Platform Option
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Object Added to Plot
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Report Added to Report Window
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Quantiles
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Box plots
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Quantiles report
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Means/Anova
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Mean diamonds
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Oneway anova reports
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Means and Std Dev
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Mean lines, error bars, and standard deviation lines
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Means and Std Deviations report
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Compare Means
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Comparison circles
(except Nonparametric Multiple Comparisons option)
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Means Comparison reports
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Quantiles
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Lists the following quantiles for each group:
• 0% (Minimum)
• 10%
• 25%
• 50% (Median)
• 75%
• 90%
• 100% (Maximum)
Activates Box Plots from the Display Options menu.
See “Quantiles”.
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Means/Anova
or
Means/Anova/Pooled t
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Fits means for each group and performs a one-way analysis of variance to test if there are differences among the means. See “Means/Anova and Means/Anova/Pooled t”.
The Means/Anova/Pooled t option appears only if the X factor has two levels.
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Means and Std Dev
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Gives summary statistics for each group. The standard errors for the means use individual group standard deviations rather than the pooled estimate of the standard deviation.
The plot now contains mean lines, error bars, and standard deviation lines. For a brief description of these elements, see “Display Options”. For more details about these elements, see “Mean Lines, Error Bars, and Standard Deviation Lines”.
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t test
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Produces a t-test report assuming that the variances are not equal. See “The t-test Report”.
This option appears only if the X factor has two levels.
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Analysis of Means Methods
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Provides four commands for performing Analysis of Means (ANOM) procedures. There are commands for comparing both means and variances. See “Analysis of Means Methods”.
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Compare Means
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Provides multiple-comparison methods for comparing sets of group means. See “Compare Means”.
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Nonparametric
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Provides nonparametric comparisons of group means. See “Nonparametric”.
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Unequal Variances
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Performs four tests for equality of group variances. Also gives the Welch test, which is an anova test for comparing means when the variances within groups are not equal. See “Unequal Variances”.
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Equivalence Test
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Tests that a difference is less than a threshold value. See “Equivalence Test”.
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Power
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Provides calculations of statistical power and other details about a given hypothesis test. See “Power”.
The Power Details window and reports also appear within the Fit Model platform. For further discussion and examples of power calculations, see the Fitting Linear Models book.
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Set a Level
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You can select an option from the most common alpha levels or specify any level with the Other selection. Changing the alpha level results in the following actions:
• recalculates confidence limits
• adjusts the mean diamonds on the plot (if they are showing)
• modifies the upper and lower confidence level values in reports
• changes the critical number and comparison circles for all Compare Means reports
• changes the critical number for all Nonparametric Multiple Comparison reports
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Normal Quantile Plot
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Provides the following options for plotting the quantiles of the data in each group:
• Plot Actual by Quantile generates a quantile plot with the response variable on the y-axis and quantiles on the x-axis. The plot shows quantiles computed within each level of the categorical X factor.
• Plot Quantile by Actual reverses the x- and y-axes.
• Line of Fit draws straight diagonal reference lines on the plot for each level of the X variable. This option is available only once you have created a plot (Actual by Quantile or Quantile by Actual).
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CDF Plot
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Plots the cumulative distribution function for all of the groups in the Oneway report. See “CDF Plot”.
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Densities
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Compares densities across groups. See “Densities”.
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Matching Column
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Specify a matching variable to perform a matching model analysis. Use this option when the data in your Oneway analysis comes from matched (paired) data, such as when observations in different groups come from the same subject.
The plot now contains matching lines that connect the matching points.
See “Matching Column”.
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Save
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Saves the following quantities as new columns in the current data table:
• Save Residuals saves values computed as the response variable minus the mean of the response variable within each level of the factor variable.
• Save Standardized saves standardized values of the response variable computed within each level of the factor variable. This is the centered response divided by the standard deviation within each level.
• Save Normal Quantiles saves normal quantile values computed within each level of the categorical factor variable.
• Save Predicted saves the predicted mean of the response variable for each level of the factor variable.
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Display Options
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Adds or removes elements from the plot. See “Display Options”.
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Script
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This menu contains options that are available to all platforms. They enable you to redo the analysis or save the JSL commands for the analysis to a window or a file. For more information, see Using JMP.
