How obtain the estimated scale parameter as in older lmer function version
On Sat, May 29, 2010 at 5:23 PM, walmes zeviani
<walmeszeviani at yahoo.com.br> wrote:
Hello, I read the article based on lme4 Doran H, Bates D, Bliese P, Dowling M (2007). ?Estimating the Multilevel Rasch Model: With the lme4 Package.? Journal of Statistical Software, 20(2). URL http://www.jstatsoft. org/v20/i02/. and I saw that the print of 'mer' class showed a estimated scale parameter. Nowadays, the print doesn't show this. I tried calculate by myself employing Pearson residuals and deviance() function but this didn't match the same result. In the article there was this output: R> data("lq2002", package = "multilevel") R> wrk <- lq2002 R> for (i in 3:16) wrk[[i]] <- ordered(wrk[[i]]) R> for (i in 17:21) wrk[[i]] <- ordered(5 - wrk[[i]]) R> lql <- reshape(wrk, varying = list(names(lq2002)[3:21]), + ? ? v.names = "fivelev", idvar = "subj", timevar = "item", + ? ? drop = names(lq2002)[c(2, 22:27)], direction = "long") R> lql$itype <- with(lql, factor(ifelse(item < 12, "Leadership", + ? ? ifelse(item < 15, "Task Sig.", "Hostility")))) R> for (i in c(1, 2, 4, 5)) lql[[i]] <- factor(lql[[i]]) R> lql$dichot <- factor(ifelse(lql$fivelev < 4, 0, 1)) R> (fm1 <- lmer(dichot ~ 0 + itype + (1 | subj) + (1 | COMPID) + + ? ? (1 | item), lql, binomial)) Generalized linear mixed model fit using Laplace Formula: dichot ~ 0 + itype + (1 | subj) + (1 | COMPID) + (1 | item) ? Data: lql ?Family: binomial(logit link) ? AIC ? BIC logLik deviance ?40722 40773 -20355 ? ?40710 Random effects: ?Groups Name ? ? ? ?Variance Std.Dev. ?subj ? (Intercept) 2.30528 1.51831 ?COMPID (Intercept) 0.25449 0.50447 ?item ? (Intercept) 0.37700 0.61400 number of obs: 38798, groups: subj, 2042; COMPID, 49; item, 19 Estimated scale (compare to ?1 ) ?0.9386558 ?#<---------------------------- this!
That quantity is the square root of the penalized residual sum of squares divided by n, the number of observations, evaluated as
sqrt(sum(c(fm1 at resid, fm1 at u)^2)/length(fm1 at resid))
[1] 0.9386649
Fixed effects: ? ? ? ? ? ? ? ?Estimate Std. Error z value Pr(>|z|) itypeHostility ? ?1.6721 ? ? 0.2883 ? 5.801 6.6e-09 itypeLeadership ?-0.4921 ? ? 0.2036 -2.417 ? ?0.0157 itypeTask Sig. ? -0.1308 ? ? 0.3654 -0.358 ? ?0.7203 Correlation of Fixed Effects: ? ? ? ? ? ?itypHs itypLd itypeLdrshp 0.117 itypeTskSg. 0.066 0.093 My actual output is:
fm1
Generalized linear mixed model fit by the Laplace approximation Formula: dichot ~ 0 + itype + (1 | subj) + (1 | COMPID) + (1 | item) ? Data: lql ? AIC ? BIC logLik deviance ?40722 40773 -20355 ? ?40710 Random effects: ?Groups Name ? ? ? ?Variance Std.Dev. ?subj ? (Intercept) 2.30573 ?1.51846 ?COMPID (Intercept) 0.25416 ?0.50415 ?item ? (Intercept) 0.37488 ?0.61227 Number of obs: 38798, groups: subj, 2042; COMPID, 49; item, 19 Fixed effects: ? ? ? ? ? ? ? ?Estimate Std. Error z value Pr(>|z|) itypeHostility ? ?1.6774 ? ? 0.2875 ? 5.834 ?5.4e-09 *** itypeLeadership ?-0.4928 ? ? 0.2031 ?-2.426 ? 0.0153 * itypeTask Sig. ? -0.1362 ? ? 0.3644 ?-0.374 ? 0.7086 --- Signif. codes: ?0 ?***? 0.001 ?**? 0.01 ?*? 0.05 ?.? 0.1 ? ? 1 Correlation of Fixed Effects: ? ? ? ? ? ?itypHs itypLd itypeLdrshp 0.118 itypeTskSg. 0.066 ?0.093
sum(residuals(fm1, type="pearson")^2)/(nrow(lql)-3-3)
[1] 0.8399116
deviance(fm1)/(nrow(lql)-3-3)
? ? ?ML 1.049437
As you can see, I can't figure out the estimated scale parameter. How can I get it? Why was this information removed from the output in newer versions of the function? Thanks in advance. ? ? ? ?[[alternative HTML version deleted]]
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