peakfit  R Documentation 
Implements the discrete mixture modelling algorithms of Galbraith and Laslett (1993) and applies them to fission track and other geochronological datasets.
peakfit(x, ...)
## Default S3 method:
peakfit(x, k = "auto", sigdig = 2, oerr = 3, log = TRUE, np = 3, ...)
## S3 method for class 'fissiontracks'
peakfit(
x,
k = 1,
exterr = FALSE,
sigdig = 2,
log = TRUE,
oerr = 3,
np = 3,
...
)
## S3 method for class 'UPb'
peakfit(
x,
k = 1,
type = 4,
cutoff.76 = 1100,
cutoff.disc = discfilter(),
common.Pb = 0,
exterr = FALSE,
sigdig = 2,
log = TRUE,
oerr = 3,
np = 3,
...
)
## S3 method for class 'PbPb'
peakfit(
x,
k = 1,
exterr = FALSE,
sigdig = 2,
log = TRUE,
common.Pb = 0,
oerr = 3,
np = 3,
...
)
## S3 method for class 'ArAr'
peakfit(
x,
k = 1,
exterr = FALSE,
sigdig = 2,
log = TRUE,
i2i = FALSE,
oerr = 3,
np = 3,
...
)
## S3 method for class 'ThPb'
peakfit(
x,
k = 1,
exterr = FALSE,
sigdig = 2,
log = TRUE,
i2i = FALSE,
oerr = 3,
np = 3,
...
)
## S3 method for class 'KCa'
peakfit(
x,
k = 1,
exterr = FALSE,
sigdig = 2,
log = TRUE,
i2i = FALSE,
oerr = 3,
np = 3,
...
)
## S3 method for class 'ReOs'
peakfit(
x,
k = 1,
exterr = FALSE,
sigdig = 2,
log = TRUE,
i2i = TRUE,
oerr = 3,
np = 3,
...
)
## S3 method for class 'SmNd'
peakfit(
x,
k = 1,
exterr = FALSE,
sigdig = 2,
log = TRUE,
i2i = TRUE,
oerr = 3,
np = 3,
...
)
## S3 method for class 'RbSr'
peakfit(
x,
k = 1,
exterr = FALSE,
sigdig = 2,
log = TRUE,
i2i = TRUE,
oerr = 3,
np = 3,
...
)
## S3 method for class 'LuHf'
peakfit(
x,
k = 1,
exterr = FALSE,
sigdig = 2,
log = TRUE,
i2i = TRUE,
oerr = 3,
np = 3,
...
)
## S3 method for class 'ThU'
peakfit(
x,
k = 1,
exterr = FALSE,
sigdig = 2,
log = TRUE,
oerr = 3,
Th0i = 0,
np = 3,
...
)
## S3 method for class 'UThHe'
peakfit(x, k = 1, sigdig = 2, log = TRUE, oerr = 3, np = 3, ...)
x 
either an 
... 
optional arguments (not used) 
k 
the number of discrete age components to be
sought. Setting this parameter to 
sigdig 
number of significant digits to be used for any legend in which the peak fitting results are to be displayed. 
oerr 
indicates whether the analytical uncertainties of the output are reported in the plot legend as:

log 
take the logs of the data before applying the mixture model? 
np 
number of parameters for the minimum age model. Must be either 3 or 4. 
exterr 
propagate the external sources of uncertainty into the component age errors? 
type 
scalar indicating whether to plot the

cutoff.76 
the age (in Ma) below which the

cutoff.disc 
discordance cutoff filter. This is an object of
class 
common.Pb 
common lead correction:

i2i 
‘isochron to intercept’: calculates the initial (aka
‘inherited’, ‘excess’, or ‘common’)

Th0i 
initial

Consider a dataset of n
dates \{t_1, t_2, ..., t_n\}
with analytical uncertainties \{s[t_1], s[t_2], ...,
s[t_n]\}
. Define z_i = \log(t_i)
and s[z_i] =
s[t_i]/t_i
. Suppose that these n
values are derived from a
mixture of k>2
populations with means
\{\mu_1,...,\mu_k\}
. Such a discrete mixture may be
mathematically described by P(z_i\mu,\omega) = \sum_{j=1}^k
\pi_j N(z_i  \mu_j, s[z_j]^2 )
where \pi_j
is the
proportion of the population that belongs to the j^{th}
component, and \pi_k=1\sum_{j=1}^{k1}\pi_j
. This equation
can be solved by the method of maximum likelihood (Galbraith and
Laslett, 1993). IsoplotR
implements the Bayes Information
Criterion (BIC) as a means of automatically choosing k
. This
option should be used with caution, as the number of peaks steadily
rises with sample size (n
). If one is mainly interested in
the youngest age component, then it is more productive to use an
alternative parameterisation, in which all grains are assumed to
come from one of two components, whereby the first component is a
single discrete age peak (\exp(m)
, say) and the second
component is a continuous distribution (as descibed by the
central
age model), but truncated at this discrete
value. IsoplotR
uses a normal likelihood function
(section 6.11 of Galbraith, 2005) for the minimum age model.
This may result in some inaccuracy for young and/or uraniumpoor
fission track samples.
Returns a list with the following items:
a 2 x k
matrix with the following rows:
t
: the ages of the k
peaks
s[t]
: the standard errors of t
a 2 x k
matrix with the following rows:
p
: the proportions of the k
peaks
s[p]
: the standard errors of p
the loglikelihood of the fit
a vector of text expressions to be used in a figure legend
Galbraith, R.F. and Laslett, G.M., 1993. Statistical models for mixed fission track ages. Nuclear Tracks and Radiation Measurements, 21(4), pp.459470.
Galbraith, R.F. 2005, Statistics for fission track analysis. Chapman and Hall/CRC, 229p.
radialplot
, central
attach(examples)
peakfit(FT1,k=2)
peakfit(LudwigMixture$x,k='min')
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