I am new to R and I am trying to build a decision tree using rpart.
However when I plotted the model using plot(fit) where fit = model, the output displayed was all lines and no texts/ no variable names. Is there anything that must be wrong with my settings?
Related
I would like to create a forest plot for the meta-regression outputs using metafor. There are several effect modifiers in the regression model I created. I am not sure if I can visualize them in one forest plot. I would like the forest plot to look as where ylab would show all the effect modifiers and xlab would show log response ratio. Would that be possible and if it is, could you please give an example?
I want to export the plot points of a cox regression survival plot so i can use it in Graphpad Prism to make a nice graph out of it.
Question
How can i export the plot points?
is there maybe an easier way to export such a graph to edit it in graphpad?
You should add a save subcommand to your analysis syntax:
/SAVE=SURVIVAL
After running the analysis you will find new column(s) containing the survival data which you can then export and plot elsewhere.
If you look in the Menu for the analysis you can see a button called - click it to see all options of new variables to save, maybe you can find other data useful.
I got some figures after I did decision tree model using part library.
This figures shows fundamental function of part library.
In these figures, I understand all excepts fourth kind of figure.
This figure don't have any powful feature. It does not show any information. How can I understand this figure?
You are right. The fourth panel shows the visualization of a tree without any splits. Thus, in this case none of the available split variables improved the cost-complexity criterion of rpart and hence only the root node remains.
The visualization using the partykit package employs stacked bar plots for every terminal node in the trees (the default visualization for binary classification in the package). Thus, there is only a single stacked bar in case of a root node only.
I'm trying to plot my model in Keras, like this:
# Plot model graph
tf.keras.utils.plot_model(model, to_file='Model1.png')
from IPython.display import Image
Image(retina=True, filename='Model1.png')
Which I get the following result: my model
But, I've seen somewhere in the internet, that someone plotted his model, like this: model I need
How can I change my code to plot like that? With the input/output information of each layer of my model?
You can use the parameter show_shapes=True.
from the tf.keras documentation:
show_shapes: whether to display shape information.
(have a closer look here: https://www.tensorflow.org/api_docs/python/tf/keras/utils/plot_model )
I'm trying to plot a cox proportional hazard model in R. (or a logit model)
I used the following code (which I copied from https://sites.google.com/site/daishizuka/toolkits/plotting-logistic-regression-in-r)
c<-coxph(formula=Surv(year, promo)~prov.yrs, data=cul)
curve(predict(c, data.frame(prov.yrs=x), type="risk"), add=TRUE)
I get the error message
Error in plot.xy(xy.coords(x, y), type = type, ...) :
invalid graphics state
I believe there is something wrong with plotting this, so I was wondering if there is a way to plot this. I get the same error message when I use glm. Any help will be appreciated!!
The example you copied from shows a logistic regression, but you are fitting a coxph model, they are very different in how they are handled.
If you just want a plot of the the hazard ratio then your code will basically work (except you are adding to a plot that is not there, which may be what generates the error, try changing add to FALSE).
If you want to plot the survival curve(s) then use the survfit function to get the predicted survival information and plot that.
The error message suggests you did not have a device open or perhaps there was some other problem with the plot you were trying to add to? That code produces a plot over a range input [0,1] with a toy example I built from the coxph help page. Perhaps your range for the 'prov.yrs' is different than an existing plot, or there is no device open? Try plot.new(), plot whatever else you were going to use, and then rerun? (The add=TRUE will suppress plotting of the box, axes and labels.)