rgr: Applied Geochemistry EDA
Version 1.1.13

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.

Browse man pages Browse package API and functions Browse package files

AuthorRobert G. Garrett
Date of publication2016-01-07 15:40:29
MaintainerRobert G. Garrett <robert.garrett@canada.ca>
LicenseGPL-2
Version1.1.13
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("rgr")

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...

Functions

ad.plot1 Man page Source code
ad.plot2 Man page Source code
ad.plot3 Man page Source code
ad.plot4 Man page Source code
ad.test Man page
alr Man page Source code
alts2dups Man page Source code
anova1 Man page Source code
anova2 Man page Source code
bwplots Man page Source code
bwplots.by.var Man page Source code
bxplot Man page Source code
caplot Man page Source code
cat2list Man page Source code
clr Man page Source code
cnpplt Man page Source code
crm.plot Man page Source code
crm.plot.new Man page Source code
crm.test Man page
crm.test.new Man page
cutter Man page Source code
df.test Man page Source code
display.ascii.o Man page Source code
display.lty Man page Source code
display.marks Man page Source code
display.rainbow Man page Source code
expit Man page Source code
fences Man page Source code
fences.summary Man page Source code
fix.test Man page
fix.test.asis Man page
framework.stats Man page Source code
framework.summary Man page Source code
gx.2dproj Man page Source code
gx.2dproj.plot Man page Source code
gx.add.chisq Man page Source code
gx.adjr2 Man page Source code
gx.cnpplts Man page Source code
gx.cnpplts.setup Man page Source code
gx.ecdf Man page Source code
gx.fractile Man page Source code
gx.hist Man page Source code
gx.hypergeom Man page Source code
gx.ks.test Man page Source code
gx.lm.vif Man page Source code
gx.md.display Man page Source code
gx.md.gait Man page Source code
gx.md.gait.closed Man page Source code
gx.md.plot Man page Source code
gx.md.plt0 Man page Source code
gx.md.print Man page Source code
gx.mf Man page Source code
gx.mva Man page Source code
gx.mva.closed Man page Source code
gx.mvalloc Man page Source code
gx.mvalloc.closed Man page Source code
gx.mvalloc.print Man page Source code
gx.ngr.ltdl Man page Source code
gx.ngr.skew Man page Source code
gx.ngr.stats Man page Source code
gx.ngr.summary Man page Source code
gx.pairs4parts Man page Source code
gx.pearson Man page Source code
gx.plot2parts Man page Source code
gx.quantile Man page Source code
gx.rma Man page Source code
gx.robmva Man page Source code
gx.robmva.closed Man page Source code
gx.rotate Man page Source code
gx.rqpca.loadplot Man page Source code
gx.rqpca.plot Man page Source code
gx.rqpca.print Man page Source code
gx.rqpca.save Man page Source code
gx.rqpca.screeplot Man page Source code
gx.runs Man page Source code
gx.scores Man page Source code
gx.sm Man page Source code
gx.sort Man page Source code
gx.sort.df Man page Source code
gx.spearman Man page Source code
gx.stats Man page Source code
gx.subset Man page Source code
gx.summary Man page Source code
gx.summary.groups Man page Source code
gx.summary.mat Man page Source code
gx.summary1 Man page Source code
gx.summary2 Man page Source code
gx.t.test Man page Source code
gx.triples.aov Man page Source code
gx.triples.fgx Man page Source code
gx.vm Man page Source code
gx.youden Man page
ilr Man page Source code
ilr.stab Man page Source code
inset Man page Source code
inset.exporter Man page Source code
kola.c Man page
kola.o Man page
logit Man page Source code
ltdl.fix Man page Source code
ltdl.fix.df Man page Source code
map.eda7 Man page Source code
map.eda8 Man page Source code
map.tags Man page Source code
map.z Man page Source code
ms.data1 Man page
ms.data2 Man page
ms.data3 Man page
ogrady Man page
ogrady.mat2open Man page
orthonorm Man page Source code
remove.na Man page Source code
rgr Man page
rgr-1.1.13 Man page
rgr-1.1.13-package Man page
rgr-package Man page
rgr_1.1.13 Man page
rgr_package Man page
rng Man page Source code
shape Man page Source code
shape.alt Man page Source code
sind Man page
sind.mat2open Man page
syms Man page Source code
syms.pfunc Man page Source code
t-test Man page
t.test Man page
tbplots Man page Source code
tbplots.by.var Man page Source code
thplot1 Man page Source code
thplot2 Man page Source code
triples.test1 Man page
triples.test2 Man page
var2fact Man page Source code
where.na Man page Source code
wtd.sums Man page Source code
xyplot.eda7 Man page Source code
xyplot.eda8 Man page Source code
xyplot.tags Man page Source code
xyplot.z Man page Source code
youden Man page
youden-plot Man page
youden.plot Man page
youden_plot Man page

