a few more doc tweaks

Author: bhaller

QtSLiM/help/SLiMHelpClasses.html

@@ -139,12 +139,12 @@
 <p class="p6"><span class="s3">If the optional </span><span class="s4">sex</span><span class="s3"> parameter is </span><span class="s4">"*"</span><span class="s3"> (the default), then the supplied hotspot map will be used for both sexes (which is the only option for hermaphroditic simulations).<span class="Apple-converted-space">  </span>In sexual simulations </span><span class="s4">sex</span><span class="s3"> may be </span><span class="s4">"M"</span><span class="s3"> or </span><span class="s4">"F"</span><span class="s3"> instead, in which case the supplied hotspot map is used only for that sex.<span class="Apple-converted-space">  </span>Note that whether sex-specific hotspot maps will be used is set by the way that the simulation is initially configured with </span><span class="s4">initializeHotspot()</span><span class="s3">, and cannot be changed with this method; so if the simulation was set up to use sex-specific hotspot maps then sex must be </span><span class="s4">"M"</span><span class="s3"> or </span><span class="s4">"F"</span><span class="s3"> here, whereas if it was set up not to, then sex must be </span><span class="s4">"*"</span><span class="s3"> or unsupplied here.<span class="Apple-converted-space">  </span>If a simulation needs sex-specific hotspot maps only some of the time, the male and female maps can simply be set to be identical the rest of the time.</span></p>
 <p class="p6"><span class="s3">The hotspot map is normally constant in simulations, so be sure you know what you are doing.</span></p>
 <p class="p3">– (void)setMutationRate(numeric rates, [Ni ends = NULL], [string$ sex = "*"])</p>
-<p class="p4">Set the mutation rate per base position per generation along the chromosome.<span class="Apple-converted-space">  </span>There are two ways to call this method.<span class="Apple-converted-space">  </span>If the optional <span class="s1">ends</span> parameter is <span class="s1">NULL</span> (the default), then <span class="s1">rates</span> must be a singleton value that specifies a single mutation rate to be used along the entire chromosome.<span class="Apple-converted-space">  </span>If, on the other hand, <span class="s1">ends</span> is supplied, then <span class="s1">rates</span> and <span class="s1">ends</span> must be the same length, and the values in <span class="s1">ends</span> must be specified in ascending order.<span class="Apple-converted-space">  </span>In that case, <span class="s1">rates</span> and <span class="s1">ends</span> taken together specify the mutation rates to be used along successive contiguous stretches of the chromosome, from beginning to end; the last position specified in <span class="s1">ends</span> should extend to the end of the chromosome (as previously determined, during simulation initialization).<span class="Apple-converted-space">  </span>See the <span class="s1">initializeMutationRate()</span> function for further discussion of precisely how these rates and positions are interpreted.</p>
+<p class="p4">Set the mutation rate per base position per <span class="s6">gamete</span>.<span class="Apple-converted-space">  </span>There are two ways to call this method.<span class="Apple-converted-space">  </span>If the optional <span class="s1">ends</span> parameter is <span class="s1">NULL</span> (the default), then <span class="s1">rates</span> must be a singleton value that specifies a single mutation rate to be used along the entire chromosome.<span class="Apple-converted-space">  </span>If, on the other hand, <span class="s1">ends</span> is supplied, then <span class="s1">rates</span> and <span class="s1">ends</span> must be the same length, and the values in <span class="s1">ends</span> must be specified in ascending order.<span class="Apple-converted-space">  </span>In that case, <span class="s1">rates</span> and <span class="s1">ends</span> taken together specify the mutation rates to be used along successive contiguous stretches of the chromosome, from beginning to end; the last position specified in <span class="s1">ends</span> should extend to the end of the chromosome (as previously determined, during simulation initialization).<span class="Apple-converted-space">  </span>See the <span class="s1">initializeMutationRate()</span> function for further discussion of precisely how these rates and positions are interpreted.</p>
 <p class="p4">If the optional <span class="s1">sex</span> parameter is <span class="s1">"*"</span> (the default), then the supplied mutation rate map will be used for both sexes (which is the only option for hermaphroditic simulations).<span class="Apple-converted-space">  </span>In sexual simulations <span class="s1">sex</span> may be <span class="s1">"M"</span> or <span class="s1">"F"</span> instead, in which case the supplied mutation rate map is used only for that sex.<span class="Apple-converted-space">  </span>Note that whether sex-specific mutation rate maps will be used is set by the way that the simulation is initially configured with <span class="s1">initializeMutationRate()</span>, and cannot be changed with this method; so if the simulation was set up to use sex-specific mutation rate maps then sex must be <span class="s1">"M"</span> or <span class="s1">"F"</span> here, whereas if it was set up not to, then sex must be <span class="s1">"*"</span> or unsupplied here.<span class="Apple-converted-space">  </span>If a simulation needs sex-specific mutation rate maps only some of the time, the male and female maps can simply be set to be identical the rest of the time.</p>