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All Graphs
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Shows or hides all graphs.
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Points
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Shows or hides data points on the plot.
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Box Plots
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Shows or hides outlier box plots for each group.
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Mean Diamonds
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Draws a horizontal line through the mean of each group proportional to its x-axis. The top and bottom points of the mean diamond show the upper and lower 95% confidence points for each group. See “Mean Diamonds and X-Axis Proportional”.
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Mean Lines
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Draws a line at the mean of each group. See “Mean Lines, Error Bars, and Standard Deviation Lines”.
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Mean CI Lines
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Draws lines at the upper and lower 95% confidence levels for each group.
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Mean Error Bars
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Identifies the mean of each group and shows error bars one standard error above and below the mean. See “Mean Lines, Error Bars, and Standard Deviation Lines”.
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Grand Mean
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Draws the overall mean of the Y variable on the plot.
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Std Dev Lines
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Shows lines one standard deviation above and below the mean of each group. See “Mean Lines, Error Bars, and Standard Deviation Lines”.
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Comparison Circles
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Shows or hides comparison circles. This option is available only when one of the Compare Means options is selected. See “Statistical Details for Comparison Circles”.
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Connect Means
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Connects the group means with a straight line.
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Mean of Means
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Draws a line at the mean of the group means.
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X-Axis proportional
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Makes the spacing on the x-axis proportional to the sample size of each level. See “Mean Diamonds and X-Axis Proportional”.
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Points Spread
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Spreads points over the width of the interval
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Points Jittered
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Adds small spaces between points that overlay on the same y value. The horizontal adjustment of points varies from 0.375 to 0.625 with a 4*(Uniform-0.5)5 distribution.
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Matching Lines
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(Only appears when the Matching Column option is selected.) Connects matching points.
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Matching Dotted Lines
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Only appears when the Matching Column option is selected.) Draws dotted lines to connect cell means from missing cells in the table. The values used as the endpoints of the lines are obtained using a two-way anova model.
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Histograms
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Draws side-by-side histograms to the right of the original plot.
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Element
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Reference
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Mean diamonds are added to the Oneway plot
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Reports
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See “The t-test Report”.
Note: This report appears only if the Means/Anova/Pooled t option is selected.
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Note: This report appears only if you have specified a Block variable in the launch window.
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Rsquare
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Measures the proportion of the variation accounted for by fitting means to each factor level. The remaining variation is attributed to random error. The R2 value is 1 if fitting the group means accounts for all the variation with no error. An R2 of 0 indicates that the fit serves no better as a prediction model than the overall response mean. For more information, see “Statistical Details for the Summary of Fit Report”.
R2 is also called the coefficient of determination.
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Adj Rsquare
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Adjusts R2 to make it more comparable over models with different numbers of parameters by using the degrees of freedom in its computation. For more information, see “Statistical Details for the Summary of Fit Report”.
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Root Mean Square Error
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Estimates the standard deviation of the random error. It is the square root of the mean square for Error found in the Analysis of Variance report.
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Mean of Response
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Overall mean (arithmetic average) of the response variable.
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Observations (or Sum Wgts)
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Number of observations used in estimating the fit. If weights are used, this is the sum of the weights.
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t Test plot
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Shows the sampling distribution of the difference in the means, assuming the null hypothesis is true. The vertical red line is the actual difference in the means. The shaded areas correspond to the p-values.
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Difference
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Shows the estimated difference between the two X levels. In the plots, the Difference value appears as a red line that compares the two levels.
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Std Err Dif
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Shows the standard error of the difference.
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Upper CL Dif
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Shows the upper confidence limit for the difference.
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Lower CL Dif
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Shows the lower confidence limit for the difference.
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Confidence
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Shows the level of confidence (1-alpha). To change the level of confidence, select a new alpha level from the Set α Level command from the platform red triangle menu.
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t Ratio
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Value of the t-statistic.
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DF
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The degrees of freedom used in the t-test.
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Prob > |t|
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The p-value associated with a two-tailed test.
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Prob > t
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The p-value associated with a lower-tailed test.
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Prob < t
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The p-value associated with an upper-tailed test.
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Source
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Lists the three sources of variation, which are the model source, Error, and C. Total (corrected total).
