standardize on "viability/survival" as the tick cycle stage name

Author: bhaller

QtSLiM/help/SLiMHelpClasses.html

@@ -810,11 +810,11 @@
 <p class="p3">individuals =&gt; (object&lt;Individual&gt;)</p>
 <p class="p6"><span class="s5">All of the individuals contained by the subpopulation.<span class="Apple-converted-space">  </span>Each individual is diploid and thus contains two </span><span class="s8">Genome</span><span class="s5"> objects.</span><span class="s3"><span class="Apple-converted-space">  </span>See the </span><span class="s4">sampleIndividuals()</span><span class="s3"> and </span><span class="s4">subsetIndividuals()</span><span class="s3"> for fast ways to get a subset of the individuals in a subpopulation.</span></p>
 <p class="p5">lifetimeReproductiveOutput =&gt; (integer)</p>
-<p class="p6">If pedigree tracking is turned on with <span class="s1">initializeSLiMOptions(keepPedigrees=T)</span>, <span class="s1">lifetimeReproductiveOutput</span> contains the value of the <span class="s1">Individual</span> property <span class="s1">reproductiveOutput</span> for all individuals in the subpopulation that died in the last selection/mortality tick cycle stage (or, for WF models, immediately after reproduction).<span class="Apple-converted-space">  </span>This allows access to the lifetime reproductive output of individuals in the subpopulation at the end of their lives.<span class="Apple-converted-space">  </span>If pedigree tracking is not on, this property is unavailable.</p>
+<p class="p6">If pedigree tracking is turned on with <span class="s1">initializeSLiMOptions(keepPedigrees=T)</span>, <span class="s1">lifetimeReproductiveOutput</span> contains the value of the <span class="s1">Individual</span> property <span class="s1">reproductiveOutput</span> for all individuals in the subpopulation that died in the last viability/survival tick cycle stage (or, for WF models, immediately after reproduction).<span class="Apple-converted-space">  </span>This allows access to the lifetime reproductive output of individuals in the subpopulation at the end of their lives.<span class="Apple-converted-space">  </span>If pedigree tracking is not on, this property is unavailable.</p>
 <p class="p5">lifetimeReproductiveOutputF =&gt; (integer)</p>
-<p class="p6">If pedigree tracking is turned on with <span class="s1">initializeSLiMOptions(keepPedigrees=T)</span>, <span class="s1">lifetimeReproductiveOutputF</span> contains the value of the <span class="s1">Individual</span> property <span class="s1">reproductiveOutput</span> for all female individuals in the subpopulation that died in the last selection/mortality tick cycle stage (or, for WF models, immediately after reproduction).<span class="Apple-converted-space">  </span>This property is undefined if separate sexes have not been enabled, or if pedigree tracking is not on.</p>
+<p class="p6">If pedigree tracking is turned on with <span class="s1">initializeSLiMOptions(keepPedigrees=T)</span>, <span class="s1">lifetimeReproductiveOutputF</span> contains the value of the <span class="s1">Individual</span> property <span class="s1">reproductiveOutput</span> for all female individuals in the subpopulation that died in the last viability/survival tick cycle stage (or, for WF models, immediately after reproduction).<span class="Apple-converted-space">  </span>This property is undefined if separate sexes have not been enabled, or if pedigree tracking is not on.</p>
 <p class="p5">lifetimeReproductiveOutputM =&gt; (integer)</p>
-<p class="p6">If pedigree tracking is turned on with <span class="s1">initializeSLiMOptions(keepPedigrees=T)</span>, <span class="s1">lifetimeReproductiveOutputM</span> contains the value of the <span class="s1">Individual</span> property <span class="s1">reproductiveOutput</span> for all male individuals in the subpopulation that died in the last selection/mortality tick cycle stage (or, for WF models, immediately after reproduction).<span class="Apple-converted-space">  </span>This property is undefined if separate sexes have not been enabled, or if pedigree tracking is not on.</p>
+<p class="p6">If pedigree tracking is turned on with <span class="s1">initializeSLiMOptions(keepPedigrees=T)</span>, <span class="s1">lifetimeReproductiveOutputM</span> contains the value of the <span class="s1">Individual</span> property <span class="s1">reproductiveOutput</span> for all male individuals in the subpopulation that died in the last viability/survival tick cycle stage (or, for WF models, immediately after reproduction).<span class="Apple-converted-space">  </span>This property is undefined if separate sexes have not been enabled, or if pedigree tracking is not on.</p>
 <p class="p5">name &lt;–&gt; (string$)</p>
 <p class="p6">A human-readable <span class="s1">string</span> name for the subpopulation.<span class="Apple-converted-space">  </span>By default, this is the subpopulation’s symbol as a <span class="s1">string</span>; for subpopulation <span class="s1">p3</span>, for example, <span class="s1">name</span> defaults to <span class="s1">"p3"</span>.<span class="Apple-converted-space">  </span>However, it may be set to whatever you wish except that subpopulation names must be unique across time (two different subpopulations may not both have the name <span class="s1">"foo"</span>, even if they never exist at the same time).<span class="Apple-converted-space">  </span>A subpopulation’s <span class="s1">name</span> may appear as a label in SLiMgui, and it can be useful in generating output, debugging, and other purposes.<span class="Apple-converted-space">  </span>When tree-sequence recording is enabled, <span class="s1">name</span> is persisted in the subpopulation’s metadata in tree-sequence output, and can then be used in Python to identify the subpopulation; if you plan to take advantage of that feature, <span class="s1">name</span> should follow the syntax of Python identifiers: starting with a letter or underscore <span class="s1">[a-zA-Z_]</span>, followed by letters, digits, or underscores <span class="s1">[a-zA-Z0-9_]</span>, without spaces, hyphens, or other characters.</p>
 <p class="p3">selfingRate =&gt; (float$)</p>

