves it to a folder named after the scenario and it produces a pdf containing all the figures.
plot_curve( raw, supplycurve_commonY, supplycurve_indiviY, infes, emu_path = "emulator", fitname = "linear", create_pdf = TRUE )plot_curve( raw, supplycurve_commonY, supplycurve_indiviY, infes, emu_path = "emulator", fitname = "linear", create_pdf = TRUE )
raw |
MAgPIE object containing the same raw data that was used to calculate the fitcoefficients. |
supplycurve_commonY |
MAgPIE object containing the points of the curve (with common y limit) (output of |
supplycurve_indiviY |
MAgPIE object containing the points of the curve (with individual y limit) (output of |
infes |
MAgPIE object containing the modelstatus (optional output of |
emu_path |
Name of the folder the figures and pdf will be saved to. |
fitname |
Name that describes the fit (default: linear) and will be used for naming the output folders. |
create_pdf |
Logical indicating whether a pdf should be produced that compiles all figures. |
David Klein
This function reads model output from mif files from the provided list of folders. It also reads the GAMS modelstatus from the fulldata.gdx and appends it to the report. If more than one folder is given it combines the contents of the multiple reports into a single magpie object and returns it. If the name of an output file is provided the object is additionally stored in this file. In each of the folders there must be a report_scenname.mif, a fulldata.gdx, a spatial_header.rda, and config.Rdata.
read_and_combine(list_of_directories, outfile = NULL)read_and_combine(list_of_directories, outfile = NULL)
list_of_directories |
Vector of strings providing the folder names from which reports will be read. |
outfile |
Path to an output file which the output of the function can optionally be stored to. |
David Klein
This function considers fits with a slope less than defined in threshold flat and tries to replace them with non-flat fits from other years.
replace_flat_fits( path_to_postfit_rdata, flat = NULL, threshold = 0.01, plot = FALSE )replace_flat_fits( path_to_postfit_rdata, flat = NULL, threshold = 0.01, plot = FALSE )
path_to_postfit_rdata |
Path to the Rdata file that contains raw data, fitted data and fitcoefficients saved by the emulator function |
flat |
If you want this function to replace further fits provide their region and year here using a vector of the form c("LAM:2020,2025", "IND:2005") |
threshold |
Defines the value of the slope (b) below which fits are considered flat |
plot |
logical. If TRUE supply curves will be saved to png files |
David Klein