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--- resources:lme [2014/09/08 21:11] – Page moved from lme to resources:lme admin
+++ resources:lme [2019/05/22 16:08] (current) – external edit 127.0.0.1
@@ Line 14: / Line 14: @@
 However, I found it easier to do this:
+<code rsplus>
 colnames(x) <- c("name1","name2"...)
+</code>
 based on guidance from:
@@ Line 24: / Line 26: @@
 http://cran.r-project.org/doc/manuals/r-devel/R-data.html
-''Column names can be given explicitly via the col.names; explicit names override the header line (if present).''
+>Column names can be given explicitly via the col.names; explicit names override the header line (if present).
@@ Line 30: / Line 32: @@
 http://cran.r-project.org/web/packages/arm/index.html
-''arm: Data Analysis Using Regression and Multilevel/Hierarchical Models
-R functions for processing lm, glm, svy.glm, merMod and polr outputs.''
+>''arm: Data Analysis Using Regression and Multilevel/Hierarchical Models''
+>
+>R functions for processing lm, glm, svy.glm, merMod and polr outputs.
-**arm** package provides the coefplot() function for plotting the regression coefficient values and std. errors.
+**arm** package provides the ''coefplot'' function for plotting the regression coefficient values and std. errors.
-Need to specify that subjects is a nominal variable, using the //factor// command:
+Need to specify that subjects is a nominal variable, using the ''factor'' command:
 http://www.statmethods.net/input/datatypes.html
-''Tell R that a variable is nominal by making it a factor. The factor stores the nominal values as a vector of integers in the range [ 1... k ] (where k is the number of unique values in the nominal variable), and an internal vector of character strings (the original values) mapped to these integers. ''
+>Tell R that a variable is nominal by making it a factor. The factor stores the nominal values as a vector of integers in the range [ 1... k ] (where k is the number of unique values in the nominal variable), and an internal vector of character strings (the original values) mapped to these integers.
 ===== Interpretation of glmer output =====
-A nice description:
+A nice description from:
 https://stat.ethz.ch/pipermail/r-sig-mixed-models/2011q1/015590.html
-    In this case the coefficient corresponds to one of the
+>In this case the coefficient corresponds to one of the
-    terms in the model and I would advocate performing a likelihood ratio
+>terms in the model and I would advocate performing a likelihood ratio
-    test comparing the two models
+>test comparing the two models
+>
-   fm <- glmer(SameSite~BreedSuc1+Sex+(1|Bird), family="binomial")
+><code rsplus>
-   fm0 <- glmer(SameSite~Sex+(1|Bird), family="binomial")  # the null
+>fm <- glmer(SameSite~BreedSuc1+Sex+(1|Bird), family="binomial")
-   hypothesis model
+>fm0 <- glmer(SameSite~Sex+(1|Bird), family="binomial")  # the null
-   anova(fm0, fm)
+>hypothesis model
+>anova(fm0, fm)
-   Even though the function is called anova it will, in this case,
+></code>
-   perform a likelihood ratio test (LRT).  It also prints the values of
+>Even though the function is called anova it will, in this case,
-   AIC and BIC if you prefer to compare models according to one of those
+>perform a likelihood ratio test (LRT).  It also prints the values of
-   criteria but I prefer using the likelihood ratio for nested models.
+>AIC and BIC if you prefer to compare models according to one of those
+>criteria but I prefer using the likelihood ratio for nested models.
-   However, before doing that comparison you should ask yourself whether
+>However, before doing that comparison you should ask yourself whether
-   you want to compare models that have the, apparently unnecessary term
+>you want to compare models that have the, apparently unnecessary term
-   for Sex in them.  The way I would approach the model building is first
+>for Sex in them.  The way I would approach the model building is first
-   to reduce the model to
+>to reduce the model to
+><code rsplus>
-   fm1 <- lmer(SameSite~BreedSuc1+(1|Bird), family="binomial")
+>fm1 <- lmer(SameSite~BreedSuc1+(1|Bird), family="binomial")
+></code>
-   You could then compare
+>You could then compare
+><code rsplus>
-   anova(fm1, fm)
+>anova(fm1, fm)
+></code>
-   which I presume will give a large p-value for the LRT, so we prefer
+>which I presume will give a large p-value for the LRT, so we prefer
-   the simpler model, fm1.  After that, I would compare
+>the simpler model, fm1.  After that, I would compare
+><code rsplus>
-   fm2 <- lmer(SameSite ~ 1 + (1|Bird), family="binomial")
+>fm2 <- lmer(SameSite ~ 1 + (1|Bird), family="binomial")
+></code>