# Questions tagged [anova]

286 questions

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### Mixed ANOVA (lme) returns error for alphabetic variable

I have a large data set with persons who answered questionnaires at several measurement points. I want to run an ANOVA using the lme function with my 'SERIAL' variable as identifying the persons (which is the serial code of a person in letters and numbers, e.g. YVEDPEPGV9). So person YVEDPEPGV9 answ...

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### How to extract residuals and read coefficients from the function Anova()?

I use the function Anova() in package car to perform a test with type III. But I have no idea how to extract the residuals or how to get the information of parameter estimates.
Is there some way to do these like residuals(model) and summary.lm(model)?

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### How to interpret glm output for quasi-binomial model

I am having difficulty interpreting the output for a quasibinomial model.
My first issue is that I have used the function 'autoplot' to test assumptions, and the normal Q-Q plot is skewed:
I am unsure whether or not it is okay to proceed with fitting the anova, or how to adjust my data if it is not...

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174

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### Why Error() in aov() gives three levels?

I'm trying to understand how to properly run an Repeated Measures or Nested ANOVA in R, without using mixed models. From consulting tutorials, the formula for a one-variable repeated measures anova is:
aov(Y ~ IV+ Error(SUBJECT/IV) )
where IV is the within subjects and subject is the identity of the...

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### How to calculate percentage change using factorial analysis? [closed]

To assess the contribution of various input factors (x, y, z) and their interactions to the response variable (A), I calculated the percentage of variance using factorial analysis in Minitab. Now I want to calculate the percentage change in A.
Say for example A is increasing when x and y are increas...

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111

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### Subsetting in multiple Imputation ANOVA in R

I'd like to ask a question considering subsetting in R. I tried to calculate Multiple Imputation ANOVA using the function mi.anova (miceadds) in R. Actually there is no possibility to only use subsets of the input.
Afterwards I tried to restructure my mids structure into a datlist, subsetting it the...

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### Multilevel / Nested ANOVA for six lakes and parasitized / non parasitized fish

I have six lakes sampled (A1, A6, A8, B2, B7, D7) with fish measurements for parasitized (1=P) and non-parasitized fish (0=NP). I want to compare similarities or differences between each lake for three different variables (Condition Factor K, Heptosomatic Index HSI, and Gonadosomatic Index GSI)
I am...

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146

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### Where is the intercept term in type II Anova function from the car package?

I have constructed a simple linear model and performed both a Type II & III analysis of variance using the Anova() function from the car package. In the output, the Type III Anova includes an intercept, whereas no intercept is included in the Type II Anova.
Type II
Anova Table (Type II tests)
Respo...

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166

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### Calculating power for repeated measures in gpower

I'm trying to calculate power for my repeated measures design in GPower. I'm confident I have the right result for my design as a single measure ANOVA:
2 factors, 3 levels each:
F tests - ANOVA: Fixed effects, special, main effects and interactions
Analysis: A priori: Compute required sample siz...

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63

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### difference between OLS and f_oneway (Anova)

I did anova test b/w 'density' : continuous, 'quality':catagorical,
but got different F-statics and p-value.
now I am confused which one should i use to reject or support null
hypothesis.
import statsmodels.formula.api as smf
import patsy
formula = 'density ~ C(quality)'
y,x = patsy.dmatrices(form...

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42

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### How to check the relationship between a character and numeric group?

I want to check the effect of a specific numeric variable on a character vector in R.
A B C D E F_PATHOLOGIC_TUMOR_STAGE AJCC_TUMOR_PATHOLOGIC_PT GRADE PRIMARY_SITE
TCGA.2J.AAB4.01 -0.2527 -1.2093 0.7556 -0.7071 -0.1310 Stage IIB...

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353

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### Eta Squared / Partial Eta Squared Using R

I've ran an ANOVA for a 2X2 mixed study design comparing the test results of a memory test, within and between a group of students. The code I used was as follows:
results

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122

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### Change vegan::adonis class to lm?

I am running a perm-manova using the adonis2 function in vegan package. I have a significant interaction in my model, so would like to perform tukey-adjusted comparisons for the interaction using the lsmeans package.
However, while lsmeans accepts many model classes, it does not accept the class of...

