Visualizing (generalized) linear mixed effects models, part 2 #rstats #lme4. In the first part on visualizing (generalized) linear mixed effects models, I showed examples of the new functions in the sjPlot package to visualize fixed and random effects (estimates and odds ratios) of (g)lmer results.
Meanwhile, I added further features to the functions, which I like to introduce here. This posting is based on the online manual of the sjPlot package. In this posting, I’d like to give examples for diagnostic and probability plots of odds ratios. The latter examples, of course, only refer to the sjp.glmer function (generalized mixed models). To reproduce these examples, you need the version 1.59 (or higher) of the package, which can be found at GitHub. Visualizing (generalized) linear mixed effects models with ggplot #rstats #lme4. In the past week, colleagues of mine and me started using the lme4-package to compute multi level models.
This inspired me doing two new functions for visualizing random effects (as retrieved by ranef()) and fixed effects (as retrieved by fixed()) of (generalized) linear mixed effect models. The upcoming version of my sjPlot package will contain two new functions to plot fitted lmer and glmer models from the lme4 package: sjp.lmer and sjp.glmer (not that surprising function names). Comparing multiple (g)lm in one graph. It’s been a while since a user of my plotting-functions asked whether it would be possible to compare multiple (generalized) linear models in one graph (see comment).
While it is already possible to compare multiple models as table output, I now managed to build a function that plots several (g)lm-objects in a single ggplot-graph. The following examples are take from my sjPlot package which is available on CRAN. Once you’ve installed the package, you can run one of the examples provided in the function’s documentation: Thanks to the help of a stackoverflow user, I now know that the order of aes-parameters matters in case you have dodged positioning of geoms on a discrete scale. An example: I use following code in my function ggplot(finalodds, aes(y=OR, x=xpos, colour=grp, alpha=pa)) to apply different colours to each model and setting an alpha-level for geoms depending on the p-level. Gefällt mir: Gefällt mir Lade... Linear in the logit graph. Binary classif. eval. in R via ROCR. A binary classifier makes decisions with confidence levels.
Usually it’s imperfect: if you put a decision threshold anywhere, items will fall on the wrong side — errors. I made this a diagram a while ago for Turker voting; same principle applies for any binary classifier. So there are a zillion ways to evaluate a binary classifier. Accuracy? Accuracy on different item types (sens, spec)?
I wanted to have a small, easy-to-use function that calls ROCR and reports the basic information I’m interested in. > binary_eval(preds, labels) These are four graphs showing variation of classifier performance as the cutoff changes. The other thing binary_eval does is show one cutoff point across all the graphs — the blue circle — and display its associated performance metrics. Predictions seem to be real-valued scores, so using naive cutoff 0: Acc = 0.531 F = 0.338 Prec = 0.780 Rec = 0.216 Spec = 0.924 Balanced Acc = 0.570 So it’s very apparent that the naive cutoff isn’t performing well here.
Plotting Odds Ratios (aka a forrestplot) with ggplot2 – Sustainable Research. Hi, if you like me work in medical research, you have to plot the results of multiple logistic regressions every once in a while.
As I have not yet found a great solution to make these plots I have put together the following short skript. Do not expect too much, it’s more of a reminder to my future self than some mind-boggling new invention. The code can be found below the resulting figure looks like this: Here comes the code. Conditionning plot. Plotting lm and glm models with ggplot. Update I followed the advice from Tim’s comment and changed the scaling in the sjPlotOdds-function to logarithmic scaling.
The screenshots below showing the plotted glm’s have been updated. Summary In this posting I will show how to plot results from linear and logistic regression models (lm and glm) with ggplot. As in my previous postings on ggplot, the main idea is to have a highly customizable function for representing data. You can download all my scripts from my script page. The inspiration source My following two functions are based on an idea which I saw at the Sustainable Research Blog. Plotting odds ratios Plotting odds ratios gives you mainly two display styles: bars or plots (dots). Odds ratios as dots, with confidence intervals, “positive” effects (> 1) in blue. In the above example, if you do not specifiy axis limits, the boundaries will be calculated according to the lowest and highest confidence interval, thus fitting the diagram to the highest possible “zoom”.