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DF
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Records an associated degrees of freedom (DF for short) for each source of variation:
• The degrees of freedom for C. Total are N - 1, where N is the total number of observations used in the analysis.
• If the X factor has k levels, then the model has k - 1 degrees of freedom.
The Error degrees of freedom is the difference between the C. Total degrees of freedom and the Model degrees of freedom (in other words, N - k).
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Sum of Squares
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Records a sum of squares (SS for short) for each source of variation:
• The total (C. Total) sum of squares of each response from the overall response mean. The C. Total sum of squares is the base model used for comparison with all other models.
• The sum of squared distances from each point to its respective group mean. This is the remaining unexplained Error (residual) SS after fitting the analysis of variance model.
The total SS minus the error SS gives the sum of squares attributed to the model. This tells you how much of the total variation is explained by the model.
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Mean Square
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Is a sum of squares divided by its associated degrees of freedom:
• The Model mean square estimates the variance of the error, but only under the hypothesis that the group means are equal.
• The Error mean square estimates the variance of the error term independently of the model mean square and is unconditioned by any model hypothesis.
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F Ratio
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Model mean square divided by the error mean square. If the hypothesis that the group means are equal (there is no real difference between them) is true, then both the mean square for error and the mean square for model estimate the error variance. Their ratio has an F distribution. If the analysis of variance model results in a significant reduction of variation from the total, the F ratio is higher than expected.
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Prob>F
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Probability of obtaining (by chance alone) an F value greater than the one calculated if, in reality, there is no difference in the population group means. Observed significance probabilities of 0.05 or less are often considered evidence that there are differences in the group means.
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Level
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Lists the levels of the X variable.
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Number
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Lists the number of observations in each group.
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Mean
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Lists the mean of each group.
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Std Error
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Lists the estimates of the standard deviations for the group means. This standard error is estimated assuming that the variance of the response is the same in each level. It is the root mean square error found in the Summary of Fit report divided by the square root of the number of values used to compute the group mean.
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Lower 95% and Upper 95%
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Lists the lower and upper 95% confidence interval for the group means.
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ANOM
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Compares group means to the overall mean. This method assumes that your data is approximately normally distributed. See “Example of an Analysis of Means Chart”.
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ANOM with Transformed Ranks
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This is the nonparametric version of the ANOM analysis. Use this method if your data is clearly non-normal and cannot be transformed to normality. Compares each group mean transformed rank to the overall mean transformed rank.
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ANOM for Variances
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Compares group standard deviations to the root mean square error. This method assumes that your data is approximately normally distributed. To use this method, each group must have at least four observations. See “Example of an Analysis of Means for Variances Chart”.
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ANOM for Variances with Levene (ADM)
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This is the nonparametric version of the ANOM for Variances analysis. Use this method if you suspect your data is non-normal and cannot be transformed to normality. Compares the group means of the absolute deviation from the median (ADM) to the overall mean ADM.
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Set Alpha Level
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Select an option from the most common alpha levels or specify any level with the Other selection. Changing the alpha level modifies the upper and lower decision limits.
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Show Summary Report
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For ANOM, creates a report showing group means and decision limits.
• For ANOM with Transformed Ranks, creates a report showing group mean transformed ranks and decision limits.
• For ANOM for Variances, creates a report showing group standard deviations (or variances) and decision limits.
• For ANOM for Variances with Levene (ADM), creates a report showing group mean ADMs and decision limits.
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Graph in Variance Scale
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(Only for ANOM for Variances) Changes the scale of the y-axis from standard deviations to variances.
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Display Options
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Display options include the following:
• Show Decision Limits shows or hides decision limit lines.
• Show Decision Limit Shading shows or hides decision limit shading.
• Show Center Line shows or hides the center line statistic.
• Show Needles shows or hides the needles.
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Option
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Description
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Reference
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Nonparametric Menu Option
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Each Pair, Student’s t
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Computes individual pairwise comparisons using Student’s t-tests. If you make many pairwise tests, there is no protection across the inferences. Therefore, the alpha-size (Type I error rate) across the hypothesis tests is higher than that for individual tests.
