Config file rate vs probability

[JorySchossau]

The comments about mutation rates in the config files are incorrect, as rate assumes reference to a quantity per unit time, that quantity of which could be greater than 1. What we mean to say is 'probability'.

[cliff-bohm]

www.merriam-webster.com disagrees...

rate noun
Definition of Rate (Entry 2 of 3)
1a : reckoned value : VALUATION
b obsolete : ESTIMATION
2 obsolete : a fixed quantity
3a : a fixed ratio between two things
b : a charge, payment, or price fixed according to a ratio, scale, or standard: such as
(1) : a charge per unit of a public-service commodity

(2) : a charge per unit of freight or passenger service

(3) : a unit charge or ratio used in assessing property taxes

(4) British : a local tax

4a : a quantity, amount, or degree of something measured per unit of something else
her typing rate was 80 words per minute
b : an amount of payment or charge based on another amount
specifically : the amount of premium per unit of insurance
5 : relative condition or quality : CLASS
at any rate
: in any case : ANYWAY

[cliff-bohm]

also, it can be greater than one.
More than one mutation per site is probably not meaningful... but it could be.

[JorySchossau]

But we use it as a probability, so this is super confusing. We should stick to using either probability or rate (given some unit of change we are specific about).

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On Sat, Sep 29, 2018 at 5:08 PM Clifford Bohm ***@***.***> wrote: also, it can be greater than one. More than one mutation per site is probably not meaningful... but it could be. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#276 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACjbeUj1eXvycJuD4Rs6onV38QtQAI9pks5uf-EzgaJpZM4XArui> .

[cliff-bohm]

But, if the mutation rate is .005, that means the rate of mutation is .005 per site or 1 mutation per 200 sites?

[JorySchossau]

The problem is that rate usually means per time. To take advantage of technicalities otherwise is confusing no matter how technically right it is. This is a useful discussion!

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On Sat., 29 Sep. 2018, 16:03 Clifford Bohm, ***@***.***> wrote: But, if the mutation rate is .005, that means the rate of mutation is .005 per site or 1 mutation per 200 sites? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#276 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACjbedRqDbPtDUvLjxsyaI0PSFm4bSdhks5uf-4sgaJpZM4XArui> .