Generic Methods for secrdesign Objects
Description
Methods to summarize simulated datasets.
Usage
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18  ## S3 method for class 'secrdesign'
summary(object, ...)
## S3 method for class 'rawdata'
summary(object, ...)
## S3 method for class 'estimatetables'
summary(object, ...)
## S3 method for class 'selectedstatistics'
summary(object, fields = c('n', 'mean',
'se'), dec = 5, alpha = 0.05, type = c('list','dataframe','array'), ...)
## S3 method for class 'selectedstatistics'
plot(x, scenarios, statistic, type =
c('hist', 'CI'), refline, xlab = NULL, ...)
header(object)

Arguments
object 
object of class simulations from 
dec 
number of decimal places in output 
fields 
character vector; names of required summary statistics (see Details) 
alpha 
alpha level for confidence intervals and quantiles 
type 
character code for type of output (see Details) 
... 
other arguments – not currently used by summary but
passed to 
x 
object of class ‘selectedstatistics’ from

scenarios 
integer indices of scenarios to plot (all plotted if not specified) 
statistic 
integer or character indices if the statistics in x for which histograms are requested 
refline 
logical; if TRUE a reference line is plotted at the true value of a parameter 
xlab 
character; optional label for xaxis 
Details
If object
inherits from ‘selectedstatistics’ then the numeric
If object
inherits from ‘selectedstatistics’ then the numeric
results from replicate simulations are summarized using the chosen
‘fields’ (by default, the number of nonmissing values, mean and standard
error), along with header information describing the
simulations. Otherwise the header alone is returned.
fields
is a vector of any selection from c(‘n’, ‘mean’, ‘sd’,
‘se’, ‘min’, ‘max’, ‘lcl’, ‘ucl’, ‘median’, ‘q’, ‘rms’), or the
character value ‘all’.
Field ‘q’ provides 1000 alpha/2
and 1000[1  alpha/2
]
quantiles qxxx and qyyy.
‘lcl’ and ‘ucl’ refer to the upper and lower limits of a 100(1  alpha)% confidence interval for the statistic, across replicates.
‘rms’ gives the rootmeansquare of the statistic  most useful for
the statistic ‘ERR’ (see select.stats
) when it
represents the overall accuracy or RMSE.
The plot
method plots either (i) histograms of the selected
statistics (type = ‘hist’) or (ii) the estimate and confidence interval for
each replicate (type = ‘CI’). The default for type = ‘hist’ is to plot
the first statistic  this is usually ‘n’ (number of detected animals)
when fit = FALSE
, and ‘estimate’ (parameter estimate) when
fit = TRUE
. If length(statistic) > 1 then more than one plot
will be produced, so a multicolumn or multirow layout should be
prepared with par
arguments ‘mfcol’ or ‘mfrow’.
For type = ‘CI’ the statistics must include ‘estimate’, ‘lcl’ and ‘ucl’ (or ‘beta’, ‘lcl’ and ‘ucl’ if outputtype = ‘coef’).
Value
List with components ‘header’
call 
original function call 
starttime 
from object 
proctime 
from object 
constants 
small dataframe with values of nonvarying inputs 
varying 
small dataframe with values of varying inputs 
fit.args 
small dataframe with values arguments for secr.fit, if specified 
and ‘OUTPUT’, a list with one component for each field. Each component may be a list or an array.
See Also
run.scenarios
,
make.array
,
select.stats
validate
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13  ## collect raw counts
scen1 < make.scenarios(D = c(5,10), sigma = 25, g0 = 0.2)
traps1 < make.grid()
tmp1 < run.scenarios(nrepl = 50, trapset = traps1, scenarios = scen1,
fit = FALSE)
opar < par(mfrow=c(2,3))
plot(tmp1, statistic = 1:3)
par(opar)
summary(tmp1)
summary(tmp1, field=c('q025', 'median', 'q975'))

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