Menu GCDkit. GCDkit I. Loads ASCII file or imports clipboard (e.g. data copied from Excel) Data are separated by tabulators, commas or semicolons The

MenuGCDkit

GCDkit I.GCDkit I.Loads ASCII file or imports clipboard

(e.g. data copied from Excel)

• Data are separated by tabulators,

commas or semicolons

• The 1st line contains unique labels

for the data columns (e.g. ‘SiO2’,

‘Fe2O3’, ‘Rb’, ‘Nd’),

the 1st column unique sample IDs

• Decimal commas are converted to

decimal points if appropriate

• Missing values are allowed

anywhere in the data file; as such

are interpreted also values ≤ 0, or

any of ‘NA’,‘N.A.’,‘-’, ‘b.d.’, ‘bd’

GCDkit I.GCDkit I.• Total iron as ferrous oxide:

‘FeOt’ or ‘FeO*’

• Structurally bound water: ‘H2O.PLUS’, ‘H2O+’,

‘H2OPLUS’ or ‘H2O_PLUS’

• Column ‘Symbol’ (if any): plotting

symbols (as codes or single

characters)

• A column whose name starts with

‘Col’ (if any): code for colour of

the symbols

• Avoid special symbols in the

column names, and accented

characters throughout the file!

GCDkit I.GCDkit I.Appends new samples (= new rows) to

the data in memory.

• The structures of both data files are,

as much as possible, matched.

• If necessary, empty columns are

introduced to either of the data sets.

File 1

File 2

GCDkit I.GCDkit I.Adds new data (columns) to the

samples stored in the memory.

• No new samples are introduced that

would occur solely in one of the

files.

File 1 File 2

GCDkit I.GCDkit I.Saves the modified data set stored in

memory under a specified filename.

• The data can be retrieved again into

GCDkit using the ‘Load data

file’ command.

GCDkit I.GCDkit I.Information about the current dataset:

• levels and frequencies for each of

the labels,

• list + no. of numeric columns,

• for each of the numeric variables

no. of available values,

• total no. of samples,

• list of samples in the selected subset

(or all samples if none is defined),

• current grouping information.

GCDkit I.GCDkit I.Prints a cross table (contingency table)

for 1-3 labels and plots

corresponding barplots.

Contingency tablesContingency tables

An example of a contingency

table involving two labels

GCDkit I.GCDkit I.Restricts the textual output to an

absolute minimum

(which is useful for large data files)

GCDkit II.GCDkit II.

GCDkit II.GCDkit II.

Data handling

Intermezzo 1: Specifying a variable in GCDkitIntermezzo 1: Specifying a variable in GCDkit

1. Enter complete name of a variable (e.g., ‘SiO2’)

2. Type only part of the variable name. If the result is ambiguous, the desired variable has to be selected from the list of the multiple matches by mouse (applies also for empty patterns)

3. Specify the variable sequence number (2 for the second one).

4. Often if a formula is entered, the results are interpreted and computed by the calculation core.

S

Intermezzo 2: Formulae & calculation coreIntermezzo 2: Formulae & calculation core

Formula can involve any combination of names of existing numerical columns,

with the constants, brackets, arithmetic operators +-*/^ and R functions.

• (Na2O+K2O)/CaO

• Rb^2

• log10(Sr)

• mean(SiO2)/10

sqrt square root

log, log10 natural/common logarithm

exp exponential function

sin, cos, tan trigonometric functions

min minimum

max maximum

length number of elements/cases

sum sum of the elements

mean mean of the elements

prod product of the elements

Examples of valid formulae:

Data handling I.Data handling I.Displays a single numeric variable or

a result of a calculation

# Works as a simple R shell too!

• summary(Rb,na.rm=T)

• cbind(SiO2/2,TiO2,Na2O+K2O)

• cbind(major)

• hist(SiO2,col="red")

• boxplot(Rb~factor(groups))

Intermezzo 3: Specifying multiple variablesIntermezzo 3: Specifying multiple variables

1. List of column name(s), in full,

separated by commas

2. Sequence numbers of variables

or their ranges (1,10:15)

3. Name of a built-in list, such as

‘LILE’, ‘REE’, ‘major’ and

‘HFSE’ or their combinations

with the column names

4. User-defined list = simple character vector. Currently only a single, stand-

alone user-defined list can be employed as a search criterion

5. For empty patterns, the correct name(s) has to be selected by mouse click(s)

(± Shift ± Ctrl) from the list of the available variables

Intermezzo 3: Specifying multiple variables - examplesIntermezzo 3: Specifying multiple variables - examples

1. Search pattern = majorSiO2, TiO2, Al2O3, Fe2O3, FeO, MnO, MgO, CaO, Na2O, K2O, P2O5

2. Search pattern = LILERb, Sr, Ba, K, Cs, Li

3. Search pattern = HFSENb, Zr, Hf, Ti, Ta, La, Ce, Y, Ga, Sc, Th, U

4. Search pattern = REELa, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu

5. Search pattern = 1:5,7Numeric data columns number 1, 2, ...5, 7

6. # User-defined listmy.elems<-c("Rb","Sr","Ba")Search pattern = my.elemsRb, Sr, Ba

Intermezzo 4: Searching and subsettingIntermezzo 4: Searching and subsetting

1. The search pattern is first tested whether it could be interpreted as a query of the sample name(s). The list of exact sample names separated by commas is allowed.

