An R package that produces a tidy output for tidymodels model evaluation!
Introduction
Sptidy implements a tidy and augment function for base R’s linear regression and Tidymodel’s kmeans clustering to ease model selection and assessment tasks. This package is a simplified reimplementation of the existing tidy and augment functions in the Broom package. Sptidy’s family of tidy functions returns a dataframe that summarizes important model information, while the augment function expands the original dataframe to include additional model specific information by observation. This package is meant to complement Sktidy, a Python package that was created to tidy up the scikit-learn package.
Features
The functions that this package currently support include:
tidy_kmeans(): Returns inertia, cluster location, and number of associated points at the level of clusters in a tidy format.tidy_lr(): Returns coefficients and corresponding feature names in a tidy format.augment_lr(): Returns predictions and residuals for each point in the training data set in a tidy format.augment_kmeans(): Returns assigned cluster and distance from cluster center for the data the kmeans algorithm was fitted with in a tidy format.
How sptidy fits into the R ecosystem
Tidymodels is a “meta-package” for modeling and statistical analysis that share the underlying design philosophy, grammar, and data structures of the tidyverse. One of the packages it includes is broom which takes the messy output of built-in functions in R, such as lm, nls, or t.test, and turns them into tidy data frames. The tidy data refers to outputting the results in a data.frame where each variable has its own column, each observation has its own row, and each value has its own cell. In sptidy, we implement the functions tidy() and augment() for the linear regression model from base R using the function lm() and the KMeans model from R stats package using the function kmeans().
Installation
This package is not yet available on CRAN, but you can install the development version from GitHub with:
devtools::install_github("UBC-MDS/sptidy")Example
This is a basic example which shows you how to solve a common problem:
When working with linear regression and kmeans clustering in R, it’s nice to:
- have a one-stop shop summary data frame on model statistics
- have a data frame with prediction, residual or cluster assignment with respect to each observation
The sptidy package provides tools that make these tasks swift and easy.
Overview
This vignette is the package-wide documentation for R package sptidy. This helps those who want to use this package better understand what sptidy does. A full usage demonstration of all functions in this package is included in this vignette.
Available functions
sptidy provides functions for model evaluation and analysis. These functions work with 2 types of models: lm() and kmeans().
- linear regression
-
tidy_lroutputs summary on lm() -
augment_lraugments a data frame with predictions and residuals
-
- kmeans clustering
-
tidy_kmeansoutputs summary on kmeans() -
augment_kmeansaugments a data frame with cluster assignments
-
Function Usage Demonstration
tidy_lr(): clean summary output for lm()
sptidy::tidy_lr() provides a tidy data frame that summarizes a fitted linear regression object lm(). The argument in the function needs to be a fitted lm() object. The output data frame has 4 columns, describing coefficient estimates, standard error, t-statistics and p-values.
my_lr <- lm(Employed~., data = longley)
sptidy::tidy_lr(my_lr)
#> coef std_err t_stats p_val
#> (Intercept) -3482.2586 890.4204 -3.9108 0.0036
#> GNP.deflator 0.0151 0.0849 0.1774 0.8631
#> GNP -0.0358 0.0335 -1.0695 0.3127
#> Unemployed -0.0202 0.0049 -4.1364 0.0025
#> Armed.Forces -0.0103 0.0021 -4.8220 0.0009
#> Population -0.0511 0.2261 -0.2261 0.8262
#> Year 1.8292 0.4555 4.0159 0.0030augment_lr(): augment data frame from lm()
sptidy::augment_lr() augments the data frame with predictions and residuals from a fitted linear regression object lm(). The first argument is the fitted lm() object. The second and third argument refer to the feature data frame and target data frame that are fitted to the lm() object. The output data frame has additional 2 columns, describing predictions and residuals with respect to each observation.