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Nonparametric > Nonparametric Multiple Comparisons > Wilcoxon Each Pair
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All Pairs, Tukey HSD
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Shows a test that is sized for all differences among the means. This is the Tukey or Tukey-Kramer HSD (honestly significant difference) test. (Tukey 1953, Kramer 1956). This test is an exact alpha-level test if the sample sizes are the same, and conservative if the sample sizes are different (Hayter 1984).
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Nonparametric > Nonparametric Multiple Comparisons > Steel-Dwass All Pairs
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With Best, Hsu MCB
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Tests whether the means are less than the unknown maximum or greater than the unknown minimum. This is the Hsu MCB test (Hsu 1981).
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See “With Best, Hsu MCB”.
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none
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With Control, Dunnett’s
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Tests whether the means are different from the mean of a control group. This is Dunnett’s test (Dunnett 1955).
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Nonparametric > Nonparametric Multiple Comparisons > Steel With Control
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Difference Matrix
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Shows a table of all differences of means.
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Confidence Quantile
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Shows the t-value or other corresponding quantiles used for confidence intervals.
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LSD Threshold Matrix
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Shows a matrix showing if a difference exceeds the least significant difference for all comparisons.
Note: For Hsu’s MCB and Dunnett’s test, only Difference Matrix, Confidence Quantile, and LSD Threshold Matrix are applicable.
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Connecting Letters Report
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Shows the traditional letter-coded report where means that are not sharing a letter are significantly different.
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Ordered Differences Report
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Shows all the positive-side differences with their confidence interval in sorted order. For the Student’s t and Tukey-Kramer comparisons, an Ordered Difference report appears below the text reports.
This report shows the ranked differences, from highest to lowest, with a confidence interval band overlaid on the plot. Confidence intervals that do not fully contain their corresponding bar are significantly different from each other.
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Detailed Comparisons Report
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Shows a detailed report for each comparison. Each section shows the difference between the levels, standard error and confidence intervals, t-ratios, p-values, and degrees of freedom. A plot illustrating the comparison appears on the right of each report.
This option is not available for All Pairs, Tukey’s HSD, and Nonparametric Multiple Comparisons.
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Wilcoxon Test1
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Performs the test based on Wilcoxon rank scores. The Wilcoxon rank scores are the simple ranks of the data. The Wilcoxon test is the most powerful rank test for errors with logistic distributions. If the factor has two or more levels, the Kruskal-Wallis test is performed.
The Wilcoxon test is also called the Mann-Whitney test.
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Median Test
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Performs the test based on Median rank scores. The Median rank scores are either 1 or 0, depending on whether a rank is above or below the median rank. The Median test is the most powerful rank test for errors with double-exponential distributions.
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van der Waerden Test
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Performs the test based on Van der Waerden rank scores. The Van der Waerden rank scores are the ranks of the data divided by one plus the number of observations transformed to a normal score by applying the inverse of the normal distribution function. The Van der Waerden test is the most powerful rank test for errors with normal distributions.
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Kolmogorov-Smirnov Test
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Performs the test based on the empirical distribution function, which tests whether the distribution of the response is the same across the groups. Both an approximate and an exact test are given. This test is available only when the X factor has two levels.
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Exact Test
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Provides options for performing exact versions of the Wilcoxon, Median, van der Waerden, and Kolmogorov-Smirnov tests. These options are available only when the X factor has two levels, and after the approximate test is requested.
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Nonparametric Multiple Comparisons
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Provides several options for performing nonparametric multiple comparisons. These tests are based on ranks, and control for the overall alpha level, except for the Wilcoxon Each Pair test. The following tests are available:
Wilcoxon Each Pair
performs the Wilcoxon test on each pair, and does not control for the overall alpha level. This is the nonparametric version of the Each Pair, Student’s t option found on the Compare Means menu.
Steel-Dwass All Pairs
performs the Steel-Dwass test on each pair. This is the nonparametric version of the All Pairs, Tukey HSD option found on the Compare Means menu.
Steel With Control
compares each level to a control level. This is the nonparametric version of the With Control, Dunnett’s option found on the Compare Means menu.
Dunn With Control for Joint Ranks
compares each level to a control level, similar to the Steel With Control option. The Dunn method is different in that it computes ranks on all the data, not just the pair being compared.