2. The pattern is assumed to correspond to a selection of sample sequence numbers.

3. Lastly the search pattern is interpreted as a Boolean condition.

4. Entering empty pattern usually

returns all the samples in the data

set.

Intermezzo 4: Searching and subsetting - examplesIntermezzo 4: Searching and subsetting - examples

1. By sample name1. By sample name

1. Search pattern = ozSamples with names Koz, KozD-5, Roz-5 …

2. Search pattern = Bl-1,Bl-2,Koz-3Samples with names Bl-1,Bl-2,Koz-3

3. Regular expressions (advanced technique, see later)


2. By sample range2. By sample range

1. Search pattern = 1:5# First to fifth samples in the data set

2. Search pattern = 1,10# First and tenth samples

3. Search pattern = 1:5, 10:11, 25# Samples number 1, 2, ...5, 10, 11, 25

In this case the search pattern is treated as a selection of sample sequence numbers

(effectively a list separated by commas that may also contain ranges

expressed by colons).


3. By Boolean conditions3. By Boolean conditions

Patterns may employ variable names and in R

common comparison operators (see Table).

• The character strings should be quoted.

• The conditions can be combined together

by logical and, or and brackets.

• Logical and can be expressed as

‘.and.’ ‘.AND.’ ‘&’

• Logical or can be expressed as

‘.or.’ ‘.OR.’ ‘|’

• Regular expressions can be employed to

search in the textual labels.

(advanced technique, see later )

< lower than

> greater than

<= lower or equal to

>= greater or equal to

=

==

equal to

!= not equal to


3. By Boolean conditions3. By Boolean conditions

1. Search pattern: Intrusion="Rhum“# Finds all analyses from Rhum

2. Search pattern: Intrusion="Rhum".and.SiO2>65Search pattern: Intrusion="Rhum".AND.SiO2>65Search pattern: Intrusion="Rhum"&SiO2>65# All analyses from Rhum with silica greater than 65# (all three expressions are equivalent)

3. Search pattern: MgO>10&(Locality="Skye"|Locality="Islay")# All analyses from Skye or Islay with MgO greater than 10

Displays specified combination of

numeric variable(s) and/or labels for

selected range of samples.

• So far only names of existing

numeric data columns and not

formulae can be handled.

Data handling I.Data handling I.

Data handling I.Data handling I.Deletes a single numeric variable or

a label.

• Some fields are mandatory and

cannot be removed.

Data handling I.Data handling I.Appends an empty numeric data column

or new label to the current data set.

Data handling I.Data handling I.Simultaneous editing of all labels for

individual samples using a

spreadsheet-like interface.

• When the desired changes have

been performed, close button is to

be clicked.



Global replacement of selected discrete

values (levels) for a given label.

Data handling I.Data handling I.Simultaneous editing of all numeric

data using a spreadsheet-like

interface.

Intermezzo 5: Regular expressionsIntermezzo 5: Regular expressions

Many enquiries in the GCDkit employ regular expressions. This is a quite powerful searching mechanism more familiar to people working in Unix.

• Most characters, including letters and digits, are regular expressions that match themselves.

• Dot ‘.’ matches any character.

• Metacharacters with a special meaning‘?’ ‘+’ ‘{’ ‘} ’ ‘|’ ‘(’ ‘) ’)must be preceded by a backslash.

• Brackets can be used to group subexpressions.


Metacharacter Matches

. Any character

x Any instance of x

^ Beginning of the expression

$ End of the expression

[ xy] Any of the characters given in square brackets

[ x-y] Range of the characters given in square brackets

x|y A logical OR operator (will match an instance of x or y)


Repetition operator

The preceding item will be matched

? At most once (i.e. is optional)

* Zero or more times

+ One or more times

{n} Exactly n times

{n,} At least n times

{n,m} At least n times, but not more than m times

Intermezzo 5: Regular expressions - examplesIntermezzo 5: Regular expressions - examples