Files

inst
inst/doc
inst/doc/rgr_func_list_1-1-13.pdf
inst/doc/What_is_in_rgr_1-1-13.pdf
inst/doc/rgr_Overview_1-1-13.pdf
NAMESPACE
data
data/ogrady.rda
data/crm.test.rda
data/crm.test.new.rda
data/ms.data3.rda
data/ms.data1.rda
data/triples.test2.rda
data/ad.test.rda
data/ogrady.mat2open.rda
data/sind.rda
data/ms.data2.rda
data/kola.o.rda
data/fix.test.rda
data/kola.c.rda
data/fix.test.asis.rda
data/sind.mat2open.rda
data/triples.test1.rda
R
R/gx.spearman.R
R/display.marks.R
R/gx.summary.R
R/gx.rotate.R
R/bwplots.R
R/gx.hypergeom.R
R/xyplot.tags.R
R/gx.sort.df.R
R/thplot2.R
R/gx.md.plt0.R
R/rng.R
R/gx.2dproj.plot.R
R/cnpplt.R
R/gx.mvalloc.R
R/framework.stats.R
R/gx.cnpplts.setup.R
R/tbplots.R
R/caplot.R
R/anova1.R
R/gx.ngr.ltdl.R
R/gx.runs.R
R/map.eda8.R
R/logit.R
R/syms.pfunc.R
R/gx.md.display.R
R/ltdl.fix.R
R/var2fact.R
R/tbplots.by.var.R
R/display.lty.R
R/gx.hist.R
R/gx.ks.test.R
R/gx.ngr.stats.R
R/gx.cnpplts.R
R/gx.add.chisq.R
R/gx.md.plot.R
R/alts2dups.R
R/gx.fractile.R
R/xyplot.eda8.R
R/gx.scores.R
R/gx.triples.aov.R
R/gx.triples.fgx.R
R/cutter.R
R/df.test.R
R/gx.sort.R
R/ad.plot1.R
R/ad.plot2.R
R/shape.R
R/gx.quantile.R
R/fences.R
R/wtd.sums.R
R/framework.summary.R
R/gx.rqpca.screeplot.R
R/cat2list.R
R/gx.plot2parts.R
R/gx.rqpca.loadplot.R
R/gx.t.test.R
R/ltdl.fix.df.R
R/ad.plot3.R
R/gx.rqpca.plot.R
R/gx.summary.mat.R
R/remove.na.R
R/gx.rma.R
R/ad.plot4.R
R/map.z.R
R/syms.R
R/map.tags.R
R/where.na.R
R/display.ascii.o.R
R/gx.adjr2.R
R/clr.R
R/crm.plot.new.R
R/inset.R
R/gx.2dproj.R
R/xyplot.eda7.R
R/gx.summary2.R
R/gx.md.gait.R
R/bxplot.R
R/gx.summary1.R
R/map.eda7.R
R/shape.alt.R
R/gx.robmva.R
R/gx.mva.closed.R
R/gx.rqpca.print.R
R/gx.mvalloc.closed.R
R/orthonorm.R
R/gx.mf.R
R/gx.md.print.R
R/inset.exporter.R
R/expit.R
R/gx.lm.vif.R
R/gx.ecdf.R
R/gx.mvalloc.print.R
R/gx.stats.R
R/gx.robmva.closed.R
R/thplot1.R
R/gx.md.gait.closed.R
R/gx.sm.R
R/bwplots.by.var.R
R/alr.R
R/gx.pairs4parts.R
R/display.rainbow.R
R/ilr.R
R/gx.pearson.R
R/gx.subset.R
R/gx.rqpca.save.R
R/gx.mva.R
R/ilr.stab.R
R/fences.summary.R
R/gx.ngr.skew.R
R/gx.ngr.summary.R
R/anova2.R
R/gx.summary.groups.R
R/gx.vm.R
R/xyplot.z.R
R/crm.plot.R
MD5
DESCRIPTION
man
man/gx.sm.Rd
man/display.marks.Rd
man/map.tags.Rd
man/gx.lm.vif.Rd
man/gx.rqpca.screeplot.Rd
man/gx.summary1.Rd
