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Major comments
- [x] 1. The introduction is generally difficult to read. To help the reader, I suggest you introduce the general concept of persistent and transient growth e.g. in line 56 before descr…
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_From [lemoine....@gmail.com](https://code.google.com/u/108397219265632109549/) on 2014-09-06T14:29:24Z_
Spyder Version: 2.2.5
Python Version: 2.7.5
Qt Version : 4.8.5, PyQt4 (API v2) 4.10.3 on…
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Hi Pablo,
I was going over `rbc_model.ipynb`, working on some edits and there are two results there that seem strange:
- The chart in Out[24] on the [original](http://nbviewer.ipython.org/github/yani…
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So it looks like the default Langevin collision rate is set to 5.0 per picosecond (https://github.com/choderalab/msmseeder/blob/master/MSMSeeder/packaging.py#L114). According to Michael's paper (http…
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I would like to monitor the rate estimates for specific branches. One way to do this is to use the treeAssembly() function and monitor the tree with the rates as branch lengths. But it seems like tree…
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```
Application Version: 5.3.14 - May 19, 2009 is on the screen when I run it
(output file just says its 5.3.1)
SVN Revision Number: 3729
Compile Date: Apr 8, 2009
Operating System…
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Need to check code for summary function in niche overlap with `ra1`and make sure it is handling extreme cases the same way for all algorithms:
``` r
# If observed index is smaller than any of the 10…
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I've implemented bootstrap confidence intervals as described in Method 1 of El-Shaarawi (2010) which is now available in the data-raw folder. I have used the code to calculate the CIs for the come exa…
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One issue with duration diagnostics is that they take such a long time to start to reach the target values. But dissolution diagnostics -- by this I mean the metric "what proportion of extant ties di…
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We have two objects, `Simulator` and `Simulation`, which have very similar names and very different purposes. I think that will be terribly confusing for users. In addition, we have a `Calculation` cl…