Dunn All Pairs for Joint Ranks
performs a comparison of each pair, similar to the Steel-Dwass All Pairs option. The Dunn method is different in that it computes ranks on all the data, not just the pair being compared.
See Dunn (1964) and Hsu (1996).
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Level
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Lists the factor levels occurring in the data.
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Count
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Records the frequencies of each level.
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Score Sum
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Records the sum of the rank score for each level.
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Expected Score
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Records the expected score under the null hypothesis that there is no difference among class levels.
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Score Mean
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Records the mean rank score for each level.
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(Mean-Mean0)/Std0
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Records the standardized score. Mean0 is the mean score expected under the null hypothesis. Std0 is the standard deviation of the score sum expected under the null hypothesis. The null hypothesis is that the group means or medians are in the same location across groups.
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ChiSquare
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Gives the values of the chi-square test statistic.
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DF
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Gives the degrees of freedom for the test.
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Prob>ChiSq
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Gives the p-value for the test.
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S
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Gives the sum of the rank scores. This is reported only when the X factor has two levels.
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Z
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Gives the test statistic for the normal approximation test. This is reported only when the X factor has two levels.
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Prob>|Z|
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Gives the p-value for the normal approximation test. This is reported only when the X factor has two levels.
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Prob≥S
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Gives a one-sided p-value for the test. This is reported only when the X factor has two levels, and the exact version of the test is requested.
Exact tests are available only in JMP Pro.
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Prob≥|S-Mean|
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Gives a two-sided p-value for the test. This is reported only when the X factor has two levels, and the exact version of the test is requested.
Exact tests are available only in JMP Pro.
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Level
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Lists the factor levels occurring in the data.
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Count
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Records the frequencies of each level.
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EDF at Maximum
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Lists the value at which the maximum deviation from the empirical distribution function (EDF) of each level and the overall EDF occurs.
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Deviation from Mean at Maximum
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Lists the value of the EDF of a sample at the maximum deviation from the mean of the EDF for the overall sample.
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KS
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A Kolmogorov-Smirnov statistic.
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KSa
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An asymptotic Kolmogorov-Smirnov statistic.
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D=max|F1-F2|
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Lists the maximum absolute deviation between the EDF of two class levels.
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Prob > D
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Lists the p-value for the test. In other words, the probability that D is greater than the observed value d, under the null hypothesis of no difference between class levels or samples.
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D+=max(F1-F2)
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Lists a one-sided test statistic that max deviation between the EDF of two class levels is positive.
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Prob > D+
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Lists the probability that D+ is greater than the observed value d+, under the null hypothesis of no difference between the two class levels.
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D-=max(F2-F1)
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Lists a one-sided test statistic that max deviation between the EDF of two class levels is negative.
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Prob > D-
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Lists the probability that D- is greater than the observed value for d-.
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q*
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Gives the quantile value used in the confidence intervals.
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Alpha
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Gives the alpha level used in the confidence intervals
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Level
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Gives the pair used in the current comparison
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Score Mean Diff
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Gives the difference of the score means.
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Std Err Dif
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Gives the standard error of the difference between the score means.
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Z
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Gives the standardized test statistic, which has an asymptotic standard normal deviation under the null hypothesis.
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p-Value
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Gives the asymptotic two-sided p-value for Z.
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Hodges-Lehmann
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Gives the Hodges-Lehmann estimator of location shift. It is the median of all paired differences between observations in the two samples.
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Lower CL
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Gives the lower confidence limit for the Hodges-Lehmann statistic.
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Upper CL
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Gives the upper confidence limit for the Hodges-Lehmann statistic.
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O’Brien
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Constructs a dependent variable so that the group means of the new variable equal the group sample variances of the original response. An anova on the O’Brien variable is actually an anova on the group sample variances (O’Brien 1979, Olejnik, and Algina 1987).
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Brown-Forsythe
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Shows the F test from an anova where the response is the absolute value of the difference of each observation and the group median (Brown and Forsythe 1974a).
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Levene
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Shows the F test from an anova where the response is the absolute value of the difference of each observation and the group mean (Levene 1960). The spread is measured as (as opposed to the SAS default ).