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### Repeated measure ANOVA (rANOVA) by MATLAB

I have 3 groups of individuals ( young (n=10), middle age (n=9), old (n=13)) in each participant 6 parameters are measured. Here is the list:
1) Heart_rate_at_rest ( block 1)
2) Heart_rate_at rest (block2)
3) Hear_rate_ after_run ( block1)
4) Heart_rate_after_run ( block2)
5) age
6) Blood pressure
I...

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261

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### comparing differences between groups with cox regression in R - anova?

I have constructed a cox regression:
Call:
coxph(formula = Surv(`infection time`, infection) ~ Treatment +
Gender + Race + Surface + head + buttock + trunk + up.leg +
low.leg + resp.tract, data = BurnData)
The p-value for the overall tests (likelihood, Wald and score) is only significant for the L...

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59

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### r repeated measures output error (main effects shown twice, between subject shown as within)

I am having trouble discerning the error strata output from a repeated measures anova in R, as they appear to be doing something funky. I have a repeated measures anova where each participant gets a score for two different roles and a score for two different valences (Role and Valence are dichotomou...

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### do partial data with the TukeyHSD

When doing a big ANOVA, sometimes we need to work with the Tukey HSD test to verify the pair significance. Since it is a time-consuming task, would like to ask for advice that How I can do partial test. I mean, I'd known the significant item after summary(aov), and I only want to do Tukey HSD on the...

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139

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### Repeated measures ANOVA and link to mixed-effect models in R

I have a problem when performing a two-way rm ANOVA in R on the following data (link : https://drive.google.com/open?id=1nIlFfijUm4Ib6TJoHUUNeEJnZnnNzO29):
subjectnbr is the id of the subject and blockType and linesTTL are the independent variables. RT2 is the dependent variable
I first performed th...

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185

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### Looking for a post hoc for a type 2 Anova (mixed-effects model)

My question is how do I run a post hoc on a type 2 Anova (mixed-effects model)? So far I am using the glmer() from the 'lme4' package, the Anova() from the 'car' package, and trying to run a HSD test from the 'agricolae' package.
After searching for some time this is the best that I could find, how...

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### in R, how can I export TukeyHSD results into rows/columns when there's multiple factors

I'm trying to export my TukeyHSD results into a file. However, the only solutions I am able to find are when it's a simple comparison and not when I also want to consider another factor.
For example, this is the type of ANOVA I'm trying to do:
dat1

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151

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### Recreate various Non-Parametric ANCOVA analyses in R

I am looking to recreate various analyses in R that can compute several types of Non-Parametric ANCOVA.
Let's use the mtcars data from the datasets package in R for example purposes. Let's say I wanted to predict MPG from Transmission while controlling for Cylinders. I would conduct a normal ANCOVA...

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### Qualitative Design of Experiments - 3 Factors 3 Levels - Categorical Response Variable

I need to perform a design of experiments where I have 3 factors with 3 levels each (all numerical). But the end response is going to be - Good, Bad, Pass sort of deal.
I need to find the factors/interactions that have the most significant contributions. Could someone suggest how to go about doing t...

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111

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### What does “inf” mean for F value in scipy.stats.f_oneway?

I ran a one-way anova, and some groups had 'inf' for the F value and '0.000000e+00' for the p value. Does this mean that the difference is significant?
I separated the dataframe using groupby and looped through, example code:
from scipy import stats
c_jobs_anova = []
for name_group in c_jobs.groupby...

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### How to test my ANOVA data analysis with Bayesian ABtesting?

I have one application that behaves in 2 ways, lets call them Dynamic and Static. I run 2 experiments to check the difference between these 2 behaviors with 50 participants for each. Assume that I have the following results:
UID AppType Q1 Q2 Q3 Q4
--------------------------
100 Dynamic 50 71 8...

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### Function to calculate ANOVA and writing basic stats in R

I am trying to write my first function in R, and I would appreciate some help.
As a researcher running experiments 2 or 3 times per year, I often have to compare the treatments using anova. I'm trying to automatize the Analysis of Variance to return a list with the results, a dataframe containing me...

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74

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### Perform several ANOVA's simultaneously on tidy data in R

I have a dataframe that looks like the following but with many additional rows. 'Content' and 'Process' can both either be 'a' or 'n'.
dv1 dv2 dv3 content process
1 3 4 a a
2 1 2 a n
5 3 5 n a
4 3 2 n n
I know how to run several A...

