ggeffects | Estimated Marginal Means and Marginal Effects | Data Visualization library
kandi X-RAY | ggeffects Summary
kandi X-RAY | ggeffects Summary
. Lüdecke D (2018). ggeffects: Tidy Data Frames of Marginal Effects from Regression Models. Journal of Open Source Software, 3(26), 772. doi: 10.21105/joss.00772.
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QUESTION
I'm trying to find the predicted values of car accidents according to age and sex and finally adjusted to population.
My data is (df):
...ANSWER
Answered 2022-Apr-07 at 13:56A Poisson glm uses a log link function, and by default the predict.glm
method returns the predictions without applying the inverse link function. You either need to use type = "response"
inside predict
, which will call the inverse link function on the predictions to give you predictions in the same units as your input data, or equivalently, since the inverse link function is essentially just exp
, you can exponentiate the results of predict
.
So you can do either:
QUESTION
I fitted a glm model and had to transform some variables with log1p. I now want to create a ggpredict plot with a backtransformed scale. I transformed the variables before using the glm function.
here's a sample of a few variables of my original data and my code:
...ANSWER
Answered 2022-Mar-02 at 23:46When I can't get the built-in plot method to do what I want, I use ggpredict()
to get the predicted values and build the plot myself. I couldn't make your model work (you only gave us responses where case=1
) so I'm making up my own, slightly simpler example.
Load package and fit model:
QUESTION
I would like to get a plot like ggplot2::geom_smooth(method = "lm", fullrange = T)
with ggeffects::ggpredict()
. The fit should only span the data and not the whole plot.
Can somebody help?
Example
...ANSWER
Answered 2021-Nov-16 at 23:16Maybe limit.range
?
QUESTION
Can someone advise how to analyse if y is significantly decreasing with increasing x using R?
...ANSWER
Answered 2021-Oct-15 at 07:15Given your new data, I think that the best course of action is to consider that these two measurements, y1 and y2, were taken in batches and so should be treated as such, i.e. coming from the same batch which may have some intra-variation. To model this intra-variation you can use a mixed model, with the batches variable as a random effect rather than a fixed effect.
QUESTION
I am working with ggeffects package I have the following syntax
...ANSWER
Answered 2022-Jan-28 at 21:54I couldn't run your code, but I rebuilt it with iris
.
Like Matt suggested, one thing would be, remove fill=F
:
QUESTION
I have a question about predictions using ggeffects, which is giving me completely different results if I use a traditional lm fit or an extracted parsnip model fit (despite having the same coefficients). Here is an example...
...ANSWER
Answered 2021-Dec-12 at 06:55You are getting different results because lmmod_simp
and lm_fit_extracted
are different models. While lm_fit
has an interaction effect on steps, lm_fit_extracted
has no idea about this interaction as it gets the data after the interaction calculation has been performed.
It is generally not recommended to pull out models from a workflow object if you plan on using it for other things than diagnostics.
QUESTION
I am not entirely sure what I am doing wrong/what to look up. My objective is to use ggpredict and ggplot to display the relationship between time and the proportion of years burnt. I'm guessing it is something to do with the time variable being log transformed?
...ANSWER
Answered 2021-Dec-07 at 18:29Okay, so I've figured out the main problem here. In the documentation of the ggpredict()
function there is an argument called back.transform
that defaults to TRUE. This means that log-transformed data will be automatically transformed back to the original response scale. This is why if you examine the ggpredict object d
, you will see that the time
variable actually does go to over 8000 in that object. So because you did not flag back.transform=FALSE
, but also specified time[exp]
, what happened was the function automatically exponentiated your values, and then you did it again.
If we look at the logged values:
QUESTION
I have a dataset in a long format of 60 repeated measurements taken within 19 patients (ID
). Patients have had a differing amount of measurements (2 measurements [n=11], followed by 5 measurements [n=5], 3 [n=1], 4 [n=1], and 6 measurements [n=1], with varying time-intervals (fu_time
measured in years). The data looks as follows:
ANSWER
Answered 2021-Nov-16 at 23:10A bit off-topic, but I suggest parameters::model_parameters()
for your summary tables:
QUESTION
I'd like to plot the relationship between the number of ladenant
response variable in function of Bioma
(categorical) and temp
(numeric) using binomial negative
generalized linear mixed models (GLMMs) without success. I try to do:
ANSWER
Answered 2021-Nov-12 at 20:23I think you just need to be careful with the different names of the variables in the two objects myds
and mydf
, and where you place them in the calls to the various geom
s:
QUESTION
These are three different ways to run an individual fixed effect method which gives more or less the same results (see below). My main question is how to get predictive probabilities or average marginal effects using the second model (model_plm
) or the third model(model_felm
). I know how to do it using the first model (model_lm
) and show an example below using ggeffects
, but that only works when i have a small sample.
As i have over a million individual, my model only works using model_plm
and model_felm
. If i use model_lm
, it takes a lot of time to run with one million individuals since they are controlled for in the model. I also get the following error: Error: vector memory exhausted (limit reached?)
. I checked many threads on StackOverflow to work around that error but nothing seems to solve it.
I was wondering whether there is an efficient way to work around this issue. My main interest is to extract the predicted probabilities of the interaction residence*union
. I usually extract predictive probabilities or average marginal effects using one of these packages: ggeffects
,emmeans
or margins
.
ANSWER
Answered 2021-Oct-22 at 17:46This potential solution uses biglm::biglm()
to fit the lm model and then uses emmeans::qdrg()
with a nuisance specified. Does this approach help in your situation?
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