wangke16
commented
5 months ago Hi,
Regarding time boundaries, I think you should check —samegrid function in plot_utils.py from MSMC-IM repository.
On 17 Apr 2024, at 11:21, Ari Löytynoja @.***> wrote:
Hello,
I'm confused about the correct way of computing M(t).
In MSMC_IM.py, they are computed using the right boundaries and then outputted in the file .MSMC_IM.estimates.txt: https://github.com/wangke16/MSMC-IM/blob/e6c5d3b13d10131a6aec7b5a9fd792a3ce09bec9/MSMC_IM.py#L79 https://github.com/wangke16/MSMC-IM/blob/e6c5d3b13d10131a6aec7b5a9fd792a3ce09bec9/MSMC_IM.py#L79 However, in plot_utils.py, they are computed using the left boundaries as only those are included in .MSMC_IM.estimates.txt:
time_boundaries,IM_N1s,IM_N2s,m_t_s = read_from_MSMC_IM(args.Input) if args.samegrid: t = time_boundaries CDF_t = cumulative_Symmigproportion(time_boundaries, m_t_s) https://github.com/wangke16/MSMC-IM/blob/e6c5d3b13d10131a6aec7b5a9fd792a3ce09bec9/plot_utils.py#L86 https://github.com/wangke16/MSMC-IM/blob/e6c5d3b13d10131a6aec7b5a9fd792a3ce09bec9/plot_utils.py#L86 As the first left boundary is zero, a consequence of the latter is that integ = 2 m[0] 0 is always zero and the first time period is ignored: https://github.com/wangke16/MSMC-IM/blob/e6c5d3b13d10131a6aec7b5a9fd792a3ce09bec9/plot_utils.py#L44 https://github.com/wangke16/MSMC-IM/blob/e6c5d3b13d10131a6aec7b5a9fd792a3ce09bec9/plot_utils.py#L44 Confusingly, the plotting function in MSMC_IM.py is different from that in plot_utils.py, and erroneous at least if xlog is used and the first x-value (log(0)) is not defined: https://github.com/wangke16/MSMC-IM/blob/e6c5d3b13d10131a6aec7b5a9fd792a3ce09bec9/MSMC_IM.py#L190 https://github.com/wangke16/MSMC-IM/blob/e6c5d3b13d10131a6aec7b5a9fd792a3ce09bec9/MSMC_IM.py#L190 There are now three ways of plotting M(t):
in plot_utils.py for making plots from the .estimates.txt data but recomputing the M values in MSMC_IM.py for plots in .fittingdetails.xlog.pdf user-made plots using the M values in .estimates.txt I personally would plot M(t) with the column 'M' from .MSMC_IM.estimates.txt and the right boundaries. One could add zeros in the vectors to start it from the corner. However, this differs from the plots generated by MSMC-IM.
Can you please tell your opinion on which one of these is the right way to do the plotting?
Best regards,
Ari
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Hello,
I'm confused about the correct way of computing M(t).
In MSMC_IM.py, they are computed using the right boundaries and then outputted in the file *.MSMC_IM.estimates.txt: https://github.com/wangke16/MSMC-IM/blob/e6c5d3b13d10131a6aec7b5a9fd792a3ce09bec9/MSMC_IM.py#L79
However, in plot_utils.py, they are computed using the left boundaries as only those are included in *.MSMC_IM.estimates.txt:
https://github.com/wangke16/MSMC-IM/blob/e6c5d3b13d10131a6aec7b5a9fd792a3ce09bec9/plot_utils.py#L86
As the first left boundary is zero, a consequence of the latter is that
integ = 2 * m[0] * 0is always zero and the first time period is ignored: https://github.com/wangke16/MSMC-IM/blob/e6c5d3b13d10131a6aec7b5a9fd792a3ce09bec9/plot_utils.py#L44Confusingly, the plotting function in MSMC_IM.py is different from that in plot_utils.py, and erroneous at least if xlog is used and the first x-value (
log(0)) is not defined:https://github.com/wangke16/MSMC-IM/blob/e6c5d3b13d10131a6aec7b5a9fd792a3ce09bec9/MSMC_IM.py#L190
There are now three ways of plotting M(t):
I personally would plot M(t) with the column 'M' from *.MSMC_IM.estimates.txt and the right boundaries. One could add zeros in the vectors to start it from the corner. However, this differs from the plots generated by MSMC-IM.
Can you please tell your opinion on which one of these is the right way to do the plotting?
Best regards,
Ari