# Searched is list of localities: Mull, Rhum, Skye, Coll, Colonsay, Hoy, Westray, Sanday, Stronsay, Tiree, Islay

• Search pattern = ol Coll, Colonsay

• Search pattern = n.aColonsay, Sanday, Stronsay

• Search pattern = ^S Skye, Sanday, Stronsay

• Search pattern = e$ Skye, Tiree

• Search pattern = [ds]ay Colonsay, Sanday, Stronsay

• Search pattern = [p-s]ayColonsay, Westray, Stronsay

Intermezzo 5: Regular expressions - examplesIntermezzo 5: Regular expressions - examples

# Searched is list of localities: Mull, Rhum, Skye, Coll, Colonsay, Hoy, Westray, Sanday, Stronsay, Tiree, Islay

• Search pattern = ol|oy Coll, Colonsay, Hoy

• Search pattern = l{2} Mull, Coll

# Sample names are: Bl-1, Bl-3, Koz-1, Koz-2, Koz-5, Koz-11, KozD-1, Ri-1

• Search pattern = oz-|Bl- Bl-1, Bl-2, Bl-3, Koz-1, Koz-2, Koz-5, Koz-11

• Search pattern = oz-[1-3] Koz-1, Koz-2, Koz-11

• Search pattern = oz-1{1,} Koz-1, Koz-11

Data handling I.Data handling I.Selecting subsets of the data stored in

memory by searching sample names

or levels of a single label.

• regular expressions implemented

Lokalita

Data handling I.Data handling I.Selecting subsets of the data stored in

memory by their range.

1:5

Data handling I.Data handling I.Selecting subsets of the current dataset

using Boolean conditions.

• queried can be both numeric fields

and labels (or combinations thereof)

• regular expressions can be

employed to search the labels

Suita=“Ricany”

Data handling I.Data handling I.Restores data for all samples in the

same form as they were loaded from

a data file.

Data handling II.Data handling II.

Grouping the data according to the

levels of a single label.

Suita


Grouping the data according to the

interval a single numerical variable

falls into.

• Enter a comma-delimited list of one

or more breakpoints defining the

intervals

• The default includes the mean, that

would be supplemented by 0 and

maximum (i.e. two intervals)

• The names of individual groups can

be specified

• The vector containing the

information on the groups can be

appended to the labels.


SiO2

52,63

Basic,Intermediate,Acid


Grouping the data using selected

classification diagram.


information on the current groups

can be appended to the labels.


Grouping the data using the cluster

analysis.

• After the dendrogram is drawn, the

user is asked how many clusters is

the dataset to be broken into.




• The groups are initially numbered

but the names can be changed

readily using the function

Edit labels as factor. 5


Enables merging several groups into

a single one.




Old

Old

YoungYoung

Intermezzo 4: Plotting symbolsIntermezzo 4: Plotting symbols

Use codes from the table or

single character vectors as ‘*’,‘B’,‘s’

Intermezzo 5: Plotting coloursIntermezzo 5: Plotting colours

NB that only numeric

codes can be used

to specify plotting

colours so far.

Data handling III.Data handling III.

Assigns plotting symbols and colours

simultaneously according to the

levels of the defined groups.

34


Assign plotting symbols or colours

according to the levels of a single

label.


Assign uniform plotting symbols or

colours to all the analyses in the

current data set.


Data handling III.Data handling III. Displays a graphical legend(s) with

current assignment of plotting

symbols and colours used by most

of the diagrams.

• If necessary, two legends are

created, for symbols and colours

separately.

Calcula-tions

Calculations I.Calculations I.Computes a single numeric variable and

appends it, under specified name, to

the numeric data in memory.

SiO2/5

My.param

Calculations I.Calculations I.Adds a formula for a single numeric

variable to the specified R script

(‘*.r’ ).

• The user is prompted for the

variable name and any comments

that should appear in the file.

• The script can be executed later

using the R command ‘File|

Source’. Alternatively, it can be

placed among the plugins into the

subdirectory ‘\Plugin’.

Calculations I.Calculations I.Recasts the selected data to a fixed sum.

Calculations I.Calculations I.Calculates millications as used for

many plots of the French school,

e.g. by De la Roche et al. (1980) or

Debon & Le Fort (1983, 1988).

• The calculated values are Si, Ti, Al,

Fe3, Fe2, Fe, Mn, Mg, Ca, Na, K, P.

nOxideMW

wtOxideElement

i

ii )(

.%)(1000

Where: MW = molecular weight of the

Oxidei, n = number of atoms of

Elementi in the formula

Calculations I.Calculations I.

Calculations II. (stats)Calculations II. (stats)

Prints statistical summary for a single

variable and the current dataset

(or its part).

• Formulae are ok.

• The statistical summary involves

no. of observations, missing values,

mean, std. deviation, minimum,

25% quartile, median (= 50%

quartile), 75% quartile and

maximum.

• The function also plots a summary

boxplot and a histogram.



Like previous, but respecting grouping.



Prints statistical summary for selected

list of elements (majors or traces,

respectively) and the current dataset

(or its part).

