rgr: Applied Geochemistry EDA

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.

Author
Robert G. Garrett
Date of publication
2016-01-07 15:40:29
Maintainer
Robert G. Garrett <robert.garrett@canada.ca>
License
GPL-2
Version
1.1.13

View on CRAN

Man pages

ad.plot1
Plot Results of Analytical Duplicate Analyses
ad.plot2
Plot Results of Analytical Duplicate Analyses, Alternate...
ad.plot3
Plot Results of Analytical Duplicate Analyses as Ratios
ad.plot4
Plot Results of Analytical Duplicate Analyses as Ratios,...
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
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
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...
crm.test
National Geochemical Reconnaissance survey QA/QC data
crm.test.new
Simulated National Geochemical Reconnaissance survey QA/QC...
cutter
Function to Identify in Which Interval a Value Falls
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
expit
Inverse-logit transformation(s)
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
gx.2dproj
Function to Compute and Display 2-d Projections for Data...
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.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.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...
gx.md.gait
Function for Multivariate Graphical Adaptive Interactive...
gx.md.gait.closed
Function for Multivariate Graphical Adaptive Interactive...
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...
gx.mva.closed
Function to undertake an Exploratory Multivariate 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...
gx.mvalloc.print
Function to display the results of Multivariate Allocation
gx.ngr.ltdl
Displays a Count of Negative Values and NAs for a Matrix or...
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...
gx.pearson
Display Pearson Correlation Coefficients and their...
gx.plot2parts
Display Plots for Two Parts from a Compositional Data Set
gx.quantile
Estimate the Quantile for a Specified Fractile
gx.rma
Estimate the Coefficients of the Reduced Major Axis
gx.robmva
Function to undertake a Robust Exploratory Multivariate Data...
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...
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...
gx.sm
Display Robust ilr Stabilities and log-ratio Medians for...
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...
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.summary1
Display a one-line Summary Statistics Report
gx.summary2
Display a ten-line Summary Statistics Report
gx.summary.groups
Displays Summary Statistics for a Variable Grouped by a...
gx.summary.mat
Displays Summary Statistics for a Matrix or Data Frame
gx.triples.aov
Carries out a 3-Level Staggered ANOVA and Estimates Variance...
gx.triples.fgx
ANOVA to Estimate if 'Triples' are a Valid Subset
gx.t.test
t-test from Means, Standard Deviations and Sample Sizes
gx.vm
Display an Aitchison Variation Matrix for Compositional Data
ilr
Isometric Log-Ratio (ilr) transformation
ilr.stab
Compute the Robust ilr Stability for Two Parts of a...
inset
An EDA Graphical and Statistical Summary
inset.exporter
Saves an EDA Graphical and Statistical Summary
kola.c
Kola Project C-horizon Soil Data
kola.o
Kola Project O-horizon Soil Data
logit
Logit transformation
ltdl.fix
Replace Negative Values Representing Less Than Detects in a...
ltdl.fix.df
Replace Negative Values Representing Less Than Detects in a...
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
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
remove.na
Remove and Count NAs
rgr_1.1.13-package
Geological Survey of Canada Applied Geochemistry EDA
rng
Undertakes a Range Transformation on the Columns of a Matrix
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
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,...
triples.test1
North American Geochemical Soil Landscapes Project QA/QC data
triples.test2
North American Geochemical Soil Landscapes Project QA/QC data
var2fact
Rearranges Data for Variables as Factors
where.na
Identify Vector Elements or Data Frame/Matrix Rows with NAs
wtd.sums
Function to Compute Weighted Sums
xyplot.eda7
Display a Third Variable in a X-Y Plot using Tukey Boxplot...
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...