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241

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### 2-way ANOVA in Python statsmodels yields different Sum of Squares than SPSS

I am learning to use Python for my statistical analyses, and while figuring out how to perform a 2-way ANOVA with statsmodels I found that my Python code yielded slightly aberrant values. Comparing the outputs you can see that the SS_Factor_1 values, and the Adjusted R2 are different for Python vs S...

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### Mixed Design ANOVA-Error: object of type 'closure' is not subsettable

I'am running a 2X3X3 mixed ANOVA design. Ive been trying to get the student-newman Kuels function to work in R, but I keep getting the error: object of type 'closure' is not subsettable. Any help would be greatly appreciated!
library(ez)
library(ggplot2)
library(nlme)
library(pastecs)
library(resha...

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### Anova table for pscl:zeroinfl

We're trying to model a count variable with excessive zeros using a zero-inflated poisson (as implemented in pscl package). Here is a (simplified) output showing both categorical and continuous explanatory variables:
library(pscl)
> m1 summary(m1)
Count model coefficients (poisson with log link):
E...

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60

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### ANOVA result is inconsistent (AIC VS deviance)

I am working on GLM models (using glmer). Now I am exploring whether I need an interaction term. I'd like to find the best model, but the following result is confusing:
Models:
g1: y ~ year + (1 | BZR/PLR)
g2: y ~ year + year * BZR + (1 | BZR/PLR)
Df AIC BIC logLik deviance Chisq Chi Df Pr...

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### Get Kruskal-Wallis Ranks from function

I'm using Kruskal-Wallis to do some analysis on non-normal/heterskedastic data and I'm keen to use Welch's t-test implementation data as described by Cribbie et al here. Their process involves performing the Welch's T-test on the ranks from K-W.
The Python part of the question is: is there a way...

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### How to compare r-squared from different ANOVAs?

I'm trying to compare the variance explained by one factor in ANOVA, across three different experimental conditions. For each condition I performed the same ANOVA, and r squared = SS_factor/SS_total. Is there a way to compared the different r squared values for different conditions?
If not, what is...

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### ggplot2: Faceting multiple regressions with slope & p-value labels

I thought I would share some code for those who ever struggled to automate adding R2, slope, intercept, p-value onto your multi-facet figures. This code shows you how to calculate your regression fits, and place them onto your figure as a labels for multiple regressions (ancova).
Bellow figure is ho...

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### account for non-homogeneity of variance (heteroskedasticity) in statsmodels ANOVA

Greeting to the community.
I am using statsmodels in order to conduct ANOVA and one of the prerequisites of ANOVA is that the independent variables should have equal variances.
I am using the levene test through scipy in order to check for the presence of the effect (i apply the test in each of the...

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49

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### How can I reorganize a data frame according to parts of the name of a column?

I am trying to do a repeated measures Analysis of Variance in R.
My orignial data is in Excel.
My within-factors are:
temperature (levels 40,50,60 and 70 degrees)
interaction type (levels TmK, BmK and WoK)
Trial (levels _1 vs _2)
My dependent variable is the time (which stands in the cells of my Ex...

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### How can I get my code to print/display SST?

I am trying to complete ANOVA calculations in Java where I have to calculate Degrees of Freedom within groups and between groups, Sum of Squares total, within groups and between groups and mean of squares within and between groups. I have completed DoF and have my calculation for the SST but I can n...

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### manova in R error message: length of 'dimnames' [1] not equal to array extent

Trying to run manova on this data:
Create a data.frame:
acc

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663

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### Apply ANOVA tests in MATLAB neural networks.toolbox

Matlab has NN toolbox as well as ANOVA tests. I want to apply ANOVA tests for the NN model after training. How to do it? Any references or examples are welcome.

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667

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### R: Anova Data - 2^5 Design, with replicates

I'm running simulations that I wish to analyse with an ANOVA methood, and I'm just having issues figuring out how to set it up.
I have a 2^5 factorial design, so I have 32 runs of my experiment with the appropriate +/- values outlining the 32 possible combinations.
However, I also have ~500 replicat...

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387

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### Perfom a one-way ANOVA using rpsychi (R) and the subsequent post-hoc pair-wise comparisons

I have 4 samples, represented by their means and standard deviations. If I consider a sample size for all of them as 100, how can I perform a one-way ANOVA using the library of rpsychi in R?
The samples are all normal distributed and independent.
These are their values:
S1: mean1=5.5, sd1=0.6
S2: me...