View source: R/create_ThetaMatrix.R
create_ThetaMatrix | R Documentation |
Create the Θ matrix with the shared uncertainties that can used as input in, e.g., AgeS_Computation and Age_OSLC14 which is used for the covariance matrix Σ (Combès \& Philippe, 2017)
create_ThetaMatrix(input, output_file = NULL, sigma_s, ...)
input |
character or data.frame (optional): input data frame or file connection
to import a CSV-file with the needed information. If nothing is provided the function returns
an input template. The argument |
output_file |
character (optional): file path for the output CSV-file, the field separator
is hard set to |
sigma_s |
numeric (required): named character with values for systematic uncertainties. Those values
are lab-specific. Can be set to |
... |
further arguments that can be passed to utils::read.table (for the CSV-file import) |
The function intends to ease the creation of the Theta matrix, which cannot be
created straight forward, e.g., base R functions such as stats::cov
.
The relationship between the covariance matrix Sigma and Theta is given with
Σ_ij = A_i * A_j * Θ_ij
For details see Combès \& Philippe, 2017 and Guérin et al. (under review).
Input modes
The function supports two different operation modes:
input
is left empty: the function returns a data.frame template that can be used as input (the option output_file
works as well)
input
is fed with a data.frame or a character
(file path), the Θ matrix is returned
Input format
The function expects either a CSV-file or a data.frame as input. To create template you can
run the function leaving the argument input
empty (see example). Please note the format
of the input table (data.frame) needs to kept as specified in the template.
The following table lists the meaning of the columns:
COLUMN | DESCRIPTION | UNIT |
SAMPLE_ID | sample name | - |
DR_BETA_K | standard error beta-dose rate K | Gy/ka |
DR_BETA_U | standard error beta-dose rate U | Gy/ka |
DR_BETA_Th | standard error beta-dose rate Th | Gy/ka |
DR_GAMMA_K | standard error gamma-dose rate K | Gy/ka |
DR_GAMMA_U | standard error gamma-dose rate U | Gy/ka |
DR_GAMMA_Th | standard error gamma-dose rate Th | Gy/ka |
DR_GAMMA_TOTAL | standard error total gamma-dose rate | Gy/ka |
DR_TOTAL | total dose rate | Gy/ka |
DR_TOTAL_X | standard error total dose rate | Gy/ka |
Note: All columns can be set to 0 or NA, no column must be left empty! If a value > 0 is provided
for DR_GAMMA_TOTAL
this value is taken and values in, e.g., DR_GAMMA_K
are discarded (set to 0)!
Systematic uncertainties
The following table provides informaton on the named argument
that can be provided via the argument sigma_s
ARGUMENT | DESCRIPTION | UNIT |
s_betaK | relative uncertainty K concentration | - |
s_betaU | relative uncertainty U concentration | - |
s_betaTh | relative uncertainty Th concentration | - |
s_gammaK | relative uncertainty K concentration | - |
s_gammaU | relative uncertainty U concentration | - |
s_gammaTh | relative uncertainty Th concentration | - |
s_gammaDR | relative uncertainty gamma-dose rate | - |
s_CAL | relative uncertainty beta-source calibration | - |
s_intDR | absolute uncertainty internal dose rate | Gy/ka |
A symetric Theta matrix or if input
is missing, a data.frame with an input
template
0.1.0
Kreutzer, S., 2022. create_ThetaMatrix(): Create Theta Matrix. Function version 0.1.0. In: Christophe, C., Philippe, A., Kreutzer, S., Guerin, G., 2022. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.2.1. https://CRAN.r-project.org/package=BayLum
Sebastian Kreutzer, IRAMAT-CRP2A, UMR 5060, CNRS-Université Bordeaux Montaigne (France), based on an 'MS Excel' sheet by Guillaume Guérin, IRAMAT-CRP2A, UMR 5060, CNRS-Université Bordeaux Montaigne (France)
Combès, B., Philippe, A., 2017. Bayesian analysis of individual and systematic multiplicative errors for estimating ages with stratigraphic constraints in optically stimulated luminescence dating. Quaternary Geochronology 39, 24–34. doi: 10.1016/j.quageo.2017.02.003
AgeS_Computation, Age_OSLC14, utils::read.table, utils::write.table
##(1) return template data.frame (no file output) create_ThetaMatrix() ## Not run: ##(2) return template as data.frame + file file_path <- tempfile(fileext = ".csv") create_ThetaMatrix(output_file = file_path ) ##NOT RUNNING EXAMPLE for sigma_s calc_ThetaMatrix(..., sigma_s = c( s_betaK = 0.010, s_betaU = 0.007, s_betaTh = 0.006, s_gammaK = 0.010, s_gammaU = 0.007, s_gammaTh = 0.006, s_gammaDR = 0.05, s_CAL = 0.020, s_intDR = 0.030)) ## End(Not run)
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