# Applied Geochemistry EDA

## Documentation for package ‘rgr’ version 1.1.15

- DESCRIPTION file.

## Help Pages

A B C D E F G I K L M N O R S T V W X Y

rgr-1.1.15-package | Geological Survey of Canada Applied Geochemistry EDA
rgr-package | Geological Survey of Canada Applied Geochemistry EDA

## -- A --

ad.plot1 | Plot Results of Analytical Duplicate Analyses
ad.plot2 | Plot Results of Analytical Duplicate Analyses, Alternate Input
ad.plot3 | Plot Results of Analytical Duplicate Analyses as Ratios
ad.plot4 | Plot Results of Analytical Duplicate Analyses as Ratios, Alternate Input
ad.test | National Geochemical Reconnaissance survey QA/QC data
alr | Additive Log-Ratio (alr) transformation
alts2dups | Create a Matrix of Duplicate Pairs from Sequential Data
anova1 | Analysis of Variance (ANOVA)
anova2 | Analysis of Variance (ANOVA), Alternate Input

## -- B --

bwplots | Plot Vertical Box-and-Whisker Plots
bwplots.by.var | Plot Vertical Box-and-Whisker Plots for Variables
bxplot | Plot a Horizontal Boxplot or Box-and-Whisker Plot

## -- C --

caplot | Prepare a Concentration-Area (C-A) Plot
cat2list | Divides Data into Subsets by Factor
clr | Centred Log-Ratio (clr) transformation
cnpplt | Cumulative Normal Percentage Probability (CPP) Plot
crm.plot | Plot Results of Control Reference Material (CRM) Analyses
crm.plot.new | Plot Results of Control Reference Material (CRM) Analyses Adding New Data
crm.test | National Geochemical Reconnaissance survey QA/QC data
crm.test.new | Simulated National Geochemical Reconnaissance survey QA/QC data
cutter | Function to Identify in Which Interval a Value Falls

## -- D --

df.test | Check for the Existence of a Data Frame
display.ascii.o | Display the Windows Latin 1 Font Octal Table
display.lty | Display Available Line Styles and Colour Codes
display.marks | Display Available Plotting Marks
display.rainbow | Display the Colours of the Rainbow(36) Pallette

## -- E --

expit | Inverse-logit transformation(s)

## -- F --

fences | Generate and Display Fence Values
fences.summary | Generate and Save Fence Values for Data Subsets
fix.test | Test Data for Function ltdl.fix.df
fix.test.asis | Test Data for Function ltdl.fix.df
framework.stats | Compile Framework/Subset Summary Statistics
framework.summary | Generate and Save Framework/Subset Summary Statistics

## -- G --

gx.2dproj | Function to Compute and Display 2-d Projections for Data Matrices
gx.2dproj.plot | Function to Display a Saved 2-d Projection Object
gx.add.chisq | Function to Add Fences to Chi-square Plots
gx.adjr2 | Function to compute Adjusted r-squared values
gx.cnpplts | Multiple (max 9) Cumulative Normal Probability (CPP) plots
gx.cnpplts.setup | Set Up and Display Symbolgy for function 'gx.cnpplts'
gx.eb | Computation of Empirical Balances
gx.ecdf | Emprical Cumulative Distribution Function (ECDF)
gx.fractile | Estimate the Fractile for a Specified Quantile
gx.hist | Plot a Histogram
gx.hypergeom | Compute Probabilities for Target Recognition
gx.ilr | Isometric Log-Ratio (ilr) transformation
gx.ks.test | Kolmogorov-Smirnov test with ECDF Plot
gx.lm.vif | Estimate Variance Inflation Factosr (VIFs)
gx.md.display | Function to Display Membership Probabilities and Other Relevant Data
gx.md.gait | Function for Multivariate Graphical Adaptive Interactive Trimming
gx.md.gait.closed | Function for Multivariate Graphical Adaptive Interactive Trimming with Compositional Data
gx.md.plot | Function to Display Chi-square Plots of Mahalanobis Distances
gx.md.plt0 | Function to Display Chi-square plots of Mahalanobis Distances
gx.md.print | Function to Display Membership Probabilities
gx.mf | Prepare a Concentration-Number (C-N) Plot
gx.mva | Function to undertake an Exploratory Multivariate Data Analysis
gx.mva.closed | Function to undertake an Exploratory Multivariate Data Analysis on Compositional, geochemical data
gx.mvalloc | 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
gx.mvalloc.print | Function to display the results of Multivariate Allocation
gx.ngr.ltdl | Displays a Count of Negative and Coded Values and NAs for a Data Frame
gx.ngr.skew | Estimate the Skewness of a Data Vector
gx.ngr.stats | Computes Summary Statistics for a NGR Report Table
gx.ngr.summary | Saves a NGR Report Summary Statistics Table to a .csv File
gx.pairs4parts | Display a Graphical Matrix for Parts of a Compositional Data Set
gx.pearson | Display Pearson Correlation Coefficients and their Significances
gx.plot2parts | Display Plots for Two Parts from a Compositional Data Set
gx.quantile | Estimate the Quantile for a Specified Fractile
gx.quantiles | Estimate the Common Quantiles
gx.rma | Estimate the Coefficients of the Reduced Major Axis
gx.robmva | Function to undertake a Robust Exploratory Multivariate Data Analysis
gx.robmva.closed | Function to undertake a Robust Closed Data Multivariate EDA
gx.rotate | Function to Perform a Kaiser Varimax Rotaion
gx.rqpca.loadplot | Function to Graphically Display PCA Loadings
gx.rqpca.plot | Function to Plot Principal Component Analysis Loadings and Scores
gx.rqpca.print | Function to Display PCA Loadings and Scores
gx.rqpca.save | Function to Save PCA Loadings and Scores as .csv files
gx.rqpca.screeplot | Display a Scree Plot
gx.runs | The Wald-Wolfowitz, 'Runs', Test
gx.scores | Function to Compute Scores on the Basis of Threshold Estimates
gx.sm | Display Robust ilr Stabilities and log-ratio Medians for Compositional Data
gx.sort | Function to Single Column Sort a Matrix or Data Frame
gx.sort.df | Function to Multi-Column Sort a Data Frame
gx.spearman | Display Spearman Correlation Coefficients and their Significances
gx.stats | Function to Compute and Display Summary Statistics
gx.subset | Extracts a Subset of Rows from a Data Frame
gx.summary | Compiles a Table of Summary Statistics
gx.summary.groups | Displays Summary Statistics for a Variable Grouped by a Factor
gx.summary.mat | Displays Summary Statistics for a Matrix or Data Frame
gx.summary1 | Display a one-line Summary Statistics Report
gx.summary2 | Display a ten-line Summary Statistics Report
gx.symm.coords | Computation of Symmetric Coordinates
gx.symm.coords.mat | Create a Matrix of Symmetric Coordinates
gx.symm.coords.plot | Display a X-Y Plot, Scatterplot, of Symmetric Balances
gx.symm.coords.r | Displays a Matrix of Correlation Coefficients based on Symmetric Balances
gx.t.test | t-test from Means, Standard Deviations and Sample Sizes
gx.triples.aov | Carries out a 3-Level Staggered ANOVA and Estimates Variance Components
gx.triples.fgx | ANOVA to Estimate if 'Triples' are a Valid Subset
gx.vm | Display an Aitchison Variation Matrix for Compositional Data
gx.youden | Estimate the Coefficients of the Reduced Major Axis

