The num.filter
parameter is a hyper-parameter which will effect the expressiveness of your model. A larger number of filters will give you a more expressive model, which can find more subtle patterns given enough data, but is also more likely to over-fit. So in general there's no "best" answer, but this is something you'll need to experiment with for your dataset.
As for building a time-series model with a CNN, again, there's no simple answer. It's certainly possible to use a CNN for time-series analysis, but I wouldn't start with an image-processing CNN like the one you link to. This question https://stats.stackexchange.com/questions/127542/convolutional-neural-network-for-time-series gives a bunch of good references on how to build time-series models with neural networks.
You might also consider using an RNN, which are generally more naturally suited for time-series analysis. Here's a good example of running an RNN in R with MXNet: http://mxnet.io/tutorials/r/charRnnModel.html