my_lr <- lm(Employed~., data = longley)
sptidy::augment_lr(my_lr, longley[1:6], as.data.frame(longley$Employed))
#> GNP.deflator GNP Unemployed Armed.Forces Population Year
#> 1947 83.0 234.289 235.6 159.0 107.608 1947
#> 1948 88.5 259.426 232.5 145.6 108.632 1948
#> 1949 88.2 258.054 368.2 161.6 109.773 1949
#> 1950 89.5 284.599 335.1 165.0 110.929 1950
#> 1951 96.2 328.975 209.9 309.9 112.075 1951
#> 1952 98.1 346.999 193.2 359.4 113.270 1952
#> 1953 99.0 365.385 187.0 354.7 115.094 1953
#> 1954 100.0 363.112 357.8 335.0 116.219 1954
#> 1955 101.2 397.469 290.4 304.8 117.388 1955
#> 1956 104.6 419.180 282.2 285.7 118.734 1956
#> 1957 108.4 442.769 293.6 279.8 120.445 1957
#> 1958 110.8 444.546 468.1 263.7 121.950 1958
#> 1959 112.6 482.704 381.3 255.2 123.366 1959
#> 1960 114.2 502.601 393.1 251.4 125.368 1960
#> 1961 115.7 518.173 480.6 257.2 127.852 1961
#> 1962 116.9 554.894 400.7 282.7 130.081 1962
#> longley$Employed predictions residuals
#> 1947 60.323 60.05566 0.26734003
#> 1948 61.122 61.21601 -0.09401394
#> 1949 60.171 60.12471 0.04628717
#> 1950 61.187 61.59711 -0.41011462
#> 1951 63.221 62.91129 0.30971459
#> 1952 63.639 63.88831 -0.24931122
#> 1953 64.989 65.15305 -0.16404896
#> 1954 63.761 63.77418 -0.01318036
#> 1955 66.019 66.00470 0.01430477
#> 1956 67.857 67.40161 0.45539409
#> 1957 68.169 68.18627 -0.01726893
#> 1958 66.513 66.55206 -0.03905504
#> 1959 68.655 68.81055 -0.15554997
#> 1960 69.564 69.64967 -0.08567131
#> 1961 69.331 68.98907 0.34193151
#> 1962 70.551 70.75776 -0.20675783tidy_kmeans(): clean summary output for kmeans()
sptidy::tidy_kmeans() provides a tidy data frame that summarizes a fitted kmeans clustering object kmenas(). The first argument is the fitted kmeans() object. The second argument refers to the data that was fitted to the kmeans() object. The output data frame has 3 columns, describing cluster number, cluster center and number of points within each cluster.
data <- iris[,1:3]
kclust <- kmeans(data, centers = 3)
tidy_kmeans(kclust, data)
#> # A tibble: 3 x 3
#> cluster_number cluster_center n_points
#> <int> <list> <int>
#> 1 1 <dbl [3]> 22
#> 2 2 <dbl [3]> 32
#> 3 3 <dbl [3]> 96augment_kmeans(): augment data frame from kmeans()
sptidy::augment_kmeans() augments the data frame with cluster assignment from a fitted kmeans clustering object kmeans(). The first argument is the fitted kmeans() object. The second argument refers to the data that was fitted to the kmeans() object. The output data frame has additional 1 column, describing cluster assignment with respect to each observation.
data <- iris[,1:3]
kclust <- kmeans(data, centers = 3)
augment_kmeans(kclust, data)
#> Sepal.Length Sepal.Width Petal.Length cluster
#> 1 5.1 3.5 1.4 3
#> 2 4.9 3.0 1.4 3
#> 3 4.7 3.2 1.3 3
#> 4 4.6 3.1 1.5 3
#> 5 5.0 3.6 1.4 3
#> 6 5.4 3.9 1.7 3
#> 7 4.6 3.4 1.4 3
#> 8 5.0 3.4 1.5 3
#> 9 4.4 2.9 1.4 3