Files in this package

rgr
rgr/inst
rgr/inst/doc
rgr/inst/doc/rgr_func_list_1-1-13.pdf
rgr/inst/doc/What_is_in_rgr_1-1-13.pdf
rgr/inst/doc/rgr_Overview_1-1-13.pdf
rgr/NAMESPACE
rgr/data
rgr/data/ogrady.rda
rgr/data/crm.test.rda
rgr/data/crm.test.new.rda
rgr/data/ms.data3.rda
rgr/data/ms.data1.rda
rgr/data/triples.test2.rda
rgr/data/ad.test.rda
rgr/data/ogrady.mat2open.rda
rgr/data/sind.rda
rgr/data/ms.data2.rda
rgr/data/kola.o.rda
rgr/data/fix.test.rda
rgr/data/kola.c.rda
rgr/data/fix.test.asis.rda
rgr/data/sind.mat2open.rda
rgr/data/triples.test1.rda
rgr/R
rgr/R/gx.spearman.R
rgr/R/display.marks.R
rgr/R/gx.summary.R
rgr/R/gx.rotate.R
rgr/R/bwplots.R
rgr/R/gx.hypergeom.R
rgr/R/xyplot.tags.R
rgr/R/gx.sort.df.R
rgr/R/thplot2.R
rgr/R/gx.md.plt0.R
rgr/R/rng.R
rgr/R/gx.2dproj.plot.R
rgr/R/cnpplt.R
rgr/R/gx.mvalloc.R
rgr/R/framework.stats.R
rgr/R/gx.cnpplts.setup.R
rgr/R/tbplots.R
rgr/R/caplot.R
rgr/R/anova1.R
rgr/R/gx.ngr.ltdl.R
rgr/R/gx.runs.R
rgr/R/map.eda8.R
rgr/R/logit.R
rgr/R/syms.pfunc.R
rgr/R/gx.md.display.R
rgr/R/ltdl.fix.R
rgr/R/var2fact.R
rgr/R/tbplots.by.var.R
rgr/R/display.lty.R
rgr/R/gx.hist.R
rgr/R/gx.ks.test.R
rgr/R/gx.ngr.stats.R
rgr/R/gx.cnpplts.R
rgr/R/gx.add.chisq.R
rgr/R/gx.md.plot.R
rgr/R/alts2dups.R
rgr/R/gx.fractile.R
rgr/R/xyplot.eda8.R
rgr/R/gx.scores.R
rgr/R/gx.triples.aov.R
rgr/R/gx.triples.fgx.R
rgr/R/cutter.R
rgr/R/df.test.R
rgr/R/gx.sort.R
rgr/R/ad.plot1.R
rgr/R/ad.plot2.R
rgr/R/shape.R
rgr/R/gx.quantile.R
rgr/R/fences.R
rgr/R/wtd.sums.R
rgr/R/framework.summary.R
rgr/R/gx.rqpca.screeplot.R
rgr/R/cat2list.R
rgr/R/gx.plot2parts.R
rgr/R/gx.rqpca.loadplot.R
rgr/R/gx.t.test.R
rgr/R/ltdl.fix.df.R
rgr/R/ad.plot3.R
rgr/R/gx.rqpca.plot.R
rgr/R/gx.summary.mat.R
rgr/R/remove.na.R
rgr/R/gx.rma.R
rgr/R/ad.plot4.R
rgr/R/map.z.R
rgr/R/syms.R
rgr/R/map.tags.R
rgr/R/where.na.R
rgr/R/display.ascii.o.R
rgr/R/gx.adjr2.R
rgr/R/clr.R
rgr/R/crm.plot.new.R
rgr/R/inset.R
rgr/R/gx.2dproj.R
rgr/R/xyplot.eda7.R
rgr/R/gx.summary2.R
rgr/R/gx.md.gait.R
rgr/R/bxplot.R
rgr/R/gx.summary1.R
rgr/R/map.eda7.R
rgr/R/shape.alt.R
rgr/R/gx.robmva.R
rgr/R/gx.mva.closed.R
rgr/R/gx.rqpca.print.R
rgr/R/gx.mvalloc.closed.R
rgr/R/orthonorm.R
rgr/R/gx.mf.R
rgr/R/gx.md.print.R
rgr/R/inset.exporter.R
rgr/R/expit.R
rgr/R/gx.lm.vif.R
rgr/R/gx.ecdf.R
rgr/R/gx.mvalloc.print.R
rgr/R/gx.stats.R
rgr/R/gx.robmva.closed.R
rgr/R/thplot1.R
rgr/R/gx.md.gait.closed.R
rgr/R/gx.sm.R
rgr/R/bwplots.by.var.R
rgr/R/alr.R
rgr/R/gx.pairs4parts.R
rgr/R/display.rainbow.R
rgr/R/ilr.R
rgr/R/gx.pearson.R
rgr/R/gx.subset.R
rgr/R/gx.rqpca.save.R
rgr/R/gx.mva.R
rgr/R/ilr.stab.R
rgr/R/fences.summary.R
rgr/R/gx.ngr.skew.R
rgr/R/gx.ngr.summary.R
rgr/R/anova2.R
rgr/R/gx.summary.groups.R
rgr/R/gx.vm.R
rgr/R/xyplot.z.R
rgr/R/crm.plot.R
rgr/MD5
rgr/DESCRIPTION
rgr/man
rgr/man/gx.sm.Rd
rgr/man/display.marks.Rd
rgr/man/map.tags.Rd
