Description Usage Arguments Details Value Examples

View source: R/multiple_binary_test.R

`multiple_binary_test`

is used to preform goodness-of-fit tests on
multiple binary chains of data of the same length to see if a Markov chain
model is appropriate.

1 2 | ```
multiple_binary_test(binary_chains, swaps = 1000, n = 1000, run = 4,
bins = 30, success = NULL)
``` |

`binary_chains` |
A two dimensional matrix, in which there are two unique values. |

`swaps` |
A positive nonzero integer value for the number of swaps to be
attempted on the chain. Larger values will tend to yield "more independent"
data. Generally, the number of swaps should be much larger then the number of
elements in the matrix |

`n` |
A positive nonzero integer representing the number of new sets of chains to be generated. |

`run` |
The length of the run to test for if one is interested in run test statistics. |

`bins` |
The number of bins to be displayed in histograms of test
statistics when one plots objects generated by |

`success` |
Denotes the data entry to be counted for run statistics. |

`multiple_binary_test`

works by taking the supplied `binary_chains`

parameter, counting the transitions between different elements, and then
generating `n`

new sets of chains with the same number of transitions.
It generates these new sets of chains by attempting to swap random elements
of the chains `swaps`

times, only doing so if the attempted swap
preserves the number of transitions between the two unique elements of the
chains. `multiple_binary_test`

then saves the chain generated by this
process, then preforms a number of swaps equivalent to the value of
`swaps`

on that chain again, then recording the result in a new entry in
a list of data. `multiple_binary_test`

does this `n`

times to
generate the `n`

new sets of chains. These new sets of chains are
effectively independent of the original one.

Once `multiple_binary_test`

has generated new data, it preforms various
tests of that data. included in the function are the likelihood ratio test,
the Pearson's chi square test, and a run test for a run of length specified
by the argument `run`

.

`multiple_binary_test`

returns a list of class
`"multiple_binary_test"`

with the following elements:

`data`

, a list of matrices, the first of which is binary_chains, and
the rest of which are the generated data.

`test_stats_lrt`

, vector of likelihood ratio test statistics for each
element of list `data`

.

`test_stats_chi_sq`

, a vector of Pearson's chi square test statistics
for each element of list `data`

.

`test_stats_run`

, a vector of run test statistics for a run of length
`run`

for each element of list `data`

.

`p_value_lrt`

, the p-value of `binary_chain`

, calculated exactly
from the distribution of `test_stats_lrt`

.

`p_value_chi_sq`

, the p-value of `binary_chain`

, calculated exactly
from the distribution of `test_stats_chi_sq`

.

`p_value_run`

, the p-value of `binary_chain`

, calculated exactly
from the distribution of `test_stats_run`

.

`call`

, the function call.

`bins`

, the number of bins specified in the function call.

`run`

, the length of run specified in the function call.

1 2 3 | ```
data <- as.matrix(maRkov::snoqualmie)
foo <- multiple_binary_test(binary_chains = data, swaps = 10000, n = 10000,
run = 3, bins = 50)
``` |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.