plotDiagnostics

Plot observation diagnostics of generalized linear regression model

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Syntax

plotDiagnostics(mdl)

plotDiagnostics(mdl,plottype)

plotDiagnostics(___,Name,Value)

plotDiagnostics(ax,___)

h = plotDiagnostics(___)

Description

plotDiagnostics creates a plot of observation diagnostics, such as leverage and Cook's distance, to identify outliers and influential observations.

plotDiagnostics(mdl) creates a leverage plot of the generalized linear regression model (mdl) observations. A dotted line in the plot represents the recommended threshold values.

example

plotDiagnostics(mdl,plottype) specifies the type of observation diagnostics plottype.

example

plotDiagnostics(___,Name,Value) specifies additional options using one or more name-value pair arguments in addition to any of the input argument combinations in the previous syntaxes. For example, you can specify the marker symbol and size for the data points.

plotDiagnostics(ax,___) plots into the axes specified by ax instead of the current axes (gca). (since R2024a)

h = plotDiagnostics(___) returns graphics objects for the lines or contour in the plot. Use h to modify the properties of a specific line or contour after you create the plot. For a list of properties, see Line Properties and Contour Properties.

Examples

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Find Outliers Using Leverage and Cook's Distance

Open Live Script

Create leverage and Cook's distance plots of a fitted generalized linear model, and find the outliers.

Generate sample data using Poisson random numbers with two underlying predictors X(:,1) and X(:,2).

rng('default') % For reproducibility
rndvars = randn(100,2);
X = [2 + rndvars(:,1),rndvars(:,2)];
mu = exp(1 + X*[1;2]);
y = poissrnd(mu);

Create a generalized linear regression model of Poisson data.

mdl = fitglm(X,y,'y ~ x1 + x2','Distribution','poisson');

Create a leverage plot.

plotDiagnostics(mdl)
legend('show') % Show the legend

Figure contains an axes object. The axes object with title Case order plot of leverage, xlabel Row number, ylabel Leverage contains 2 objects of type line. One or more of the lines displays its values using only markers These objects represent Leverage, Reference Line.

The dotted line represents the recommended threshold value 2*p/n, where p is the number of coefficients, and n is the number of observations. Find the threshold value using the NumCoefficients and NumObservations properties.

t_leverage = 2*mdl.NumCoefficients/mdl.NumObservations

t_leverage = 
0.0600

Find the observations with leverage values that exceed the threshold value.

find(mdl.Diagnostics.Leverage > t_leverage)

You can also find an observation number by using a data tip. Select the data points above the threshold line to display their data tips. The data tip includes the x-axis and y-axis values for the selected point, along with the observation number.

Plot the Cook's distance values.

plotDiagnostics(mdl,'cookd')

Figure contains an axes object. The axes object with title Case order plot of Cook's distance, xlabel Row number, ylabel Cook's distance contains 2 objects of type line. One or more of the lines displays its values using only markers These objects represent Cook's distance, Reference Line.

The dotted line represents the recommended threshold value. Compute the threshold value t_cookd.

t_cookd = 3*mean(mdl.Diagnostics.CooksDistance')

t_cookd = 
0.0294

Find the observations with the Cook's distance values that exceed the threshold value.

find(mdl.Diagnostics.CooksDistance > t_cookd)

Three observations (21, 65, and 70) are outliers by both measures, but some points (9, 15, 27, and 64) are outliers by only one measure.

Input Arguments

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`mdl` — Generalized linear regression model
`GeneralizedLinearModel` object

Generalized linear regression model, specified as a GeneralizedLinearModel object created using fitglm or stepwiseglm.

`plottype` — Type of plot
`'leverage'` (default) | `'contour'` | `'cookd'`

Type of plot, specified as one of the values in this table.

Value	Plot Type	Dotted Reference Line in Plot	Purpose
`'contour'`	Residual vs. leverage with overlaid contours of Cook's distance	Contours of Cook's distance	Identify observations with large residual values, high leverage, and large Cook's distance values.
`'cookd'`	Cook's distance	Recommended threshold, computed by `3*mean(mdl.Diagnostics.CooksDistance)`	Identify observations with large Cook's distance values.
`'leverage'`	Leverage	Recommended threshold, computed by `2*p/n`, where `p` is the number of coefficients (`mdl.NumCoefficients`) and `n` is the number of observations (`mdl.NumObservations`)	Identify high leverage observations.

