Utilities for Developing R Software • oeli

This R package provides helper functions I found useful when developing R code - perhaps you will too! The released package version can be installed via:

install.packages("oeli")

The following shows some demos. Click the headings for references on all available helpers in each category.

Distributions

The package has density and sampling functions for some distributions not included in base R, like the Dirichlet:

ddirichlet(x = c(0.2, 0.3, 0.5), concentration = 1:3)
#> [1] 4.5
rdirichlet(concentration = 1:3)
#> [1] 0.2832878 0.5086812 0.2080309

For faster computation, Rcpp implementations are also available:

microbenchmark::microbenchmark(
  "R"    = rmvnorm(mean = c(0, 0, 0), Sigma = diag(3)),
  "Rcpp" = rmvnorm_cpp(mean = c(0, 0, 0), Sigma = diag(3))
)
#> Unit: microseconds
#>  expr   min     lq    mean median     uq    max neval
#>     R 275.3 295.65 345.847  310.1 332.45 2386.5   100
#>  Rcpp   2.7   3.20   6.245    4.8   5.40  164.2   100

Function helpers

Retrieving default arguments of a function:

f <- function(a, b = 1, c = "", ...) { }
function_defaults(f)
#> $b
#> [1] 1
#> 
#> $c
#> [1] ""

Indexing helpers

Create all possible permutations of vector elements:

permutations(LETTERS[1:3])
#> [[1]]
#> [1] "A" "B" "C"
#> 
#> [[2]]
#> [1] "A" "C" "B"
#> 
#> [[3]]
#> [1] "B" "A" "C"
#> 
#> [[4]]
#> [1] "B" "C" "A"
#> 
#> [[5]]
#> [1] "C" "A" "B"
#> 
#> [[6]]
#> [1] "C" "B" "A"

Package helpers

Quickly have a basic logo for your new package:

logo <- package_logo("my_package", brackets = TRUE)
print(logo)

How to print a matrix without filling up the entire console?

x <- matrix(rnorm(10000), ncol = 100, nrow = 100)
print_matrix(x, rowdots = 4, coldots = 4, digits = 2, label = "what a big matrix")
#> what a big matrix : 100 x 100 matrix of doubles 
#>         [,1]  [,2]  [,3] ... [,100]
#> [1,]    0.79 -0.43 -0.87 ...  -2.12
#> [2,]   -1.11  1.98 -2.42 ...   1.65
#> [3,]    1.66  1.76  0.25 ...  -2.97
#> ...      ...   ...   ... ...    ...
#> [100,]  0.44  0.28  0.53 ...  -1.75

And what about a data.frame?

x <- data.frame(x = rnorm(1000), y = LETTERS[1:10])
print_data.frame(x, rows = 7, digits = 0)
#>      x  y
#> 1     0 A
#> 2    -1 B
#> 3     0 C
#> 4     0 D
#> <993 rows hidden>
#>          
#> 998   0 H
#> 999   0 I
#> 1000  0 J

Simulation helpers

Let’s simulate correlated regressor values from different marginal distributions:

labels <- c("P", "C", "N1", "N2", "U")
n <- 100
marginals <- list(
  "P" = list(type = "poisson", lambda = 2),
  "C" = list(type = "categorical", p = c(0.3, 0.2, 0.5)),
  "N1" = list(type = "normal", mean = -1, sd = 2),
  "U" = list(type = "uniform", min = -2, max = -1)
)
correlation <- matrix(
  c(1, -0.3, -0.1, 0, 0.5,
    -0.3, 1, 0.3, -0.5, -0.7,
    -0.1, 0.3, 1, -0.3, -0.3,
    0, -0.5, -0.3, 1, 0.1,
    0.5, -0.7, -0.3, 0.1, 1),
  nrow = 5, ncol = 5
)
data <- correlated_regressors(
  labels = labels, n = n, marginals = marginals, correlation = correlation
)
head(data)
#>   P C        N1          N2         U
#> 1 1 2 -3.619643  1.24813328 -1.782100
#> 2 1 3 -4.117207  0.19133009 -1.585383
#> 3 2 1  2.146791 -0.08796485 -1.290140
#> 4 2 3 -3.501855  0.60817726 -1.688658
#> 5 1 3  2.707852 -2.17507050 -1.912338
#> 6 2 1 -2.222701  2.28324260 -1.646795
cor(data)
#>              P          C          N1          N2           U
#> P   1.00000000 -0.3164384 -0.08426915 -0.03743832  0.54776279
#> C  -0.31643843  1.0000000  0.19326415 -0.50596805 -0.75090001
#> N1 -0.08426915  0.1932641  1.00000000 -0.30000000 -0.26643345
#> N2 -0.03743832 -0.5059680 -0.30000000  1.00000000  0.09397231
#> U   0.54776279 -0.7509000 -0.26643345  0.09397231  1.00000000

Transformation helpers

The group_data.frame() function groups a given data.frame based on the values in a specified column:

df <- data.frame("label" = c("A", "B"), "number" = 1:10)
group_data.frame(df = df, by = "label")
#> $A
#>   label number
#> 1     A      1
#> 3     A      3
#> 5     A      5
#> 7     A      7
#> 9     A      9
#> 
#> $B
#>    label number
#> 2      B      2
#> 4      B      4
#> 6      B      6
#> 8      B      8
#> 10     B     10

Validation helpers

Is my matrix a proper transition probability matrix?

matrix <- diag(4)
matrix[1, 2] <- 1
check_transition_probability_matrix(matrix)
#> [1] "Must have row sums equal to 1"