## -- I --

ilr | Isometric Log-Ratio (ilr) transformation
ilr.stab | Compute the Robust ilr Stability for Two Parts of a Composition
inset | An EDA Graphical and Statistical Summary
inset.exporter | Saves an EDA Graphical and Statistical Summary

## -- K --

kola.c | Kola Project C-horizon Soil Data
kola.o | Kola Project O-horizon Soil Data

## -- L --

logit | Logit transformation
ltdl.fix | Replace Negative Values Representing Less Than Detects in a Vector
ltdl.fix.df | Replace Negative Values Representing Less Than Detects in a Data Frame
ltdl.summary | Displays a Count of Negative and Coded Values and NAs for a Data Frame

## -- M --

map.eda7 | Plot a Symbol Map of Data Based on the Tukey Boxplot
map.eda8 | Plot a Symbol Map of Data Based on their Percentiles
map.tags | Plot a Map of Posted Values
map.z | Plot a Map of Data using Proportional Symbols
ms.data1 | Measurement Variability Test Data
ms.data2 | Measurement Variability Test Data
ms.data3 | Measurement Variability Test Data

## -- N --

Nockolds | The Nockolds average igneous plutonic rock compositions
nockolds | The Nockolds average igneous plutonic rock compositions

## -- O --

ogrady | Lithogeochemical Data Set from the O'Grady Pluton, NWT, 1970
ogrady.mat2open | Lithogeochemical Data Set from the O'Grady Pluton, NWT, 1970
orthonorm | Computation of an Orthonormal Basis Matrix

## -- R --

remove.na | Remove and Count NAs
rgr | Geological Survey of Canada Applied Geochemistry EDA
rgr-1.1.15 | Geological Survey of Canada Applied Geochemistry EDA
rgr_1.1.15 | Geological Survey of Canada Applied Geochemistry EDA
rgr_package | Geological Survey of Canada Applied Geochemistry EDA
rng | Undertakes a Range Transformation on the Columns of a Matrix

## -- S --

shape | An EDA Graphical Summary
shape.alt | An Alternate EDA Graphical Summary
sind | Sinding-Larsen Norwegian Stream Sediment Test Data Set
sind.mat2open | Sinding-Larsen Norwegian Stream Sediment Test Data Set
syms | Function to Compute the Diameters of Proportional Symbols
syms.pfunc | Function to Demonstrate the Effect of Different Values of p

## -- T --

t-test | t-test from Means, Standard Deviations and Sample Sizes
t.test | t-test from Means, Standard Deviations and Sample Sizes
tbplots | Plot Vertical Tukey Boxplots
tbplots.by.var | Plot Vertical Tukey Boxplots for Variables
thplot1 | Display a Thompson-Howarth Plot of Duplicate Measurements
thplot2 | Display a Thompson-Howarth Plot of Duplicate Measurements, Alternate Input
triples.test1 | North American Geochemical Soil Landscapes Project QA/QC data
triples.test2 | North American Geochemical Soil Landscapes Project QA/QC data

## -- V --

var2fact | Rearranges Data for Variables as Factors

## -- W --

where.na | Identify Vector Elements or Data Frame/Matrix Rows with NAs
wtd.sums | Function to Compute Weighted Sums

## -- X --

xyplot.eda7 | Display a Third Variable in a X-Y Plot using Tukey Boxplot Symbology
xyplot.eda8 | Display a Third Variable in a X-Y Plot as Percentiles
xyplot.tags | Display a Plot of Posted Values for a Third Variable
xyplot.z | Display a Third Variable in a X-Y Plot using Proportional Symbols

## -- Y --

youden | Estimate the Coefficients of the Reduced Major Axis
youden-plot | Estimate the Coefficients of the Reduced Major Axis
youden.plot | Estimate the Coefficients of the Reduced Major Axis
youden_plot | Estimate the Coefficients of the Reduced Major Axis