R Anova Mean Square Error
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this post in threaded view ♦ ♦ | Report Content as Inappropriate ♦ ♦ extraction of mean square value from ANOVA Hello, I am randomly generating values and then using an how to get mse in r ANOVA table to find the mean square value. I would like to form
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a loop that extracts the mean square value from ANOVA in each iteration. Below is an example of what I am how to use ezanova doing. a<-rnorm(10) b<-factor(c(1,1,2,2,3,3,4,4,5,5)) c<-factor(c(1,2,1,2,1,2,1,2,1,2)) mylm<-lm(a~b+c) anova(mylm) Since I would like to use a loop to generate this several times it would be helpful to know how to extract the mean square value from ANOVA.
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Thanks [[alternative HTML version deleted]] ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code. Rolf Turner-3 Threaded Open this post in threaded view ♦ ♦ | Report Content as Inappropriate ♦ ♦ Re: extraction of mean square value from ANOVA On 20/05/11 13:46, Cheryl Johnson wrote: > Hello, > > I am randomly generating values ezanova example and then using an ANOVA table to find the > mean square value. I would like to form a loop that extracts the mean square > value from ANOVA in each iteration. Below is an example of what I am doing. > > a<-rnorm(10) > b<-factor(c(1,1,2,2,3,3,4,4,5,5)) > c<-factor(c(1,2,1,2,1,2,1,2,1,2)) > > mylm<-lm(a~b+c) > anova(mylm) > > Since I would like to use a loop to generate this several times it would be > helpful to know how to extract the mean square value from ANOVA. anova(mylm)[["Mean Sq"]] strangely enough. :-) This gives you a *vector* (of length 3 in your setting), the last entry of which is the error (or residual) mean square, which is probably what you want since you refer the ``mean square value'' (singular). cheers, Rolf Turner ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code. Cheryl Johnson Threaded Open this post in threaded view ♦ ♦ | Report Content as Inappropriate ♦ ♦ Re: extraction of mean square value from ANOVA Thanks for your help. How would I extract each of the 3 values in the vector individually? Thanks again On Thu, May 19, 2
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Join the Stack Overflow Community Stack Overflow is a community of 6.2 million programmers, just like you, helping each other. Join them; it only interpreting anova in r takes a minute: Sign up Best way to extract Mean Square Values from aov object in r up vote 3 down vote favorite 2 I'm trying to write a function to automate doing a variance analysis, part of which involves http://r.789695.n4.nabble.com/extraction-of-mean-square-value-from-ANOVA-td3537450.html doing some further calculations. The method I've been using isn't very robust, if variable names change then it stops working. For this dummy data > dput(assayvar,"") structure(list(Run = structure(c(1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 4L, 4L, 4L), .rk.invalid.fields = list(), .Label = c("1", "2", "3", "4"), class = "factor"), Actual = c(246.3, 253.6, 247.6, 249, 249, 251.3, 254.9, 254.1, 253.2, 250, 248.9, 250.3)), .Names = c("Run", "Actual"), row.names = c(NA, 12L), class = "data.frame") > assayaov<-aov(Actual~Run+Error(Run),data=assayvar) > str(summary(assayaov)) http://stackoverflow.com/questions/1423472/best-way-to-extract-mean-square-values-from-aov-object-in-r List of 2 $ Error: Run :List of 1 ..$ :Classes ‘anova’ and 'data.frame': 1 obs. of 3 variables: .. ..$ Df : num 3 .. ..$ Sum Sq : num 46.5 .. ..$ Mean Sq: num 15.5 ..- attr(*, "class")= chr [1:2] "summary.aov" "listof" $ Error: Within:List of 1 ..$ :Classes ‘anova’ and 'data.frame': 1 obs. of 5 variables: .. ..$ Df : num 8 .. ..$ Sum Sq : num 36.4 .. ..$ Mean Sq: num 4.55 .. ..$ F value: num NA .. ..$ Pr(>F) : num NA ..- attr(*, "class")= chr [1:2] "summary.aov" "listof" - attr(*, "class")= chr "summary.aovlist" But for this dummy data > dput(BGBottles,"") structure(list(Machine = structure(c(1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 4L, 4L, 4L), .rk.invalid.fields = structure(list(), .Names = character(0)), .Label = c("1", "2", "3", "4"), class = "factor"), Weight = c(14.23, 14.96, 14.85, 16.46, 16.74, 15.94, 14.98, 14.88, 14.87, 15.94, 16.07, 14.91 )), .Names = c("Machine", "Weight"), row.names = c(NA, 12L), class = "data.frame") > bgaov<-aov(Weight~Machine+Error(Machine),data=BGBottles) > str(summary(bgaov)) List of 2 $ Error: Machine:List of 1 ..$ :Classes ‘anova’ and 'data.frame': 1 obs. of 3 variables: .. ..$ Df : num 3 .. ..$ Sum Sq : num 5.33 .. ..$ Mean Sq: num 1.78 ..- attr(*, "class")= chr [1:2] "summary.aov" "listof" $ Error: Within :List of 1 ..$ :Classes ‘anova’ and 'data.frame': 1 obs. of 5 variables: .. ..$ Df : num 8 .. ..$ Sum Sq : n