• The statistical summary involves

no. of observations, missing values,

mean, std. deviation, minimum,

25% quartile, median (= 50%

quartile), 75% quartile and

maximum.

• Optionally the function also plots

summary boxplots and/or

histograms.



Like previous, but respecting grouping.



Displays a binary diagram of two

elements/oxides, in which are

plotted averages for the individual

groups with whiskers corresponding

to the standard deviations.



Plots a matrix of scatterplots in the

lower panel and one of other pre-

defined panel functions in the upper.

panel.corr Prints correlations, with size proportional to their magnitude

panel.cov Prints covariances

panel.smooth Fits smooth trend lines

panel.hist Plots histograms of frequencies




Produces, for each group a separate, set

of plots of correlation coefficient

patterns (Rollinson 1993 and

references therein).

• Similarity in patterns between two

or more elements indicates their

analogous geochemical behaviour,

potentially controlled by the same

geochemical process (fractional

crystallization, partial melting,

weathering, hydrothermal

alteration...)



Performs principal components analysis

(scaled variables, covariance or

correlation matrix) and plots a

biplot (Gabriel, 1971).

• The length of the individual arrows

is proportional to the relative

variation of each of the variables.

• Comparable direction of two arrows

implies that both variables are

positively correlated; the opposite

one indicates a strong negative

correlation.

(Buccianti & Peccerillo, 1999)



Hierarchical cluster analysis on a set of

dissimilarities.

• The user is asked to specify a label

for the individual samples, default

are their names.

• After the dendrogram is drawn, the

individual clusters can be identified.

• For each sample falling into the

given group, specified information

(e.g. Locality, Rock type and/or

Author) can be printed.


Calculations III.Calculations III.

Cationic parameters of Niggli (1948).

Various modifications of the CIPW

norm (Hutchison 1974, 1975)

Eine bessere Mesonorm for

granitoids (Mielke & Winkler 1979).

If desired, the Q'-ANOR diagram of

Streckeisen & Le Maitre (1979) is

plotted.

Niggli's Molecular Norm (Catanorm),

the algorithm is by Hutchison (1974).


Least-squares approximations of the

mode given major-element

compositions of the rock and its

main mineral constituents.

• Both unconstrained and constrained

solutions are produced (see

Albarede 1995 and the help file).

• Mineral compositions are to be

provided in a separate tab-delimited

text file.

• The output includes computed

modal proportions of the individual

minerals, the calculated

composition of the rock and

residuals.



Recalculates whole-rock analyses to

Debon & Le Fort's (1983, 1988)

multicationic values.

Recasts whole-rock data into

R1-R2 values of De La Roche et al.

(1980).


Various petrochemical indexes, such as:

• Total iron as Fe2O3

• Fe2O3/FeO, Na2O/K2O and

K2O/Na2O ratios

• Differentiation index (Larsen 1938)

• Solidification index (Kuno 1959)


Saves the variable ‘results’ ,

returned by most calculation

algorithms, to a tab-delimited text

(ASCII) file.


Appends the most recently calculated

values (variable ‘results’) to

the numeric data stored in memory,

e.g. for plotting or statistical

evaluation.


Copies the most recently calculated

results to a clipboard.

Plugin Saturation.rPlugin Saturation.r

Zircon saturation: yields temperatures for the observed major-element and Zr

contents. Returns also Zr saturation levels for the given major-element

compositions and assumed magma temperature (Watson & Harrison, 1983).

Monazite saturation computes saturation temperatures for given major-element

compositions and LREE contents of the magma (Montel, 1993).

Apatite saturation calculates saturation temperatures for observed whole-rock

major-element compositions (including P2O5 contents). Returns also a

phosphorus saturation levels for the given major-element compositions and

assumed magma temperature (Harrison & Watson, 1984; Bea et al., 1992;

Pichavant et al., 1992).

(Menu Calculations)

Plugin html_tables.rPlugin html_tables.r

Both functions output the specified data with (optional) labels into HTML. This

format is useful for importing into spreadsheets, word processors or publishing

on the WWW.

• The plugin attempts to format sub- and superscripts in the variable names.

• The created file ‘htmltable.html’ is placed in the subdirectory ‘\

R2HTM’ of the main GCDkit directory; when finished, it is previewed in a

browser. The style for the table is determined by the cascade style file

R2HTML.css in the subdirectory ‘\Plugin’.

• The plugin exploits R2HTML library by Eric Lecoutre, which must be

downloaded from CRAN and properly installed.

(Menu Calculations)

(Menu Data handling)

Plugin html_tables.rPlugin html_tables.r

Documents

Menu GCDkit. GCDkit I. Loads ASCII file or imports clipboard (e.g. data copied from Excel) Data are separated by tabulators, commas or semicolons The