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rgr (version 1.1.15)

Applied Geochemistry EDA

Description

Geological Survey of Canada (GSC) functions for exploratory data analysis with applied geochemical data, with special application to the estimation of background ranges and identification of outliers, 'anomalies', to support mineral exploration and environmental studies. Additional functions are provided to support analytical data QA/QC, ANOVA for investigations of field sampling and analytical variability, and utility tasks. NOTE: function caplot() for concentration-area plots employs package 'akima', however, 'akima' is only licensed for not-for-profit use. Therefore, not-for-profit users of 'rgr' will have to independently make package 'akima' available through library(....); and use of function caplot() by for-profit users will fail.

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Version

Install

install.packages('rgr')

Monthly Downloads

235

Version

1.1.15

License

GPL-2

Maintainer

Last Published

March 5th, 2018

Functions in rgr (1.1.15)

Plot Results of Analytical Duplicate Analyses

Plot Vertical Box-and-Whisker Plots for Variables

Plot a Horizontal Boxplot or Box-and-Whisker Plot

display.ascii.o

Display the Windows Latin 1 Font Octal Table

gx.cnpplts.setup

Set Up and Display Symbolgy for function gx.cnpplts

Display Available Line Styles and Colour Codes

National Geochemical Reconnaissance survey QA/QC data

Additive Log-Ratio (alr) transformation

Prepare a Concentration-Area (C-A) Plot

Computation of Empirical Balances

Isometric Log-Ratio (ilr) transformation

Divides Data into Subsets by Factor

Inverse-logit transformation(s)

Generate and Display Fence Values

Test Data for Function ltdl.fix.df

Create a Matrix of Duplicate Pairs from Sequential Data

framework.stats

Compile Framework/Subset Summary Statistics

Analysis of Variance (ANOVA)

Centred Log-Ratio (clr) transformation

Kolmogorov-Smirnov test with ECDF Plot

Function to Display Membership Probabilities and Other Relevant Data

Cumulative Normal Percentage Probability (CPP) Plot

Estimate Variance Inflation Factosr (VIFs)

Function to Display Chi-square Plots of Mahalanobis Distances

Generate and Save Fence Values for Data Subsets

Function to Display a Saved 2-d Projection Object

Test Data for Function ltdl.fix.df

gx.mvalloc.print

Function to display the results of Multivariate Allocation

Function to Display Chi-square plots of Mahalanobis Distances

Plot a Histogram

Function to Add Fences to Chi-square Plots

Compute Probabilities for Target Recognition

Estimate the Skewness of a Data Vector

Function for Allocation on the basis of Multivariate Data

gx.mvalloc.closed

Function for Allocation on the basis of Multivariate Data for closed Compositional Data

Analysis of Variance (ANOVA), Alternate Input

Plot Vertical Box-and-Whisker Plots

Display a Graphical Matrix for Parts of a Compositional Data Set

Plot Results of Control Reference Material (CRM) Analyses

Estimate the Quantile for a Specified Fractile

Display Plots for Two Parts from a Compositional Data Set

Display Pearson Correlation Coefficients and their Significances

The Wald-Wolfowitz, ‘Runs’, Test

Function to Compute Scores on the Basis of Threshold Estimates

Function to Multi-Column Sort a Data Frame

Plot Results of Control Reference Material (CRM) Analyses Adding New Data

Function to undertake a Robust Exploratory Multivariate Data Analysis

Display Spearman Correlation Coefficients and their Significances

Function to Identify in Which Interval a Value Falls

gx.robmva.closed

Function to undertake a Robust Closed Data Multivariate EDA

Check for the Existence of a Data Frame

Display Robust ilr Stabilities and log-ratio Medians for Compositional Data

Function to compute Adjusted r-squared values

gx.symm.coords.mat

Create a Matrix of Symmetric Coordinates

Function to Save PCA Loadings and Scores as .csv files

gx.symm.coords.plot

Display a X-Y Plot, Scatterplot, of Symmetric Balances

Logit transformation

Kola Project O-horizon Soil Data

Function to Single Column Sort a Matrix or Data Frame

gx.rqpca.screeplot

Display a Scree Plot

Multiple (max 9) Cumulative Normal Probability (CPP) plots

Emprical Cumulative Distribution Function (ECDF)