For 'cookd' and 'leverage', the x-axis is the row number (case order) of observations.

The Diagnostics property of mdl contains the diagnostic values used by plotDiagnostics to create plots.

For more information about observation diagnostics, see Cook’s Distance and Leverage.

`ax` — Target axes
`Axes` object

Since R2024a

Target axes, specified as an Axes object. If you do not specify the axes, then plotDiagnostics uses the current axes (gca).

Name-Value Arguments

Specify optional pairs of arguments as Name1=Value1,...,NameN=ValueN, where Name is the argument name and Value is the corresponding value. Name-value arguments must appear after other arguments, but the order of the pairs does not matter.

Before R2021a, use commas to separate each name and value, and enclose Name in quotes.

Example: 'Color','blue','Marker','o'

Note

The graphical properties listed here are only a subset. For a complete list, see Line Properties. The specified properties determine the appearance of diagnostic data points.

`Color` — Line color
RGB triplet | hexadecimal color code | color name | short name

Line color, specified as the comma-separated pair consisting of 'Color' and an RGB triplet, hexadecimal color code, color name, or short name for one of the color options listed in the following table.

The 'Color' name-value pair argument also determines marker outline color and marker fill color if 'MarkerEdgeColor' is 'auto' (default) and 'MarkerFaceColor' is 'auto'.

For a custom color, specify an RGB triplet or a hexadecimal color code.

An RGB triplet is a three-element row vector whose elements specify the intensities of the red, green, and blue components of the color. The intensities must be in the range [0,1], for example, [0.4 0.6 0.7].
A hexadecimal color code is a string scalar or character vector that starts with a hash symbol (#) followed by three or six hexadecimal digits, which can range from 0 to F. The values are not case sensitive. Therefore, the color codes "#FF8800", "#ff8800", "#F80", and "#f80" are equivalent.

Alternatively, you can specify some common colors by name. This table lists the named color options, the equivalent RGB triplets, and hexadecimal color codes.

Color Name	Short Name	RGB Triplet	Hexadecimal Color Code	Appearance
`"red"`	`"r"`	`[1 0 0]`	`"#FF0000"`
`"green"`	`"g"`	`[0 1 0]`	`"#00FF00"`
`"blue"`	`"b"`	`[0 0 1]`	`"#0000FF"`
`"cyan"`	`"c"`	`[0 1 1]`	`"#00FFFF"`
`"magenta"`	`"m"`	`[1 0 1]`	`"#FF00FF"`
`"yellow"`	`"y"`	`[1 1 0]`	`"#FFFF00"`
`"black"`	`"k"`	`[0 0 0]`	`"#000000"`
`"white"`	`"w"`	`[1 1 1]`	`"#FFFFFF"`
`"none"`	Not applicable	Not applicable	Not applicable	No color

Here are the RGB triplets and hexadecimal color codes for the default colors MATLAB^® uses in many types of plots.

RGB Triplet	Hexadecimal Color Code	Appearance
`[0 0.4470 0.7410]`	`"#0072BD"`
`[0.8500 0.3250 0.0980]`	`"#D95319"`
`[0.9290 0.6940 0.1250]`	`"#EDB120"`
`[0.4940 0.1840 0.5560]`	`"#7E2F8E"`
`[0.4660 0.6740 0.1880]`	`"#77AC30"`
`[0.3010 0.7450 0.9330]`	`"#4DBEEE"`
`[0.6350 0.0780 0.1840]`	`"#A2142F"`

Example: 'Color','blue'

`LineWidth` — Line width
positive value

Line width, specified as the comma-separated pair consisting of 'LineWidth' and a positive value in points. If the line has markers, then the line width also affects the marker edges.

Example: 'LineWidth',0.75

`Marker` — Marker symbol
`'o'` | `'+'` | `'*'` | `'.'` | `'x'` | ...

Marker symbol, specified as the comma-separated pair consisting of 'Marker' and one of the values in this table.