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Bartlett
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Compares the weighted arithmetic average of the sample variances to the weighted geometric average of the sample variances. The geometric average is always less than or equal to the arithmetic average with equality holding only when all sample variances are equal. The more variation there is among the group variances, the more these two averages differ. A function of these two averages is created, which approximates a χ2-distribution (or, in fact, an F distribution under a certain formulation). Large values correspond to large values of the arithmetic or geometric ratio, and therefore to widely varying group variances. Dividing the Bartlett Chi-square test statistic by the degrees of freedom gives the F value shown in the table. Bartlett’s test is not very robust to violations of the normality assumption (Bartlett and Kendall 1946).
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Level
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Lists the factor levels occurring in the data.
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Count
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Records the frequencies of each level.
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Std Dev
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Records the standard deviations of the response for each factor level. The standard deviations are equal to the means of the O’Brien variable. If a level occurs only once in the data, no standard deviation is calculated.
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MeanAbsDif to Mean
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Records the mean absolute difference of the response and group mean. The mean absolute differences are equal to the group means of the Levene variable.
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MeanAbsDif to Median
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Records the absolute difference of the response and group median. The mean absolute differences are equal to the group means of the Brown-Forsythe variable.
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Test
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Lists the names of the tests performed.
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F Ratio
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Records a calculated F statistic for each test.
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DFNum
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Records the degrees of freedom in the numerator for each test. If a factor has k levels, the numerator has k - 1 degrees of freedom. Levels occurring only once in the data are not used in calculating test statistics for O’Brien, Brown-Forsythe, or Levene. The numerator degrees of freedom in this situation is the number of levels used in calculations minus one.
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DFDen
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Records the degrees of freedom used in the denominator for each test. For O’Brien, Brown-Forsythe, and Levene, a degree of freedom is subtracted for each factor level used in calculating the test statistic. One more degree of freedom is subtracted for the overall mean. If a factor has k levels, the denominator degrees of freedom is n - k - 1.
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p-Value
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Probability of obtaining, by chance alone, an F value larger than the one calculated if in reality the variances are equal across all levels.
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F Ratio
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Shows the F test statistic for the equal variance test.
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DFNum
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Records the degrees of freedom in the numerator of the test. If a factor has k levels, the numerator has k - 1 degrees of freedom. Levels occurring only once in the data are not used in calculating the Welch anova. The numerator degrees of freedom in this situation is the number of levels used in calculations minus one.
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DFDen
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Records the degrees of freedom in the denominator of the test.
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Prob>F
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Probability of obtaining, by chance alone, an F value larger than the one calculated if in reality the means are equal across all levels. Observed significance probabilities of 0.05 or less are considered evidence of unequal means across the levels.
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t Test
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Shows the relationship between the F ratio and the t Test. Calculated as the square root of the F ratio. Appears only if the X factor has two levels.
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Alpha (α)
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Significance level, between 0 and 1 (usually 0.05, 0.01, or 0.10). Initially, a value of 0.05 shows.
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Sigma (σ)
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Standard error of the residual error in the model. Initially, RMSE, the estimate from the square root of the mean square error is supplied here.
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Delta (δ)
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Raw effect size. For details about effect size computations, see the Fitting Linear Models book. The first position is initially set to the square root of the sums of squares for the hypothesis divided by n; that is, .
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Number (n)
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Total sample size across all groups. Initially, the actual sample size is put in the first position.
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Solve for Power
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Solves for the power (the probability of a significant result) as a function of all four values: α, σ, δ, and n.
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Solve for Least Significant Number
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Solves for the number of observations needed to achieve approximately 50% power given α, σ, and δ.
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Solve for Least Significant Value
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Solves for the value of the parameter or linear test that produces a p-value of α. This is a function of α, σ, n, and the standard error of the estimate. This feature is available only when the X factor has two levels and is usually used for individual parameters.
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Adjusted Power and Confidence Interval
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When you look at power retrospectively, you use estimates of the standard error and the test parameters.
• Adjusted power is the power calculated from a more unbiased estimate of the non-centrality parameter.
• The confidence interval for the adjusted power is based on the confidence interval for the non-centrality estimate.
Adjusted power and confidence limits are computed only for the original Delta, because that is where the random variation is.
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