ogrady.mat2open

Lithogeochemical Data Set from the O'Grady Pluton, NWT, 1970

Undertakes a Range Transformation on the Columns of a Matrix

Computation of an Orthonormal Basis Matrix

Function to Compute and Display Summary Statistics

Extracts a Subset of Rows from a Data Frame

Estimate the Fractile for a Specified Quantile

An EDA Graphical Summary

Display a Thompson-Howarth Plot of Duplicate Measurements, Alternate Input

Display a ten-line Summary Statistics Report

North American Geochemical Soil Landscapes Project QA/QC data

Computation of Symmetric Coordinates

gx.symm.coords.r

Displays a Matrix of Correlation Coefficients based on Symmetric Balances

Plot Results of Analytical Duplicate Analyses as Ratios

Function to Display Membership Probabilities

Plot Results of Analytical Duplicate Analyses as Ratios, Alternate Input

National Geochemical Reconnaissance survey QA/QC data

Prepare a Concentration-Number (C-N) Plot

Display Available Plotting Marks

Carries out a 3-Level Staggered ANOVA and Estimates Variance Components

display.rainbow

Display the Colours of the Rainbow(36) Pallette

Simulated National Geochemical Reconnaissance survey QA/QC data

framework.summary

Generate and Save Framework/Subset Summary Statistics

ANOVA to Estimate if ‘Triples’ are a Valid Subset

t-test from Means, Standard Deviations and Sample Sizes

Function to Compute and Display 2-d Projections for Data Matrices

Estimate the Common Quantiles

Displays a Count of Negative and Coded Values and NAs for a Data Frame

Function for Multivariate Graphical Adaptive Interactive Trimming

Estimate the Coefficients of the Reduced Major Axis

gx.md.gait.closed

Function for Multivariate Graphical Adaptive Interactive Trimming with Compositional Data

Plot a Symbol Map of Data Based on their Percentiles

Plot a Symbol Map of Data Based on the Tukey Boxplot

rgr_1.1.15-package

Geological Survey of Canada Applied Geochemistry EDA

Remove and Count NAs

Plot a Map of Posted Values

Plot Vertical Tukey Boxplots for Variables

Function to undertake an Exploratory Multivariate Data Analysis

Function to Plot Principal Component Analysis Loadings and Scores

Identify Vector Elements or Data Frame/Matrix Rows with NAs

Display a Thompson-Howarth Plot of Duplicate Measurements

Function to undertake an Exploratory Multivariate Data Analysis on Compositional, geochemical data

Function to Compute Weighted Sums

The Nockolds average igneous plutonic rock compositions

Lithogeochemical Data Set from the O'Grady Pluton, NWT, 1970

Sinding-Larsen Norwegian Stream Sediment Test Data Set

Function to Display PCA Loadings and Scores

Computes Summary Statistics for a NGR Report Table

North American Geochemical Soil Landscapes Project QA/QC data

Displays Summary Statistics for a Matrix or Data Frame

Function to Compute the Diameters of Proportional Symbols

Rearranges Data for Variables as Factors

Display a one-line Summary Statistics Report

Saves a NGR Report Summary Statistics Table to a .csv File

Display an Aitchison Variation Matrix for Compositional Data

Function to Perform a Kaiser Varimax Rotaion

gx.rqpca.loadplot

Function to Graphically Display PCA Loadings

Isometric Log-Ratio (ilr) transformation

Replace Negative Values Representing Less Than Detects in a Vector

Compiles a Table of Summary Statistics

Replace Negative Values Representing Less Than Detects in a Data Frame

gx.summary.groups

Displays Summary Statistics for a Variable Grouped by a Factor

Measurement Variability Test Data

Measurement Variability Test Data

An Alternate EDA Graphical Summary

Sinding-Larsen Norwegian Stream Sediment Test Data Set

Compute the Robust ilr Stability for Two Parts of a Composition

Display a Plot of Posted Values for a Third Variable

Display a Third Variable in a X-Y Plot using Proportional Symbols

An EDA Graphical and Statistical Summary

Saves an EDA Graphical and Statistical Summary

Kola Project C-horizon Soil Data

Plot a Map of Data using Proportional Symbols

Measurement Variability Test Data

Function to Demonstrate the Effect of Different Values of p

Display a Third Variable in a X-Y Plot using Tukey Boxplot Symbology

Plot Vertical Tukey Boxplots

Display a Third Variable in a X-Y Plot as Percentiles

Plot Results of Analytical Duplicate Analyses, Alternate Input