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POConverting mixed model formula from SAS to R
 

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  1. POConverting mixed model formula from SAS to R
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    <p>I want to fit a mixed model using nlme package in R which is equivalent to following SAS codes:</p> <pre><code>proc mixed data = one; class var1 var2 year loc rep; model yld = var1 * var2; random loc year(loc) rep*year(loc); </code></pre> <p>EDITS: Explanation of what is experiment about </p> <p>the same combination of var1 and var2 were tested in replicates (rep- replicates are numbered 1:3). The replicates (rep) is considered random. This set of experiment is repeated over locations (loc) and years (year). Although replicates are numbered 1:3 within each location and year for covinience because they do not have any name, replication 1 within a location and a year doesnot have correlation replication 1 within other location and other year</p> <p>I tried the following codes:</p> <pre><code> require(nlme) fm1 &lt;- lme(yld ~ var1*var2, data = one, random = loc + year / loc + rep * year / loc) </code></pre> <p>Is my codes correct? </p> <p>EDITS: data and model based on suggestions you can download the example data file from the following link: <a href="https://sites.google.com/site/johndatastuff/mydata1.csv">https://sites.google.com/site/johndatastuff/mydata1.csv</a></p> <pre><code>data$var1 &lt;- as.factor(data$var1) data$var2 &lt;- as.factor(data$var2) data$year &lt;- as.factor(data$year) data$loc &lt;- as.factor(data$loc) data$rep &lt;- as.factor(data$rep) following suggestions from the comments below: fm1 &lt;- lme(yld ~ var1*var2, data = data, random = ~ loc + year / loc + rep * year / loc) Error in getGroups.data.frame(dataMix, groups) : Invalid formula for groups </code></pre> <p>EXPECTED BASED ON SAS OUTPUT</p> <pre><code>Type 3 tests of fixed effects var1*var2 14 238 F value 16.12 Pr &gt;F = &lt; 0.0001 Covariance parameters: loc = 0, year(loc) = 922161, year*rep(loc) = 2077492, residual = 1109238 </code></pre> <p>I tried the following model, I still getting some errors: </p> <pre><code>Edits: Just for information I tried the following model require(lme4) fm1 &lt;- lmer(yld ~ var1*var2 + (1|loc) + (1|year / loc) + (1|rep : (year / loc)), data = data) Error in rep:`:` : NA/NaN argument In addition: Warning message: In rep:`:` : numerical expression has 270 elements: only the first used </code></pre>
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    1. COWhat happened when you tried it? Can you make a small reproducible example?
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    2. CODid you try adding a ~ in the formula? fm1 <- lme(yld ~ var1*var2, data = one, random = ~ loc + year / loc + rep * year / loc)
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    3. COHmm... I haven't used lme/lmer but anything more advanced than lmer(yld ~ var1*var2 +(1|year), data=data) fails.
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