SLiMgui/SLiMHelpClasses.rtf

@@ -5838,8 +5838,7 @@ Beginning with SLiM 3.3, the
 \f4\i0  include the nucleotides associated with any nucleotide-based mutations; the 
 \f3\fs18 ancestralNucleotides
 \f4\fs20  flag governs only the ancestral sequence.\
-\pard\pardeftab543\li547\ri720\sb60\sa60\partightenfactor0
-\cf2 \kerning1\expnd0\expndtw0 Beginning with SLiM 3.5, the 
+\kerning1\expnd0\expndtw0 Beginning with SLiM 3.5, the 
 \f3\fs18 pedigreeIDs
 \f4\fs20  parameter may be used to request that pedigree IDs be written out (and read in by 
 \f3\fs18 readFromPopulationFile()
@@ -5969,8 +5968,7 @@ As of SLiM 3.0, this method will read and restore the ages of individuals if tha
 As of SLiM 3.3, this method will restore the nucleotides of nucleotide-based mutations, and will restore the ancestral nucleotide sequence, if that information is present in the output file.  Loading an output file that contains nucleotide information in a non-nucleotide-based model, and 
 \f1\i vice versa
 \f4\i0 , will produce an error.\
-\pard\pardeftab543\li547\ri720\sb60\sa60\partightenfactor0
-\cf2 \kerning1\expnd0\expndtw0 As of SLiM 3.5, this method will read and restore the pedigree IDs of individuals and genomes if that information is present in the output file (as requested with 
+\kerning1\expnd0\expndtw0 As of SLiM 3.5, this method will read and restore the pedigree IDs of individuals and genomes if that information is present in the output file (as requested with 
 \f3\fs18 outputFull(pedigreeIDs=T)
 \f4\fs20 ) 
 \f1\i and
@@ -6835,7 +6833,7 @@ fitnessScaling <\'96> (float$)\
 \f3\fs18 Individual
 \f4\fs20  property 
 \f3\fs18 reproductiveOutput
-\f4\fs20  for all individuals in the subpopulation that died in the last selection/mortality tick cycle stage (or, for WF models, immediately after reproduction).  This allows access to the lifetime reproductive output of individuals in the subpopulation at the end of their lives.  If pedigree tracking is not on, this property is unavailable.\
+\f4\fs20  for all individuals in the subpopulation that died in the last viability/survival tick cycle stage (or, for WF models, immediately after reproduction).  This allows access to the lifetime reproductive output of individuals in the subpopulation at the end of their lives.  If pedigree tracking is not on, this property is unavailable.\
 \pard\pardeftab720\li720\fi-446\ri720\sb180\sa60\partightenfactor0
 
 \f3\fs18 \cf2 lifetimeReproductiveOutputF => (integer)\
@@ -6849,7 +6847,7 @@ fitnessScaling <\'96> (float$)\
 \f3\fs18 Individual
 \f4\fs20  property 
 \f3\fs18 reproductiveOutput
-\f4\fs20  for all female individuals in the subpopulation that died in the last selection/mortality tick cycle stage (or, for WF models, immediately after reproduction).  This property is undefined if separate sexes have not been enabled, or if pedigree tracking is not on.\
+\f4\fs20  for all female individuals in the subpopulation that died in the last viability/survival tick cycle stage (or, for WF models, immediately after reproduction).  This property is undefined if separate sexes have not been enabled, or if pedigree tracking is not on.\
 \pard\pardeftab720\li720\fi-446\ri720\sb180\sa60\partightenfactor0
 
 \f3\fs18 \cf2 lifetimeReproductiveOutputM => (integer)\
@@ -6863,7 +6861,7 @@ fitnessScaling <\'96> (float$)\
 \f3\fs18 Individual
 \f4\fs20  property 
 \f3\fs18 reproductiveOutput
-\f4\fs20  for all male individuals in the subpopulation that died in the last selection/mortality tick cycle stage (or, for WF models, immediately after reproduction).  This property is undefined if separate sexes have not been enabled, or if pedigree tracking is not on.\
+\f4\fs20  for all male individuals in the subpopulation that died in the last viability/survival tick cycle stage (or, for WF models, immediately after reproduction).  This property is undefined if separate sexes have not been enabled, or if pedigree tracking is not on.\
 \pard\pardeftab720\li720\fi-446\ri720\sb180\sa60\partightenfactor0
 
