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README.md

@@ -86,6 +86,7 @@ General simulation parameters:
 * `tburnin` (0) is the duration of the burn-in period, in generations
 * `tend` (10) is the number of generations to simulate (after burn-in)
 * `tsave` (10) is the frequency at which to record the data
+* `tcalcri` (0) is the frequency at which to record reproductive isolation (RI). RI is on a separate timeline than the rest of the variables because its computation involves sampling random numbers (it samples mating events and records effective mating preferences). Therefore, measuring RI affects the course of events because it affects the random numbers that will be generated down the line. This means that two simulations run with the same `seed` (see below) will not be identical if they compute RI at different times. To ensure that simulations could be replicated and recorded at different resolutions we therefore keep the computation of RI on a separate timeline. So, you can run two identical simulations sampled at different temporal resolutions, just make sure that `tcalcri` is identical between the two. Note that it is thus the other variables that may be sampled at different frequencies, not RI (there is no way around it: two simulations computing RI at different frequencies *will* be different). If `tcalcri` is set to zero, it takes the value of `tsave` and RI is recorded at the same time as the other variables, provided that `datsave` is one and "RI" is written in the order file `whattosave.txt` (see below).
 * `tcomplete` (1000000) is the time at which to force complete reproductive isolation between the two ecotypes (can mimic e.g. genomic incompatibilities between the two species, or the evolution of very good species recognition abilities)
 * `talkative` (1) is either 0 or 1 and sets whether the simulation should print status information to the prompt
 * `choosewhattosave` (0) is either 0 or 1 and sets whether the variables to save are specified in a separate file, the order file `whattosave.txt` (see below). If 0 all of the output variables are saved every `tsave` generations except for whole genomes