View source: R/print.ContTable.R

print.ContTable | R Documentation |

`ContTable`

class objects`print`

method for the `ContTable`

class objects created by `CreateContTable`

function.

## S3 method for class 'ContTable' print( x, digits = 2, pDigits = 3, quote = FALSE, missing = FALSE, explain = TRUE, printToggle = TRUE, noSpaces = FALSE, nonnormal = NULL, minMax = FALSE, insertLevel = FALSE, test = TRUE, smd = FALSE, formatOptions = list(scientific = FALSE), ... )

`x` |
Object returned by |

`digits` |
Number of digits to print in the table. |

`pDigits` |
Number of digits to print for p-values (also used for standardized mean differences). |

`quote` |
Whether to show everything in quotes. The default is FALSE. If TRUE, everything including the row and column names are quoted so that you can copy it to Excel easily. |

`missing` |
Whether to show missing data information. |

`explain` |
Whether to add explanation to the variable names, i.e., (mean (SD) or median [IQR]) is added to the variable names. |

`printToggle` |
Whether to print the output. If FALSE, no output is created, and a matrix is invisibly returned. |

`noSpaces` |
Whether to remove spaces added for alignment. Use this option if you prefer to align numbers yourself in other software. |

`nonnormal` |
A character vector to specify the variables for which the p-values should be those of nonparametric tests. By default all p-values are from normal assumption-based tests (oneway.test). |

`minMax` |
Whether to use [min,max] instead of [p25,p75] for nonnormal variables. The default is FALSE. |

`insertLevel` |
Whether to add an empty level column to the left of strata. |

`test` |
Whether to show p-values. TRUE by default. If FALSE, only the numerical summaries are shown. |

`smd` |
Whether to show standardized mean differences. FALSE by default. If there are more than one contrasts, the average of all possible standardized mean differences is shown. For individual contrasts, use |

`formatOptions` |
A list of options, which will be passed to |

`...` |
For compatibility with generic. Ignored. |

A matrix object containing what you see is also invisibly returned. This can be assinged a name and exported via `write.csv`

.

Kazuki Yoshida, Alexander Bartel

`CreateTableOne`

, `CreateContTable`

, `summary.ContTable`

## Load library(tableone) ## Load Mayo Clinic Primary Biliary Cirrhosis Data library(survival) data(pbc) ## Check variables head(pbc) ## Create an overall table for continuous variables contVars <- c("time","age","bili","chol","albumin","copper", "alk.phos","ast","trig","platelet","protime") contTableOverall <- CreateContTable(vars = contVars, data = pbc) ## Simply typing the object name will invoke the print.ContTable method, ## which will show the sample size, means and standard deviations. contTableOverall ## To further examine the variables, use the summary.ContTable method, ## which will show more details. summary(contTableOverall) ## c("age","chol","copper","alk.phos","trig","protime") appear highly skewed. ## Specify them in the nonnormal argument, and the display changes to the median, ## and the [25th, 75th] percentile. nonNormalVars <- c("age","chol","copper","alk.phos","trig","protime") print(contTableOverall, nonnormal = nonNormalVars) ## To show median [min,max] for nonnormal variables, use minMax = TRUE print(contTableOverall, nonnormal = nonNormalVars, minMax = TRUE) ## The table can be stratified by one or more variables contTableBySexTrt <- CreateContTable(vars = contVars, strata = c("sex","trt"), data = pbc) ## print now includes p-values which are by default calculated by oneway.test (t-test ## equivalent in the two group case). It is formatted at the decimal place specified ## by the pDigits argument (3 by default). It does <0.001 for you. contTableBySexTrt ## The nonnormal argument toggles the p-values to the nonparametric result from ## kruskal.test (wilcox.test equivalent for the two group case). print(contTableBySexTrt, nonnormal = nonNormalVars) ## The minMax argument toggles whether to show median [range] print(contTableBySexTrt, nonnormal = nonNormalVars, minMax = TRUE) ## summary now includes both types of p-values summary(contTableBySexTrt) ## If your work flow includes copying to Excel and Word when writing manuscripts, ## you may benefit from the quote argument. This will quote everything so that ## Excel does not mess up the cells. print(contTableBySexTrt, nonnormal = nonNormalVars, quote = TRUE) ## If you want to center-align values in Word, use noSpaces option. print(contTableBySexTrt, nonnormal = nonNormalVars, quote = TRUE, noSpaces = TRUE)

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