Marker	Description	Resulting Marker
`"o"`	Circle
`"+"`	Plus sign
`"*"`	Asterisk
`"."`	Point
`"x"`	Cross
`"_"`	Horizontal line
`"\|"`	Vertical line
`"square"`	Square
`"diamond"`	Diamond
`"^"`	Upward-pointing triangle
`"v"`	Downward-pointing triangle
`">"`	Right-pointing triangle
`"<"`	Left-pointing triangle
`"pentagram"`	Pentagram
`"hexagram"`	Hexagram
`"none"`	No markers	Not applicable

Example: 'Marker','+'

`MarkerEdgeColor` — Marker outline color
`'auto'` (default) | `'none'` | RGB triplet | hexadecimal color code | color name | short name

Marker outline color, specified as the comma-separated pair consisting of 'MarkerEdgeColor' and an RGB triplet, hexadecimal color code, color name, or short name for one of the color options listed in the Color name-value pair argument.

The default value of 'auto' uses the same color specified by using 'Color'.

Example: 'MarkerEdgeColor','blue'

`MarkerFaceColor` — Marker fill color
`'none'` (default) | `'auto'` | RGB triplet | hexadecimal color code | color name | short name

Marker fill color, specified as the comma-separated pair consisting of 'MarkerFaceColor' and an RGB triplet, hexadecimal color code, color name, or short name for one of the color options listed in the Color name-value pair argument.

The 'auto' value uses the same color specified by using 'Color'.

Example: 'MarkerFaceColor','blue'

`MarkerSize` — Marker size
`6` (default) | positive value

Marker size, specified as the comma-separated pair consisting of 'MarkerSize' and a positive value in points.

Example: 'MarkerSize',2

Output Arguments

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`h` — Graphics objects
graphics array

Graphics objects corresponding to the lines or contour in the plot, returned as a graphics array. Use dot notation to query and set properties of the graphics objects. For details, see Line Properties and Contour Properties.

You can use name-value pair arguments to specify the appearance of diagnostic data points corresponding to the first graphics object h(1).

More About

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Cook’s Distance

Cook’s distance is the scaled change in fitted values, which is useful for identifying outliers in the observations for predictor variables. Cook’s distance shows the influence of each observation on the fitted response values. An observation with Cook’s distance larger than three times the mean Cook’s distance might be an outlier.

The Cook’s distance D_i of observation i is

$D_{i} = w_{i} \frac{e_{i}^{2}}{p \hat{φ}} \frac{h_{i i}}{{(1 - h_{i i})}^{2}},$

where

$\hat{φ}$ is the dispersion parameter (estimated or theoretical).
e_i is the linear predictor residual, $g (y_{i}) - x_{i} \hat{β}$ , where
- g is the link function.
- y_i is the observed response.
- x_i is the observation.
- $\hat{β}$ is the estimated coefficient vector.
p is the number of coefficients in the regression model.
h_ii is the ith diagonal element of the Hat Matrix H.

Leverage

Leverage is a measure of the effect of a particular observation on the regression predictions due to the position of that observation in the space of the inputs.

The leverage of observation i is the value of the ith diagonal term h_ii of the hat matrix H. Because the sum of the leverage values is p (the number of coefficients in the regression model), an observation i can be considered an outlier if its leverage substantially exceeds p/n, where n is the number of observations.

Hat Matrix

The hat matrix is a projection matrix that projects the vector of response observations onto the vector of predictions.

The hat matrix H is defined in terms of the data matrix X and a diagonal weight matrix W:

H = X(X^TWX)^–1X^TW^T.

W has diagonal elements w_i:

$w_{i} = \frac{g^{'} (μ_{i})}{\sqrt{V (μ_{i})}},$

where

g is the link function mapping y_i to x_ib.
$g^{'}$ is the derivative of the link function g.
V is the variance function.
μ_i is the ith mean.

The diagonal elements H_ii satisfy

$\begin{array}{l} 0 \leq h_{i i} \leq 1 \\ \sum_{i = 1}^{n} h_{i i} = p, \end{array}$

where n is the number of observations (rows of X), and p is the number of coefficients in the regression model.

Tips

The data cursor displays the values of the selected plot point in a data tip (small text box located next to the data point). The data tip includes the x-axis and y-axis values for the selected point, along with the observation name or number.
Use legend('show') to show the pre-populated legend.

Alternative Functionality

A GeneralizedLinearModel object provides multiple plotting functions.

