do_corr — do_corr • biostat

do_corr

do_corr(
  x,
  y = NULL,
  method = c("spearman", "kendall", "pearson")[1],
  use = "complete.cases",
  conf = 0.95,
  R = 999,
  sim = "balanced",
  ci_type = c("bca"),
  p_adjust_method = p.adjust.methods[1],
  ss = p05plus
)

# S3 method for do_corr
print(
  x,
  ...,
  digits = 2,
  digits_p = 3,
  ss = attr(x, "ss"),
  p_col = c("p", "p.adj")
)

# S3 method for do_corr
pander(
  x,
  ...,
  caption = "The results of correlation analysis",
  digits = 2,
  digits_p = 3,
  ss = attr(x, "ss"),
  p_col = c("p", "p.adj")
)

Arguments

x, y, method, use, conf, R, sim, ci_type, p_adjust_method, ss	`# FIXME:` not documented

Examples

data(iris)
ans <- do_corr(iris[, -5])
ans
#>                     variables   cor ci_low ci_upp          p      p.adj   n
#> 1  Sepal.Length - Sepal.Width -0.17  -0.32  -0.02  0.041 *    0.041 *   150
#> 2 Sepal.Length - Petal.Length  0.88   0.84   0.91 <0.001 *** <0.001 *** 150
#> 3  Sepal.Length - Petal.Width  0.83   0.78   0.87 <0.001 *** <0.001 *** 150
#> 4  Sepal.Width - Petal.Length -0.31  -0.46  -0.15 <0.001 *** <0.001 *** 150
#> 5   Sepal.Width - Petal.Width -0.29  -0.44  -0.12 <0.001 *** <0.001 *** 150
#> 6  Petal.Length - Petal.Width  0.94   0.92   0.95 <0.001 *** <0.001 *** 150
#>     method
#> 1 spearman
#> 2 spearman
#> 3 spearman
#> 4 spearman
#> 5 spearman
#> 6 spearman

library(pander)
pander(ans)
#> 
#> --------------------------------------------------------------------
#>           variables             cor    ci_low   ci_upp       p      
#> ----------------------------- ------- -------- -------- ------------
#>  Sepal.Length - Sepal.Width    -0.17   -0.32    -0.02     0.041 *   
#> 
#>  Sepal.Length - Petal.Length   0.88     0.84     0.91    <0.001 *** 
#> 
#>  Sepal.Length - Petal.Width    0.83     0.78     0.87    <0.001 *** 
#> 
#>  Sepal.Width - Petal.Length    -0.31   -0.46    -0.15    <0.001 *** 
#> 
#>   Sepal.Width - Petal.Width    -0.29   -0.44    -0.12    <0.001 *** 
#> 
#>  Petal.Length - Petal.Width    0.94     0.92     0.95    <0.001 *** 
#> --------------------------------------------------------------------
#> 
#> Table: The results of correlation analysis (continued below)
#> 
#>  
#> -----------------------------
#>    p.adj       n     method  
#> ------------ ----- ----------
#>   0.041 *     150   spearman 
#> 
#>  <0.001 ***   150   spearman 
#> 
#>  <0.001 ***   150   spearman 
#> 
#>  <0.001 ***   150   spearman 
#> 
#>  <0.001 ***   150   spearman 
#> 
#>  <0.001 ***   150   spearman 
#> -----------------------------
#>