updates to lmer 1 and 2

17-linear_mixed_effects_models1.Rmd

@@ -273,11 +273,11 @@ fit.augmented = lmer(formula = value ~ 1 + condition + (1 | participant),
                      data = df.original)
 
 # compare models
-# note: the lmer model has to be supplied first 
+# note: the lmer model has to be entered as the first argument
 anova(fit.augmented, fit.compact) 
 ```
 
-Yes, the likelihood of the data given the linear mixed effects model is significantly higher compared to its likelihood given the linear model. 
+Yes, the linear mixed effects model explains the data better than the linear model. 
 
 ## Additional resources
 

18-linear_mixed_effects_models2.Rmd

@@ -289,8 +289,10 @@ df.complete_pooling =  fit.complete_pooling %>%
 df.no_pooling = df.sleep %>% 
   group_by(subject) %>% 
   nest(data = c(days, reaction)) %>% 
-  mutate(fit = map(data, ~ lm(reaction ~ days, data = .)),
-         augment = map(fit, augment)) %>% 
+  mutate(fit = map(.x = data, 
+                   .f = ~ lm(reaction ~ days, data = .x)),
+         augment = map(.x = fit, 
+                       .f = ~ augment(.x))) %>% 
   unnest(c(augment)) %>% 
   ungroup() %>% 
   clean_names() %>% 
@@ -400,8 +402,10 @@ df.partial_pooling = fit.random_intercept_slope %>%
 df.plot = df.sleep %>% 
   group_by(subject) %>% 
   nest(data = c(days, reaction)) %>% 
-  mutate(fit = map(data, ~ lm(reaction ~ days, data = .)),
-         tidy = map(fit, tidy)) %>% 
+  mutate(fit = map(.x = data, 
+                   .f = ~ lm(reaction ~ days, data = .x)),
+         tidy = map(.x = fit, 
+                    .f = ~ tidy(.x))) %>% 
   unnest(c(tidy)) %>% 
   select(subject, term, estimate) %>% 
   pivot_wider(names_from = term,
@@ -517,7 +521,7 @@ Let's fit a model to this data now and take a look at the summary output:
 ```{r}
 # fit model
 fit.mixed = lmer(formula = value ~ 1 + condition + (1 | participant),
-                data = df.mixed)
+                 data = df.mixed)
 
 summary(fit.mixed)
 ```
@@ -687,7 +691,8 @@ n_observations = 10
 slope = -10 
 sd_error = 0.4
 sd_participant = 5
-intercept = rnorm(n_participants, sd = sd_participant) %>% sort()
+intercept = rnorm(n_participants, sd = sd_participant) %>% 
+  sort()
 
 df.simpson = tibble(x = runif(n_participants * n_observations, min = 0, max = 1)) %>%
   arrange(x) %>% 
@@ -753,7 +758,7 @@ Let's fit a linear mixed effects model with random intercepts:
 
 ```{r}
 fit.lmer = lmer(formula = y ~ 1 + x + (1 | participant),
-     data = df.simpson)
+                data = df.simpson)
 
 fit.lmer %>% 
   summary()
@@ -762,7 +767,6 @@ fit.lmer %>%
 As we can see, the fixed effect for `x` is now negative! 
 
 ```{r}
-
 fit.lmer %>% 
   augment() %>% 
   clean_names() %>% 

docs/404.html

@@ -23,7 +23,7 @@
 <meta name="author" content="Tobias Gerstenberg" />
 
 
-<meta name="date" content="2024-02-16" />
+<meta name="date" content="2024-02-22" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -51,12 +51,6 @@
 <link href="libs/anchor-sections-1.1.0/anchor-sections.css" rel="stylesheet" />
 <link href="libs/anchor-sections-1.1.0/anchor-sections-hash.css" rel="stylesheet" />
 <script src="libs/anchor-sections-1.1.0/anchor-sections.js"></script>
-<script src="libs/htmlwidgets-1.6.4/htmlwidgets.js"></script>
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-<script src="libs/kePrint-0.0.1/kePrint.js"></script>
-<link href="libs/lightable-0.0.1/lightable.css" rel="stylesheet" />
 
 
 <style type="text/css">
@@ -128,28 +122,6 @@
 
   div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
 </style>
-<style type="text/css">
-/* Used with Pandoc 2.11+ new --citeproc when CSL is used */
-div.csl-bib-body { }
-div.csl-entry {
-  clear: both;
-}
-.hanging div.csl-entry {
-  margin-left:2em;
-  text-indent:-2em;
-}
-div.csl-left-margin {
-  min-width:2em;
-  float:left;
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-div.csl-right-inline {
-  margin-left:2em;
-  padding-left:1em;
-}
-div.csl-indent {
-  margin-left: 2em;
-}
-</style>
 
 <link rel="stylesheet" href="style.css" type="text/css" />
 </head>
@@ -929,20 +901,6 @@ <h1>Page not found</h1>
 });
 </script>
 
-<!-- dynamically load mathjax for compatibility with self-contained -->
-<script>
-  (function () {
-    var script = document.createElement("script");
-    script.type = "text/javascript";
-    var src = "true";
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-    script.src = src;
-    document.getElementsByTagName("head")[0].appendChild(script);
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-</script>
 </body>
 
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