 <p class="p4">The mutation rate intervals are normally a constant in simulations, so be sure you know what you are doing.</p>
 <p class="p6"><span class="s3">In nucleotide-based models, </span><span class="s4">setMutationRate()</span><span class="s3"> may not be called.<span class="Apple-converted-space">  </span>If variation in the mutation rate along the chromosome is desired, </span><span class="s4">setHotspotMap()</span><span class="s3"> should be used.</span></p>
 <p class="p3">– (void)setRecombinationRate(numeric rates, [Ni ends = NULL], [string$ sex = "*"])</p>
-<p class="p4">Set the recombination rate per base position per generation along the chromosome.<span class="Apple-converted-space">  </span><span class="s6">All rates must be in the interval [</span><span class="s7">0.0</span><span class="s6">, </span><span class="s7">0.5</span><span class="s6">].<span class="Apple-converted-space">  </span></span>There are two ways to call this method.<span class="Apple-converted-space">  </span>If the optional <span class="s1">ends</span> parameter is <span class="s1">NULL</span> (the default), then <span class="s1">rates</span> must be a singleton value that specifies a single recombination rate to be used along the entire chromosome.<span class="Apple-converted-space">  </span>If, on the other hand, <span class="s1">ends</span> is supplied, then <span class="s1">rates</span> and <span class="s1">ends</span> must be the same length, and the values in <span class="s1">ends</span> must be specified in ascending order.<span class="Apple-converted-space">  </span>In that case, <span class="s1">rates</span> and <span class="s1">ends</span> taken together specify the recombination rates to be used along successive contiguous stretches of the chromosome, from beginning to end; the last position specified in <span class="s1">ends</span> should extend to the end of the chromosome (as previously determined, during simulation initialization).<span class="Apple-converted-space">  </span>See the <span class="s1">initializeRecombinationRate()</span> function for further discussion of precisely how these rates and positions are interpreted.</p>
+<p class="p4">Set the recombination rate per base position per <span class="s6">gamete</span>.<span class="Apple-converted-space">  </span><span class="s6">All rates must be in the interval [</span><span class="s7">0.0</span><span class="s6">, </span><span class="s7">0.5</span><span class="s6">].<span class="Apple-converted-space">  </span></span>There are two ways to call this method.<span class="Apple-converted-space">  </span>If the optional <span class="s1">ends</span> parameter is <span class="s1">NULL</span> (the default), then <span class="s1">rates</span> must be a singleton value that specifies a single recombination rate to be used along the entire chromosome.<span class="Apple-converted-space">  </span>If, on the other hand, <span class="s1">ends</span> is supplied, then <span class="s1">rates</span> and <span class="s1">ends</span> must be the same length, and the values in <span class="s1">ends</span> must be specified in ascending order.<span class="Apple-converted-space">  </span>In that case, <span class="s1">rates</span> and <span class="s1">ends</span> taken together specify the recombination rates to be used along successive contiguous stretches of the chromosome, from beginning to end; the last position specified in <span class="s1">ends</span> should extend to the end of the chromosome (as previously determined, during simulation initialization).<span class="Apple-converted-space">  </span>See the <span class="s1">initializeRecombinationRate()</span> function for further discussion of precisely how these rates and positions are interpreted.</p>
 <p class="p4">If the optional <span class="s1">sex</span> parameter is <span class="s1">"*"</span> (the default), then the supplied recombination rate map will be used for both sexes (which is the only option for hermaphroditic simulations).<span class="Apple-converted-space">  </span>In sexual simulations <span class="s1">sex</span> may be <span class="s1">"M"</span> or <span class="s1">"F"</span> instead, in which case the supplied recombination map is used only for that sex.<span class="Apple-converted-space">  </span>Note that whether sex-specific recombination maps will be used is set by the way that the simulation is initially configured with <span class="s1">initializeRecombinationRate()</span>, and cannot be changed with this method; so if the simulation was set up to use sex-specific recombination maps then sex must be <span class="s1">"M"</span> or <span class="s1">"F"</span> here, whereas if it was set up not to, then sex must be <span class="s1">"*"</span> or unsupplied here.<span class="Apple-converted-space">  </span>If a simulation needs sex-specific recombination maps only some of the time, the male and female maps can simply be set to be identical the rest of the time.</p>
 <p class="p4">The recombination intervals are normally a constant in simulations, so be sure you know what you are doing.</p>
 <p class="p1"><b>5.3<span class="Apple-converted-space">  </span>Class Community</b></p>