Description Usage Arguments Value Examples

Perform multiscale test of independence for multivariate vectors. See vignettes for further examples.

1 2 3 4 5 6 7 | ```
MultiFIT(xy, x = NULL, y = NULL, p_star = NULL, R_max = NULL,
R_star = 1, rank.transform = TRUE, ranking.approximation = FALSE,
M = 10, apply.stopping.rule = FALSE, alpha = 0.05,
test.method = "Fisher", correct = TRUE, min.tbl.tot = 25L,
min.row.tot = 10L, min.col.tot = 10L, p.adjust.methods = c("H",
"Hcorrected"), compute.all.holm = TRUE, return.all.pvs = TRUE,
verbose = FALSE)
``` |

`xy` |
A list, whose first element corresponds to the matrix x as below, and
its second element corresponds to the matrix y as below. If |

`x` |
A matrix, number of columns = dimension of random vector, number of rows = number of observations. |

`y` |
A matrix, number of columns = dimension of random vector, number of rows = number of observations. |

`p_star` |
Numeric, cuboids associated with tests whose |

`R_max` |
A positive integer (or Inf), the maximal number of
resolutions to scan (algorithm will stop at a lower resolution if
all tables in it do not meet the criteria specified at |

`R_star` |
A positive integer, if set to an integer
between 0 and |

`rank.transform` |
Logical, if |

`ranking.approximation` |
Logical, if |

`M` |
A positive integer (or Inf), the number of top ranking tests to continue to split at each resolution. FWER control not guaranteed for this method. |

`apply.stopping.rule` |
Logical. If TRUE, an adjusted |

`alpha` |
Numeric. Threshold below which resolution-specific |

`test.method` |
String, choose "Fisher" for Fisher's exact test (slowest), "chi.sq" for Chi-squared test, "LR" for likelihood-ratio test and "norm.approx" for approximating the hypergeometric distribution with a normal distribution (fastest). |

`correct` |
Logical, if |

`min.tbl.tot` |
Non-negative integer, the minimal number of observations
per table below which a |

`min.row.tot` |
Non-negative integer, the minimal number of observations for row totals in the 2x2 contingency tables below which a contingency table will not be tested. |

`min.col.tot` |
Non-negative integer, the minimal number of observations for column totals in the 2x2 contingency tables below which a contingency table will not be tested. |

`p.adjust.methods` |
String, choose between "H" for Holm, "Hcorrected" for Holm with
the correction as specified in |

`compute.all.holm` |
Logical, if |

`return.all.pvs` |
Logical, if TRUE, a data frame with all |

`verbose` |
Logical. |

`p.values.holistic`

, a named numerical vector containing the holistic `p`

-values of
for the global null hypothesis (i.e. x independent of y).

`p.values.resolution.specific`

, a named numerical vector containing the
reslution specific `p`

-values of for the global null hypothesis (i.e. x independent of y).

`res.by.res.pvs`

, a dta frame that contains the raw and Bonferroni adjusted
resolution specific `p`

-values.

`all.pvs`

, a data frame that contains all `p`

-values and adjusted
`p`

-values that are computed. Returned if `return.all.pvs`

is `TRUE`

.

`all`

, a nested list. Each entry is named and contains data about a resolution
that was tested. Each resolution is a list in itself, with `cuboids`

, a summary of
all tested cuboids in a resolution, `tables`

, a summary of all 2x2
contingency tables in a resolution, `pv`

, a numerical vector containing the
`p`

-values from the tests of independence on 2x2 contingency table in `tables`

that meet the criteria defined by `min.tbl.tot`

, `min.row.tot`

and `min.col.tot`

.
The length of `pv`

is equal to the number of rows of `tables`

. `pv.correct`

,
similar to the above `pv`

, corrected `p`

-values are computed and returned when
`correct`

is `TRUE`

. `rank.tests`

, logical vector that indicates
whether or not a test was ranked among the top `M`

tests in a resolution. The
length of `rank.tests`

is equal to the number of rows of `tables`

. `parent.cuboids`

,
an integer vector, indicating which cuboids in a resolution are associated with
the ranked tests, and will be further halved in the next higher resolution.
`parent.tests`

, a logical vector of the same length as the
number of rows of `tables`

, indicating whether or not a test was chosen as a parent
test (same tests may have multiple children).

1 2 3 4 5 6 7 8 9 10 11 | ```
set.seed(1)
n = 300
Dx = Dy = 2
x = matrix(0, nrow = n, ncol = Dx)
y = matrix(0, nrow = n, ncol = Dy)
x[,1] = rnorm(n)
x[,2] = runif(n)
y[,1] = rnorm(n)
y[,2] = sin(5 * pi * x[ , 2]) + 1 / 5 * rnorm(n)
fit = MultiFIT(x = x, y = y, verbose = TRUE)
w = MultiSummary(x = x, y = y, fit = fit, alpha = 0.0001)
``` |

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