man/alts2dups.Rd
man/gx.ngr.summary.Rd
man/var2fact.Rd
man/triples.test1.Rd
man/xyplot.eda8.Rd
man/gx.ngr.skew.Rd
man/gx.hypergeom.Rd
man/xyplot.z.Rd
man/gx.ngr.stats.Rd
man/display.lty.Rd
man/caplot.Rd
man/fix.test.Rd
man/gx.stats.Rd
man/ogrady.Rd
man/gx.md.gait.closed.Rd
man/gx.md.plot.Rd
man/gx.mva.Rd
man/xyplot.eda7.Rd
man/display.ascii.o.Rd
man/gx.triples.fgx.Rd
man/gx.md.plt0.Rd
man/sind.mat2open.Rd
man/crm.test.new.Rd
man/gx.robmva.Rd
man/tbplots.by.var.Rd
man/gx.cnpplts.Rd
man/syms.pfunc.Rd
man/framework.summary.Rd
man/alr.Rd
man/rng.Rd
man/ltdl.fix.df.Rd
man/gx.vm.Rd
man/gx.mvalloc.print.Rd
man/gx.pearson.Rd
man/gx.rqpca.plot.Rd
man/gx.summary2.Rd
man/remove.na.Rd
man/cnpplt.Rd
man/clr.Rd
man/gx.ngr.ltdl.Rd
man/gx.rma.Rd
man/gx.spearman.Rd
man/tbplots.Rd
man/crm.plot.Rd
man/thplot1.Rd
man/anova2.Rd
man/ad.plot3.Rd
man/display.rainbow.Rd
man/gx.plot2parts.Rd
man/crm.test.Rd
man/gx.mf.Rd
man/ilr.Rd
man/fences.Rd
man/bwplots.Rd
man/bwplots.by.var.Rd
man/map.eda8.Rd
man/fix.test.asis.Rd
man/wtd.sums.Rd
man/gx.summary.Rd
man/kola.c.Rd
man/map.z.Rd
man/gx.adjr2.Rd
man/anova1.Rd
man/gx.t.test.Rd
man/expit.Rd
man/logit.Rd
man/gx.scores.Rd
man/gx.md.gait.Rd
man/rgr_1.1.13-package.Rd
man/inset.Rd
man/shape.alt.Rd
man/gx.fractile.Rd
man/gx.robmva.closed.Rd
man/gx.runs.Rd
man/framework.stats.Rd
man/gx.mva.closed.Rd
man/gx.mvalloc.Rd
man/ltdl.fix.Rd
man/inset.exporter.Rd
man/syms.Rd
man/fences.summary.Rd
man/bxplot.Rd
man/gx.cnpplts.setup.Rd
man/ad.plot4.Rd
man/ms.data1.Rd
man/gx.hist.Rd
man/gx.rotate.Rd
man/gx.quantile.Rd
man/shape.Rd
man/thplot2.Rd
man/gx.rqpca.loadplot.Rd
man/gx.ecdf.Rd
man/ogrady.mat2open.Rd
man/gx.pairs4parts.Rd
man/gx.rqpca.save.Rd
man/crm.plot.new.Rd
man/triples.test2.Rd
man/ms.data2.Rd
man/gx.subset.Rd
man/cat2list.Rd
man/orthonorm.Rd
man/gx.add.chisq.Rd
man/map.eda7.Rd
man/gx.triples.aov.Rd
man/kola.o.Rd
man/gx.summary.mat.Rd
man/gx.sort.df.Rd
man/ilr.stab.Rd
man/where.na.Rd
man/sind.Rd
man/ad.plot2.Rd
man/gx.md.print.Rd
man/gx.2dproj.plot.Rd
man/gx.md.display.Rd
man/gx.ks.test.Rd
man/gx.2dproj.Rd
man/gx.rqpca.print.Rd
man/ad.test.Rd
man/cutter.Rd
man/gx.sort.Rd
man/ms.data3.Rd
man/ad.plot1.Rd
man/df.test.Rd
man/xyplot.tags.Rd
man/gx.mvalloc.closed.Rd
man/gx.summary.groups.Rd
rgr documentation built on May 19, 2017, 5:56 p.m.