# Options for Dimodal package Analysis, test, and display parameters for the Dimodal package. Modeled on the `par` options storage. ```r Diopt(...) Diopt.local(...) ``` ## Arguments - `...`: access or change or override options ## Details Diopt provides a global database of options for the Dimodal analysis. The function can be called in five ways: - **`Diopt()`**: returns the current options set as a list of tag=value pairs - **`Diopt(NULL)`**: resets all options to the package defaults, returning values before reset - **`Diopt(tag1=val1, tag2=val2, ...)`**: checks the option values and stores those that are valid, returning in a list the old values of the tags or NULL if a value is rejected - **`Diopt(list(tag1=val1, tag2=val2, ...))`**: checks the option values and stores those that are valid, returning in a list the old values of the tags or NULL if a value is rejected - **`Diopt("tag1", "tag2", ...)`**: returns the requested option(s) in a list The function does sanity checking on the passed values for each option, and is preferred to directly modifying the elements in the returned list. Like `par`, `Diopt(Diopt(tag1=val1, tag2=val2))` will restore the original state. Diopt.local returns all current values of the options overridden by the tag=value pairs in the argument, if the values are valid. Like Diopt, the arguments can be wrapped in an unnamed list. The options stored do not change; this is for a local, one-off edit to the values. Do not use Diopt when setting an `opt` argument for other functions, which expect the full list of values and not just those changed. String options are partially matched. Fraction values are between 0 and 1, exclusive. ## Returns As described in Details. ## Parameters: Data Preparation - **`analysis` **: which type of spacing to analyze, one or more of "lp", "diw", and "cpt" (case-insensitive) for using a low-pass filter, interval spacing, or raw spacing and changepoints - **`data.midq` **: approximation method to convert quantiles or indices to original data, if 0 determines automatically ## Parameters: Low-Pass Filter Setup - **`lp.kernel` **: filter type, one of "kaiser", "triangular" or "bartlett" (synonyms), "hanning", "hamming", "gaussian" or "normal" (synonyms), "blackman" (case-insensitive) - **`lp.window` **: kernel size, either as fraction of the data or in points - **`lp.tests` **: tests to run on detected features, one or more of "ht", "pkexcur", "len", and "ftexcur" (case-insensitive) - **`lp.param` **: list of tag=value pairs of detector or test or acceptance parameters that will be overridden for the low-pass spacing checks ## Parameters: Interval Spacing Setup - **`diw.window` **: interval size, either as a fraction of the data or in points - **`diw.tests` **: tests to run on detected features, one or more of "pkexcur", "runht", "nrun", "runlen", "ftexcur" (case-insensitive) - **`diw.param` **: list of tag=value pairs of detector or test or acceptance parameters to override for the interval spacing checks ## Parameters: Local Extrema Detector - **`peak.fht` **: minimum peak height as a fraction of the signal's range - **`peak.frelht` **: minimum peak height as a fraction of the average with the adjacent minima - **`peak.fhttie` **: maximum relative difference to treat values around extrema as the same - **`peak.fhsupp` **: fraction of peak height to determine the support range, used for excursion test (ex. 0.5 is the Full Width at Half Maximum, 1.0 extends to the minima) ## Parameters: Flat Detector - **`flat.fripple` **: ripple specification as fraction of the signal's range - **`flat.minlen` **: shortest length of flats in data points - **`flat.fminlen` **: shortest length of flats as fraction of the data - **`flat.noutlier` **: number of outliers beyond the ripple allowed between source of flat and each endpoint - **`flat.distrib` **: null distribution model for length model test, one of "logistic", "weibull", "normal" or "gaussian" (synonyms), or "gumbel" (case-insensitive) ## Parameters: Excursion/Permutation Tests - **`excur.nrep` **: number of trial draws for peak and flat excursion tests - **`excur.ntop` **: number of points at start and end of data to ignore if they are the largest, to avoid adding