Consider adding arguments trait and ind to setPheno()?

[gregorgorjanc]

Possible future features, but discussion needed.

Sometimes we would like to phenotype individuals only for a specific trait. Currently setPheno() generates phenotypes for all traits for all individuals in a population.

Addition of an argument trait to setPheno() would allow for more flexibility, but the code would likely be more complicated in the case of environmental covariances - if we would want to keep an already simulated phenotype we would have to do conditional simulation taking the previously simulated error for the previous trait into account. It would also mean it would not replace existing phenotype as it does currently.

Related to this is the fact that we currently phenotype all individuals in a population. What if we want to phenotype just a subset. Currently this is best done by splitting the population into two - phenotyped and non-phenotyped or by post-processing phenotypes (setting NA in the pop@pheno or in other containers outside of the pop). For example selectInd() has an candidates argument for similar reasons.

[gregorgorjanc]

In one project we used a traitIndMask - we create a custom setPhenoCow() function anyway (that calls setPheno()) and we added an argument traitIndMask, which is a logical matrix that a user provides (if NULL we don't do anything) and we then set phenotypes to NA based on the logicals. This means we can then decide which individuals gets phenotypes for which traits. This is very relevant for some species and breeding programmes, where only some individuals are phenotyped for some traits.

One can do all this differently, but since its quite a common operation it would make sense to have an AlphaSimR solution.

[gaynorr]

The functionality to set a subset of traits is being added with the "traits" arguments. It will default to doing all traits and thus maintain current behavior without additional arguments.