Using Itrax Data in R
Preface
0.1
The itraxR Package
0.2
Prerequisites
0.3
Example Data
0.4
Utility Data
0.5
Citing This Work
1
Data Structure
1.1
Metadata
1.2
XRF Data
1.3
Optical Images
1.4
Radiographic Images
1.5
Magnetic Susceptability
2
Importing Data
2.1
Metadata
2.2
XRF Data
2.2.1
Processed Data
2.2.2
Joining XRF Data
2.2.3
Raw Data
2.3
Optical Images
2.4
Radiographic Images
2.5
Importing Everything
3
Tidying Data
3.1
Low Count Rates
3.2
Model Errors (MSE)
3.3
Surface Slope
3.4
High Argon
3.5
Combining “Validity” Flags
3.6
Tube current
3.7
Dead Time
3.8
Correcting for Water Content
3.9
Correcting Grain Size
3.10
Uncertainties
3.11
Noisy Data
3.12
Reversing Data
3.13
Visualising Raw Data
4
Plotting
4.1
Plotting XRF Data
4.2
Plotting Images
4.3
Combining Images with XRF Data
5
Transforming Data
5.1
Ratios and Normalisation
5.2
Running Mean and Other Window Functions
6
Multivariate Methods
6.1
Preparing Data for Multivariate Data Analysis
6.2
Principal Component Analysis
6.3
Using
ordr
for PCA
6.4
Unconstrained Cluster Analysis
6.5
Constrained Cluster Analysis
7
Calibrating Data
7.1
Suitable Methods
7.2
Selecting Samples
7.3
Preparing Data
7.4
Linear Methods
7.5
Log-Ratio Methods
8
Exporting Data
8.1
Exporting Peak Area Data
8.2
Creating
sumspectra.spe
Files
References
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Using Itrax Data in R
7.5
Log-Ratio Methods
We often find that log-ratio methods work better.