the large tails of the spacing to the draw pool; can compare the first and last spacings against its standard deviation - **`excur.seed` **: RNG seed for each excursion test, 0 to not set - **`excur.nrep` **: number of trial draws for run permutation test - **`excur.seed` **: RNG seed for each permutation test, 0 to not set ## Parameters: Test Significance (Acceptance) Levels - **`alpha.ht` **: acceptance level of the peak height model test - **`alpha.pkexcur.lp` **: acceptance level of the peak height excursion (bootstrap) test for features found in the low-pass spacing - **`alpha.pkexcur.diw` **: acceptance level of the peak height excursion (bootstrap) test for features found in the interval spacing - **`alpha.len` **: acceptance level of the flat length model test - **`alpha.ftexcur.lp` **: acceptance level of the flat height excursion (bootstrap) test for features found in the low-pass spacing - **`alpha.ftexcur.diw` **: acceptance level of the flat height excursion (bootstrap) test for features found in the interval spacing - **`alpha.runht` **: acceptance level of the runs permutation test - **`alpha.nrun` **: acceptance level of the runs count statistics test - **`alpha.runlen` **: acceptance level of the longest run test ## Parameters: Changepoint Detectors - **`cpt.libs` **: vector of changepoint packages to use (name preceded by +) or ignore (by -) - **`cpt.maxfncpt` **: maximum fraction of data allowed to be changepoints, before ignoring library results - **`cpt.qvote` **: vector of two quantiles specifying range of number of changepoints per library allowed based on counts from all libraries - **`cpt.fsep` **: maximum separation between changepoints as fraction of data to consider as same point - **`cpt.sep` **: separation in data (number of points) between changepoints before merging or treating library results as one - **`cpt.libsep` **: separation in data (number of points) between changepoints when merging the variants within a library, if zero take union of all points - **`cpt.timeout` **: time-out in seconds per CPT algorithm before abandoning library method, 0 for no limit ## Parameters: Other - **`track.maxwindow` **: maximum low-pass or interval window size for Ditrack variations ## Parameters: Display - **`palette` **: the color palette to use when plotting the spacing or histogram and marking features, either a name from `palette.pals` or if starting with the string "hcl:" from `hcl.pals`, where the matching of the name follows the same rules as the palette functions - **`colID.data` **: index in the palette (of the 8 colors generated) for drawing the data or its spacing - **`colID.filter` **: index in the palette for drawing the LP or interval spacing - **`colID.hist` **: index in the palette for drawing the bars in the data histogram - **`colID.cdf` **: index in the palette for drawing the distribution atop the histogram, and the decile axes to align the spacing index with the data - **`colID.peak` **: index in the palette when marking the peaks with vertical dashed or dotted lines - **`colID.flat` **: index in the palette when marking the flats with boxes around the feature - **`colID.cpt` **: index in the palette when marking the changepoints with ticks along the upper edge of the graph - **`digits` **: number of significant digits to use when printing raw values, if 0 then use `options("digits")` - **`mark.alpha` **: TRUE to use ANSI escape codes when printing probabilities to compare them against the alpha levels, FALSE to not add any formatting - **`mark.flat` **: how to indicate flats in a plot, one of "box" or "bar" (case-insensitive) ## See Also `Dimodal`, `palette.pals`, `hcl.pals` ## Examples ```r ## Use the triangular kernel spanning 10% of the data for the ## low-pass analysis. Set the interval to 30 and override the ## ripple spec in the interval spacing but not for the low-pass. Diopt(lp.kernel='bartlett', lp.window=0.10, diw.window=30, diw.param=list(flat.fripple=0.02)) ## Diopt()$lp.kernel also accesses the new value. Diopt('lp.kernel', 'diw.window') ## Temporarily override the kernel, without changing default. Diopt.local(list(lp.kernel='Hanning'))$lp.kernel Diopt()$lp.kernel ## Reset. Diopt(NULL) ```

Diopt function