When verifying a model, use plotDiagnostics to find questionable data and to understand the effect of each observation. Also, use plotResiduals to analyze the residuals of the model.
After fitting a model, use plotPartialDependence to understand the effect of a particular predictor. Also, use plotSlice to plot slices through the prediction surface.

References

[1] Neter, J., M. H. Kutner, C. J. Nachtsheim, and W. Wasserman. Applied Linear Statistical Models, Fourth Edition. Chicago: McGraw-Hill Irwin, 1996.

Extended Capabilities

GPU Arrays
Accelerate code by running on a graphics processing unit (GPU) using Parallel Computing Toolbox™.

This function fully supports GPU arrays. For more information, see Run MATLAB Functions on a GPU (Parallel Computing Toolbox).

Version History

Introduced in R2012a

expand all

R2024a: Specify target axes

Specify the target axes for the plot by using the ax input argument.

plotDiagnostics

Syntax

Description

Examples

Find Outliers Using Leverage and Cook's Distance

Input Arguments

`mdl` — Generalized linear regression model
`GeneralizedLinearModel` object

`plottype` — Type of plot
`'leverage'` (default) | `'contour'` | `'cookd'`

`ax` — Target axes
`Axes` object

Name-Value Arguments

`Color` — Line color
RGB triplet | hexadecimal color code | color name | short name

`LineWidth` — Line width
positive value

`Marker` — Marker symbol
`'o'` | `'+'` | `'*'` | `'.'` | `'x'` | ...

`MarkerEdgeColor` — Marker outline color
`'auto'` (default) | `'none'` | RGB triplet | hexadecimal color code | color name | short name

`MarkerFaceColor` — Marker fill color
`'none'` (default) | `'auto'` | RGB triplet | hexadecimal color code | color name | short name

`MarkerSize` — Marker size
`6` (default) | positive value

Output Arguments

`h` — Graphics objects
graphics array

More About

Cook’s Distance

Leverage

Hat Matrix

Tips

Alternative Functionality

References

Extended Capabilities

GPU Arrays
Accelerate code by running on a graphics processing unit (GPU) using Parallel Computing Toolbox™.

Version History

R2024a: Specify target axes

See Also

Topics

plotDiagnostics

Syntax

Description

Examples

Find Outliers Using Leverage and Cook's Distance

Input Arguments

mdl — Generalized linear regression model GeneralizedLinearModel object

plottype — Type of plot 'leverage' (default) | 'contour' | 'cookd'

ax — Target axes Axes object

Name-Value Arguments

Color — Line color RGB triplet | hexadecimal color code | color name | short name

LineWidth — Line width positive value

Marker — Marker symbol 'o' | '+' | '*' | '.' | 'x' | ...

MarkerEdgeColor — Marker outline color 'auto' (default) | 'none' | RGB triplet | hexadecimal color code | color name | short name

MarkerFaceColor — Marker fill color 'none' (default) | 'auto' | RGB triplet | hexadecimal color code | color name | short name

MarkerSize — Marker size 6 (default) | positive value

Output Arguments

h — Graphics objects graphics array

More About

Cook’s Distance

Leverage

Hat Matrix

Tips

Alternative Functionality

References

Extended Capabilities

GPU Arrays Accelerate code by running on a graphics processing unit (GPU) using Parallel Computing Toolbox™.

Version History

R2024a: Specify target axes

See Also

Topics

`mdl` — Generalized linear regression model
`GeneralizedLinearModel` object

`plottype` — Type of plot
`'leverage'` (default) | `'contour'` | `'cookd'`

`ax` — Target axes
`Axes` object

`Color` — Line color
RGB triplet | hexadecimal color code | color name | short name

`LineWidth` — Line width
positive value

`Marker` — Marker symbol
`'o'` | `'+'` | `'*'` | `'.'` | `'x'` | ...

`MarkerEdgeColor` — Marker outline color
`'auto'` (default) | `'none'` | RGB triplet | hexadecimal color code | color name | short name

`MarkerFaceColor` — Marker fill color
`'none'` (default) | `'auto'` | RGB triplet | hexadecimal color code | color name | short name

`MarkerSize` — Marker size
`6` (default) | positive value

`h` — Graphics objects
graphics array

GPU Arrays
Accelerate code by running on a graphics processing unit (GPU) using Parallel Computing Toolbox™.