 \f3\fs18 \cf2 name <\'96> (string$)\

core/interaction_type.cpp

@@ -4031,7 +4031,7 @@ EidosValue_SP InteractionType::ExecuteMethod_evaluate(EidosGlobalStringID p_meth
 	if ((community_.CycleStage() == SLiMCycleStage::kWFStage2GenerateOffspring) ||
 		(community_.CycleStage() == SLiMCycleStage::kNonWFStage1GenerateOffspring) ||
 		(community_.CycleStage() == SLiMCycleStage::kNonWFStage4SurvivalSelection))
-		EIDOS_TERMINATION << "ERROR (InteractionType::ExecuteMethod_evaluate): evaluate() may not be called during the offspring generation or selection/mortality cycle stages." << EidosTerminate();
+		EIDOS_TERMINATION << "ERROR (InteractionType::ExecuteMethod_evaluate): evaluate() may not be called during the offspring generation or viability/survival cycle stages." << EidosTerminate();
 
 	// Get the requested subpops
 	int requested_subpop_count = subpops_value->Count();

core/population.cpp

@@ -405,7 +405,7 @@ void Population::RemoveSubpopulation(Subpopulation &p_subpop)
 // move individuals as requested by survival() callbacks
 void Population::ResolveSurvivalPhaseMovement(void)
 {
-	// So, we have a survival() callback that has requested that some individuals move during the selection/viability phase.
+	// So, we have a survival() callback that has requested that some individuals move during the viability/survival phase.
 	// We want to handle this as efficiently as we can; we could have many individuals moving between subpops in arbitrary
 	// ways.  We will remove all moving individuals from their current subpops in a single pass, and then add them to their
 	// new subpops in a single pass.  If just one individual is moving, this will be inefficient since the algorithm is O(N)
@@ -422,7 +422,7 @@ void Population::ResolveSurvivalPhaseMovement(void)
 		for (Individual *individual : (subpop_pair.second)->nonWF_survival_moved_individuals_)
 			individual->scratch_ = 1;
 
-	// loop through subpops and remove all individuals that are leaving, compacting downwards; similar to Subpopulation::ViabilitySelection()
+	// loop through subpops and remove all individuals that are leaving, compacting downwards; similar to Subpopulation::ViabilitySurvival()
 	for (std::pair<const slim_objectid_t,Subpopulation*> &subpop_pair : subpops_)
 	{ 
 		Subpopulation *subpop = subpop_pair.second;

core/species.cpp

@@ -2368,7 +2368,7 @@ void Species::nonWF_ViabilitySurvival(void)
 		std::vector<SLiMEidosBlock*> no_survival_callbacks;
 
 		for (std::pair<const slim_objectid_t,Subpopulation*> &subpop_pair : population_.subpops_)
-			subpop_pair.second->ViabilitySelection(no_survival_callbacks);
+			subpop_pair.second->ViabilitySurvival(no_survival_callbacks);
 	}
 	else
 	{
@@ -2389,7 +2389,7 @@ void Species::nonWF_ViabilitySurvival(void)
 			}
 
 			// Handle survival, using the callbacks
-			subpop->ViabilitySelection(subpop_survival_callbacks);
+			subpop->ViabilitySurvival(subpop_survival_callbacks);
 		}
 
 		// Callbacks could have requested that individuals move rather than dying; check for that

core/subpopulation.cpp

@@ -3604,7 +3604,7 @@ bool Subpopulation::ApplySurvivalCallbacks(std::vector<SLiMEidosBlock*> &p_survi
 	return p_surviving;
 }
 
-void Subpopulation::ViabilitySelection(std::vector<SLiMEidosBlock*> &p_survival_callbacks)
+void Subpopulation::ViabilitySurvival(std::vector<SLiMEidosBlock*> &p_survival_callbacks)
 {
 	// Loop through our individuals and do draws based on fitness to determine who dies; dead individuals get compacted out
 	Genome **genome_data = parent_genomes_.data();

core/subpopulation.h

@@ -388,7 +388,7 @@ class Subpopulation : public EidosDictionaryUnretained
 	void ReproduceSubpopulation(void);
 	void MergeReproductionOffspring(void);
 	bool ApplySurvivalCallbacks(std::vector<SLiMEidosBlock*> &p_survival_callbacks, Individual *p_individual, double p_fitness, double p_draw, bool p_surviving);
-	void ViabilitySelection(std::vector<SLiMEidosBlock*> &p_survival_callbacks);
+	void ViabilitySurvival(std::vector<SLiMEidosBlock*> &p_survival_callbacks);
 	void IncrementIndividualAges(void);
 	IndividualSex _GenomeConfigurationForSex(EidosValue *p_sex_value, GenomeType &p_genome1_type, GenomeType &p_genome2_type, bool &p_genome1_null, bool &p_genome2_null);
 	inline __attribute__((always_inline)) EidosValue_SP _ResultAfterModifyChildCallbacks(bool p_proposed_child_accepted, Individual *p_individual, Genome *p_genome1, Genome *p_genome2)