Description Usage Arguments Details Value Author(s) See Also Examples

Create a contingency table from cross-classifying factors, usually contained in a data frame, using a formula interface.

1 2 |

`formula` |
a |

`data` |
an optional matrix or data frame (or similar: see |

`rdrop, cdrop` |
logical (should zero marginal rows/columns be removed after cross tabulation), character or numeric (what rows/columns should be removed). |

`subset` |
an optional vector specifying a subset of observations to be used. |

`na.action` |
a function which indicates what should happen when the data contain NAs. |

`exclude` |
a vector of values to be excluded when forming the set of levels of the classifying factors. |

`drop.unused.levels` |
a logical indicating whether to drop unused levels in the classifying factors. If this is FALSE and there are unused levels, the table will contain zero marginals, and a subsequent chi-squared test for independence of the factors will not work. |

The function creates two- or three-way cross tabulation. Only works for two or three factors.

If a left hand side is given in formula, its entries are simply summed over the cells corresponding to the right hand side; this also works if the left hand side does not give counts.

A sparse numeric matrix inheriting from `sparseMatrix`

, specifically an object of S4 class `dgCMatrix`

.

For three factors, a list of sparse matrices.

This function is a slight modification of the `xtabs`

function in the stats package.

Modified by Peter Solymos <solymos@ualberta.ca>

See also `xtabs`

in stats package.

`sum_by`

for sums over a classes ('one-way table'),
and `Melt`

for the inverse operation of `Xtab`

.

`"mefa"`

S3 class: `mefa`

in mefa package.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 | ```
x <- data.frame(
sample = paste("Sample", c(1,1,2,2,3,4), sep="."),
species = c(paste("Species", c(1,1,1,2,3), sep="."), "zero.pseudo"),
count = c(1,2,10,3,4,0),
stringsAsFactors = TRUE)
x
## Xtab class, counts by repetitions in RHS
(x0 <- Xtab(~ sample + species, x))
## counts by LHS and repetitions in RHS
(x1 <- Xtab(count ~ sample + species, x))
## drop all empty rows
(x2 <- Xtab(count ~ sample + species, x, cdrop=FALSE,rdrop=TRUE))
## drop all empty columns
Xtab(count ~ sample + species, x, cdrop=TRUE,rdrop=FALSE)
## drop specific columns by placeholder
Xtab(count ~ sample + species, x, cdrop="zero.pseudo")
## 2 and 3 way crosstabs
xx <- data.frame(
sample = paste("Sample", c(1,1,2,2,3,4), sep="."),
species = c(paste("Species", c(1,1,1,2,3), sep="."), "zero.pseudo"),
count = c(1,2,10,3,4,0),
segment = letters[c(6,13,6,13,6,6)],
stringsAsFactors = TRUE)
xx
Xtab(count ~ sample + species, xx)
Xtab(count ~ sample + species + segment, xx)
``` |

```
sh: 1: cannot create /dev/null: Permission denied
Loading required package: Matrix
mefa4 0.3-7 2020-02-28
sample species count
1 Sample.1 Species.1 1
2 Sample.1 Species.1 2
3 Sample.2 Species.1 10
4 Sample.2 Species.2 3
5 Sample.3 Species.3 4
6 Sample.4 zero.pseudo 0
4 x 4 sparse Matrix of class "dgCMatrix"
Species.1 Species.2 Species.3 zero.pseudo
Sample.1 2 . . .
Sample.2 1 1 . .
Sample.3 . . 1 .
Sample.4 . . . 1
4 x 4 sparse Matrix of class "dgCMatrix"
Species.1 Species.2 Species.3 zero.pseudo
Sample.1 3 . . .
Sample.2 10 3 . .
Sample.3 . . 4 .
Sample.4 . . . .
3 x 4 sparse Matrix of class "dgCMatrix"
Species.1 Species.2 Species.3 zero.pseudo
Sample.1 3 . . .
Sample.2 10 3 . .
Sample.3 . . 4 .
4 x 3 sparse Matrix of class "dgCMatrix"
Species.1 Species.2 Species.3
Sample.1 3 . .
Sample.2 10 3 .
Sample.3 . . 4
Sample.4 . . .
4 x 3 sparse Matrix of class "dgCMatrix"
Species.1 Species.2 Species.3
Sample.1 3 . .
Sample.2 10 3 .
Sample.3 . . 4
Sample.4 . . .
sample species count segment
1 Sample.1 Species.1 1 f
2 Sample.1 Species.1 2 m
3 Sample.2 Species.1 10 f
4 Sample.2 Species.2 3 m
5 Sample.3 Species.3 4 f
6 Sample.4 zero.pseudo 0 f
4 x 4 sparse Matrix of class "dgCMatrix"
Species.1 Species.2 Species.3 zero.pseudo
Sample.1 3 . . .
Sample.2 10 3 . .
Sample.3 . . 4 .
Sample.4 . . . .
$f
4 x 4 sparse Matrix of class "dgCMatrix"
Species.1 Species.2 Species.3 zero.pseudo
Sample.1 1 . . .
Sample.2 10 . . .
Sample.3 . . 4 .
Sample.4 . . . .
$m
4 x 4 sparse Matrix of class "dgCMatrix"
Species.1 Species.2 Species.3 zero.pseudo
Sample.1 2 . . .
Sample.2 . 3 . .
Sample.3 . . . .
Sample.4 . . . .
```

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