rgr/man/gx.lm.vif.Rd
rgr/man/gx.rqpca.screeplot.Rd
rgr/man/gx.summary1.Rd
rgr/man/alts2dups.Rd
rgr/man/gx.ngr.summary.Rd
rgr/man/var2fact.Rd
rgr/man/triples.test1.Rd
rgr/man/xyplot.eda8.Rd
rgr/man/gx.ngr.skew.Rd
rgr/man/gx.hypergeom.Rd
rgr/man/xyplot.z.Rd
rgr/man/gx.ngr.stats.Rd
rgr/man/display.lty.Rd
rgr/man/caplot.Rd
rgr/man/fix.test.Rd
rgr/man/gx.stats.Rd
rgr/man/ogrady.Rd
rgr/man/gx.md.gait.closed.Rd
rgr/man/gx.md.plot.Rd
rgr/man/gx.mva.Rd
rgr/man/xyplot.eda7.Rd
rgr/man/display.ascii.o.Rd
rgr/man/gx.triples.fgx.Rd
rgr/man/gx.md.plt0.Rd
rgr/man/sind.mat2open.Rd
rgr/man/crm.test.new.Rd
rgr/man/gx.robmva.Rd
rgr/man/tbplots.by.var.Rd
rgr/man/gx.cnpplts.Rd
rgr/man/syms.pfunc.Rd
rgr/man/framework.summary.Rd
rgr/man/alr.Rd
rgr/man/rng.Rd
rgr/man/ltdl.fix.df.Rd
rgr/man/gx.vm.Rd
rgr/man/gx.mvalloc.print.Rd
rgr/man/gx.pearson.Rd
rgr/man/gx.rqpca.plot.Rd
rgr/man/gx.summary2.Rd
rgr/man/remove.na.Rd
rgr/man/cnpplt.Rd
rgr/man/clr.Rd
rgr/man/gx.ngr.ltdl.Rd
rgr/man/gx.rma.Rd
rgr/man/gx.spearman.Rd
rgr/man/tbplots.Rd
rgr/man/crm.plot.Rd
rgr/man/thplot1.Rd
rgr/man/anova2.Rd
rgr/man/ad.plot3.Rd
rgr/man/display.rainbow.Rd
rgr/man/gx.plot2parts.Rd
rgr/man/crm.test.Rd
rgr/man/gx.mf.Rd
rgr/man/ilr.Rd
rgr/man/fences.Rd
rgr/man/bwplots.Rd
rgr/man/bwplots.by.var.Rd
rgr/man/map.eda8.Rd
rgr/man/fix.test.asis.Rd
rgr/man/wtd.sums.Rd
rgr/man/gx.summary.Rd
rgr/man/kola.c.Rd
rgr/man/map.z.Rd
rgr/man/gx.adjr2.Rd
rgr/man/anova1.Rd
rgr/man/gx.t.test.Rd
rgr/man/expit.Rd
rgr/man/logit.Rd
rgr/man/gx.scores.Rd
rgr/man/gx.md.gait.Rd
rgr/man/rgr_1.1.13-package.Rd
rgr/man/inset.Rd
rgr/man/shape.alt.Rd
rgr/man/gx.fractile.Rd
rgr/man/gx.robmva.closed.Rd
rgr/man/gx.runs.Rd
rgr/man/framework.stats.Rd
rgr/man/gx.mva.closed.Rd
rgr/man/gx.mvalloc.Rd
rgr/man/ltdl.fix.Rd
rgr/man/inset.exporter.Rd
rgr/man/syms.Rd
rgr/man/fences.summary.Rd
rgr/man/bxplot.Rd
rgr/man/gx.cnpplts.setup.Rd
rgr/man/ad.plot4.Rd
rgr/man/ms.data1.Rd
rgr/man/gx.hist.Rd
rgr/man/gx.rotate.Rd
rgr/man/gx.quantile.Rd
rgr/man/shape.Rd
rgr/man/thplot2.Rd
rgr/man/gx.rqpca.loadplot.Rd
rgr/man/gx.ecdf.Rd
rgr/man/ogrady.mat2open.Rd
rgr/man/gx.pairs4parts.Rd
rgr/man/gx.rqpca.save.Rd
rgr/man/crm.plot.new.Rd
rgr/man/triples.test2.Rd
rgr/man/ms.data2.Rd
rgr/man/gx.subset.Rd
rgr/man/cat2list.Rd
rgr/man/orthonorm.Rd
rgr/man/gx.add.chisq.Rd
rgr/man/map.eda7.Rd
rgr/man/gx.triples.aov.Rd
rgr/man/kola.o.Rd
rgr/man/gx.summary.mat.Rd
rgr/man/gx.sort.df.Rd
rgr/man/ilr.stab.Rd
rgr/man/where.na.Rd
rgr/man/sind.Rd
rgr/man/ad.plot2.Rd
rgr/man/gx.md.print.Rd
rgr/man/gx.2dproj.plot.Rd
rgr/man/gx.md.display.Rd
rgr/man/gx.ks.test.Rd
rgr/man/gx.2dproj.Rd
rgr/man/gx.rqpca.print.Rd
rgr/man/ad.test.Rd
rgr/man/cutter.Rd
rgr/man/gx.sort.Rd
rgr/man/ms.data3.Rd
rgr/man/ad.plot1.Rd
rgr/man/df.test.Rd
rgr/man/xyplot.tags.Rd
rgr/man/gx.mvalloc.closed.Rd
rgr/man/gx.summary.groups.Rd