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.

AuthorRobert G. Garrett
Date of publication2016-01-07 15:40:29
MaintainerRobert G. Garrett <robert.garrett@canada.ca>
LicenseGPL-2
Version1.1.13

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...

Functions

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

Files

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

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