This package gives a number of functions to aid common data analysis processes and reporting statistical results in an RMarkdown file. Data analysis functions combine multiple base R functions used to describe simple bivariate relationships into a single, easy to use function. Reporting functions will return character strings to report p-values, confidence intervals, and hypothesis test and regression results. Strings will be LaTeX-formatted as necessary and will knit pretty in an RMarkdown document. The package also provides a wrapper for the CreateTableOne function in the tableone package to make the results knitable.

Suppose we have the following data:

```
pred1 = sample(letters[1:3], size=50, replace=TRUE)
out1 = sample(letters[4:6], size=50, replace=TRUE)
out2 = rnorm(50)
```

We can investigate the relationship between `pred1`

and `out1`

using `cat_compare()`

:

```
## Warning in chisq.test(tab_no_miss): Chi-squared approximation may be incorrect
## $counts
## y
## x d e f Sum
## a 8 7 3 18
## b 6 2 9 17
## c 7 4 4 15
## Sum 21 13 16 50
##
## $chisq
##
## Pearson's Chi-squared test
##
## data: tab_no_miss
## X-squared = 6.5486, df = 4, p-value = 0.1618
##
##
## $CramersV
## [1] 0.2559017
##
## $plot
```

We can investigate the distribution of `out2`

across levels of `pred1`

using `num_compare()`

:

```
## $summary_stats
## n obs mis mean stdev med q1 q3
## a 18 18 0 0.006755781 1.0851542 0.04793630 -0.4201223 0.8188215
## b 17 17 0 0.001604250 0.8911016 0.07865256 -0.2591153 0.5775767
## c 15 15 0 0.198539217 1.0332958 -0.07142822 -0.2773362 0.6744763
##
## $decomp
## Call:
## aov(formula = y ~ grp, data = mydat)
##
## Terms:
## grp Residuals
## Sum of Squares 0.39657 47.67131
## Deg. of Freedom 2 47
##
## Residual standard error: 1.007116
## Estimated effects may be unbalanced
##
## $eta_sq
## [1] 0.008250299
##
## $plot
```

`inline`

and `write`

functions`inline_test()`

`inline_reg()`

`inline_coef()`

`inline_anova()`

`write_int()`

`write_p()`

`as_perc()`

Using the data above, we can obtain some inferential results:

```
x = rnorm(50)
y = rnorm(50)
a = sample(letters[1:3], size=50, replace=TRUE)
b = sample(letters[1:3], size=50, replace=TRUE)
test1 = t.test(x)
test2 = chisq.test(table(a,b))
model1 = lm(y ~ x)
model2 = lm(y ~ a)
```

We can then report the results of the hypothesis test inline using `inline_test(test1)`

and get the following: (t(49) = -0.7), (p = 0.49). Simiarly, `inline_test(test2)`

will report the results of the chi-squared test: (^2(4) = 4.85), (p = 0.3). So far `inline_test`

only works for (t) and chi-squared tests, but the goal is to add more functionality - requests gladly accepted.

The regression results can be reported with `inline_reg(model1)`

and `inline_coef(model1, 'x')`

to get (R^2 = 0.02), (F(1,48) = 0.81), (p = 0.37) and (b = -0.14), (t(48) = -0.9), (p = 0.37), respectively. In addition, `inline_anova(model2)`

will report the ANOVA F statistic and relevant results: (F(2,47) = 2.81), (p = 0.07). So far `inline_reg`

and `inline_coef`

currently work for `lm`

and `glm`

objects; `inline_anova`

only works for `lm`

objects.

We can also report the confidence intervals using `write_int()`

with a length-2 vector of interval endpoints. For example, `write_int(c(3.04, 4.7))`

and `write_int(test1$conf.int)`

yield (3.04, 4.70) and (-0.37, 0.18), respectively. If a 2-column matrix is provided to `write_int()`

, the entries in each row will be formatted into an interval and a character vector will be returned.

P-values can be reported using `write_p()`

. This function will take either a numeric value or a list-like object with an element named `p.value`

. For example, `write_p(0.00002)`

gives (p < 0.01) and `write_p(test1)`

gives (p = 0.49).

Many R functions produce proportions, though analysts may want to report the output as a percentage. `as_perc()`

will do this. For example, `as_perc(0.01)`

will produce 1%.

See the help files of all functions described above for more details and options. For example, all test and regression reporting functions have wrappers ending in `_p`

which report only the p-value of the input.

`KreateTableOne`

The package also provides the function `KreateTableOne`

, a wrapper for `CreateTableOne`

from the `tableone`

package which makes the results knitable. First use `KreateTableOne`

in an R chunk with `results='hide'`

(or ouside the RMarkdown document), then recall the saved data frame in a new chunk. For example:

```
table1 = KreateTableOne(x=mtcars, strata='am',
factorVars='vs')
colnames(table1)[1:2] = c('am = 0', 'am = 1')
```

Then

am = 0 | am = 1 | p | |
---|---|---|---|

n | 19 | 13 | |

mpg (mean (SD)) | 17.15 (3.83) | 24.39 (6.17) | <0.001 |

cyl (mean (SD)) | 6.95 (1.54) | 5.08 (1.55) | 0.002 |

disp (mean (SD)) | 290.38 (110.17) | 143.53 (87.20) | <0.001 |

hp (mean (SD)) | 160.26 (53.91) | 126.85 (84.06) | 0.180 |

drat (mean (SD)) | 3.29 (0.39) | 4.05 (0.36) | <0.001 |

wt (mean (SD)) | 3.77 (0.78) | 2.41 (0.62) | <0.001 |

qsec (mean (SD)) | 18.18 (1.75) | 17.36 (1.79) | 0.206 |

vs = 1 (%) | 7 (36.8) | 7 (53.8) | 0.556 |

am (mean (SD)) | 0.00 (0.00) | 1.00 (0.00) | <0.001 |

gear (mean (SD)) | 3.21 (0.42) | 4.38 (0.51) | <0.001 |

carb (mean (SD)) | 2.74 (1.15) | 2.92 (2.18) | 0.754 |