#> 10 4.9 3.1 1.5 3
#> 11 5.4 3.7 1.5 3
#> 12 4.8 3.4 1.6 3
#> 13 4.8 3.0 1.4 3
#> 14 4.3 3.0 1.1 3
#> 15 5.8 4.0 1.2 3
#> 16 5.7 4.4 1.5 3
#> 17 5.4 3.9 1.3 3
#> 18 5.1 3.5 1.4 3
#> 19 5.7 3.8 1.7 3
#> 20 5.1 3.8 1.5 3
#> 21 5.4 3.4 1.7 3
#> 22 5.1 3.7 1.5 3
#> 23 4.6 3.6 1.0 3
#> 24 5.1 3.3 1.7 3
#> 25 4.8 3.4 1.9 3
#> 26 5.0 3.0 1.6 3
#> 27 5.0 3.4 1.6 3
#> 28 5.2 3.5 1.5 3
#> 29 5.2 3.4 1.4 3
#> 30 4.7 3.2 1.6 3
#> 31 4.8 3.1 1.6 3
#> 32 5.4 3.4 1.5 3
#> 33 5.2 4.1 1.5 3
#> 34 5.5 4.2 1.4 3
#> 35 4.9 3.1 1.5 3
#> 36 5.0 3.2 1.2 3
#> 37 5.5 3.5 1.3 3
#> 38 4.9 3.6 1.4 3
#> 39 4.4 3.0 1.3 3
#> 40 5.1 3.4 1.5 3
#> 41 5.0 3.5 1.3 3
#> 42 4.5 2.3 1.3 3
#> 43 4.4 3.2 1.3 3
#> 44 5.0 3.5 1.6 3
#> 45 5.1 3.8 1.9 3
#> 46 4.8 3.0 1.4 3
#> 47 5.1 3.8 1.6 3
#> 48 4.6 3.2 1.4 3
#> 49 5.3 3.7 1.5 3
#> 50 5.0 3.3 1.4 3
#> 51 7.0 3.2 4.7 1
#> 52 6.4 3.2 4.5 2
#> 53 6.9 3.1 4.9 1
#> 54 5.5 2.3 4.0 2
#> 55 6.5 2.8 4.6 2
#> 56 5.7 2.8 4.5 2
#> 57 6.3 3.3 4.7 2
#> 58 4.9 2.4 3.3 2
#> 59 6.6 2.9 4.6 2
#> 60 5.2 2.7 3.9 2
#> 61 5.0 2.0 3.5 2
#> 62 5.9 3.0 4.2 2
#> 63 6.0 2.2 4.0 2
#> 64 6.1 2.9 4.7 2
#> 65 5.6 2.9 3.6 2
#> 66 6.7 3.1 4.4 2
#> 67 5.6 3.0 4.5 2
#> 68 5.8 2.7 4.1 2
#> 69 6.2 2.2 4.5 2
#> 70 5.6 2.5 3.9 2
#> 71 5.9 3.2 4.8 2
#> 72 6.1 2.8 4.0 2
#> 73 6.3 2.5 4.9 2
#> 74 6.1 2.8 4.7 2
#> 75 6.4 2.9 4.3 2
#> 76 6.6 3.0 4.4 2
#> 77 6.8 2.8 4.8 1
#> 78 6.7 3.0 5.0 1
#> 79 6.0 2.9 4.5 2
#> 80 5.7 2.6 3.5 2
#> 81 5.5 2.4 3.8 2
#> 82 5.5 2.4 3.7 2
#> 83 5.8 2.7 3.9 2
#> 84 6.0 2.7 5.1 2
#> 85 5.4 3.0 4.5 2
#> 86 6.0 3.4 4.5 2
#> 87 6.7 3.1 4.7 1
#> 88 6.3 2.3 4.4 2
#> 89 5.6 3.0 4.1 2
#> 90 5.5 2.5 4.0 2
#> 91 5.5 2.6 4.4 2
#> 92 6.1 3.0 4.6 2
#> 93 5.8 2.6 4.0 2
#> 94 5.0 2.3 3.3 2
#> 95 5.6 2.7 4.2 2
#> 96 5.7 3.0 4.2 2
#> 97 5.7 2.9 4.2 2
#> 98 6.2 2.9 4.3 2
#> 99 5.1 2.5 3.0 2
#> 100 5.7 2.8 4.1 2
#> 101 6.3 3.3 6.0 1
#> 102 5.8 2.7 5.1 2
#> 103 7.1 3.0 5.9 1
#> 104 6.3 2.9 5.6 1
#> 105 6.5 3.0 5.8 1
#> 106 7.6 3.0 6.6 1
#> 107 4.9 2.5 4.5 2
#> 108 7.3 2.9 6.3 1
#> 109 6.7 2.5 5.8 1
#> 110 7.2 3.6 6.1 1
#> 111 6.5 3.2 5.1 1
#> 112 6.4 2.7 5.3 1
#> 113 6.8 3.0 5.5 1
#> 114 5.7 2.5 5.0 2
#> 115 5.8 2.8 5.1 2
#> 116 6.4 3.2 5.3 1
#> 117 6.5 3.0 5.5 1
#> 118 7.7 3.8 6.7 1
#> 119 7.7 2.6 6.9 1
#> 120 6.0 2.2 5.0 2
#> 121 6.9 3.2 5.7 1
#> 122 5.6 2.8 4.9 2
#> 123 7.7 2.8 6.7 1
#> 124 6.3 2.7 4.9 2
#> 125 6.7 3.3 5.7 1
#> 126 7.2 3.2 6.0 1
#> 127 6.2 2.8 4.8 2
#> 128 6.1 3.0 4.9 2
#> 129 6.4 2.8 5.6 1
#> 130 7.2 3.0 5.8 1
#> 131 7.4 2.8 6.1 1
#> 132 7.9 3.8 6.4 1
#> 133 6.4 2.8 5.6 1
#> 134 6.3 2.8 5.1 1
#> 135 6.1 2.6 5.6 1
#> 136 7.7 3.0 6.1 1
#> 137 6.3 3.4 5.6 1
#> 138 6.4 3.1 5.5 1
#> 139 6.0 3.0 4.8 2
#> 140 6.9 3.1 5.4 1
#> 141 6.7 3.1 5.6 1
#> 142 6.9 3.1 5.1 1
#> 143 5.8 2.7 5.1 2
#> 144 6.8 3.2 5.9 1
#> 145 6.7 3.3 5.7 1
#> 146 6.7 3.0 5.2 1
#> 147 6.3 2.5 5.0 2
#> 148 6.5 3.0 5.2 1
#> 149 6.2 3.4 5.4 1
#> 150 5.9 3.0 5.1 2