women with low daily calcium intakes (400 mg) assigned at random to one of three treatments--placebo, calcium carbonate, calcium citrate maleate). Class Levels Values http://www.jerrydallal.com/lhsp/aov1out.htm GROUP 3 CC CCM P Dependent Variable: DBMD05 Sum of Source DF Squares http://www.weibull.com/hotwire/issue95/relbasics95.htm Mean Square F Value Pr > F Model 2 44.0070120 22.0035060 5.00 0.0090 Error 78 343.1110102 4.3988591 Corrected Total 80 387.1180222 R-Square Coeff Var Root MSE DBMD05 Mean 0.113679 -217.3832 2.097346 -0.964815 Source DF Type I SS Mean Square F Value Pr > F GROUP 2 44.00701202 22.00350601 5.00 0.0090 Source DF how to Type III SS Mean Square F Value Pr > F GROUP 2 44.00701202 22.00350601 5.00 0.0090 Standard Parameter Estimate Error t Value Pr > |t| Intercept -1.520689655 B 0.38946732 -3.90 0.0002 GROUP CC 0.075889655 B 0.57239773 0.13 0.8949 GROUP CCM 1.597356322 B 0.56089705 2.85 0.0056 GROUP P 0.000000000 B . . . NOTE: The X'X matrix has been found to be singular, and a generalized r anova mean inverse was used to solve the normal equations. Terms whose estimates are followed by the letter 'B' are not uniquely estimable. The GLM Procedure Least Squares Means DBMD05 LSMEAN GROUP LSMEAN Number CC -1.44480000 1 CCM 0.07666667 2 P -1.52068966 3 Least Squares Means for effect GROUP Pr > |t| for H0: LSMean(i)=LSMean(j) i/j 1 2 3 1 0.0107 0.8949 2 0.0107 0.0056 3 0.8949 0.0056 NOTE: To ensure overall protection level, only probabilities associated with pre-planned comparisons should be used. Adjustment for Multiple Comparisons: Tukey-Kramer Least Squares Means for effect GROUP Pr > |t| for H0: LSMean(i)=LSMean(j) i/j 1 2 3 1 0.0286 0.9904 2 0.0286 0.0154 3 0.9904 0.0154 The Analysis of Variance Table The Analysis of Variance table is just like any other ANOVA table. The Total Sum of Squares is the uncertainty that would be present if one had to predict individual responses without any other information. The best one could do is predict each observation to be equal to the overall sample mean. The ANOVA table partitions this variability into two parts. One portion is accounted for (some say "explained by") the model. It's the reduction in uncertain
of variance, or ANOVA, is a powerful statistical technique that involves partitioning the observed variance into different components to conduct various significance tests. This article discusses the application of ANOVA to a data set that contains one independent variable and explains how ANOVA can be used to examine whether a linear relationship exists between a dependent variable and an independent variable. Sum of Squares and Mean Squares The total variance of an observed data set can be estimated using the following relationship: where: s is the standard deviation. yi is the ith observation. n is the number of observations. is the mean of the n observations. The quantity in the numerator of the previous equation is called the sum of squares. It is the sum of the squares of the deviations of all the observations, yi, from their mean, . In the context of ANOVA, this quantity is called the total sum of squares (abbreviated SST) because it relates to the total variance of the observations. Thus: The denominator in the relationship of the sample variance is the number of degrees of freedom associated with the sample variance. Therefore, the number of degrees of freedom associated with SST, dof(SST), is (n-1). The sample variance is also referred to as a mean square because it is obtained by dividing the sum of squares by the respective degrees of freedom. Therefore, the total mean square (abbreviated MST) is: When you attempt to fit a model to the observations, you are trying to explain some of the variation of the observations using this model. For the case of simple linear regression, this model is a line. In other words, you would be trying to see if the relationship between the independent variable and the dependent variable is a straight line. If the model is such that the resulting line passes through all of the observations, then you would have a "perfect" model, as shown in Figure 1. Figure 1: Perfect Model Passing Through All Observed Data Points The model explains all of the variability of the observations. Therefore, in this case, the model sum of squares (abbreviated SSR) equals the total sum of squares: For the perfect model, the model sum of squares, SSR, equals the total sum of squares, SST, because all estimated values obtained using the model, , will equal the corresponding observations, yi. The model sum of squares, SSR, can be calculated using a relationship similar to the one used to obtain SST. For SSR, we simply replace the yi in the r