Updates to standardize and simplify

[patrickbarks]

Updates primarily to standardize code and documentation, and simplify or split complicated functions.

Resolves the following issues: #7, #13, #16, #19, #23, #24, #25, #26, #27, #28, #29, #30, #31, #32, #33; and partly addresses #12 (I believe Iain is handling the rest of that one). Also pulls matrix-level functions from Rcompadre into Rage, as per jonesor/Rcompadre#28.

[patrickbarks]

@RobSalGo I added a new version of vitalRatePerturbation based on the version you sent. This version has two main updates corresponding to two 'tricky' scenarios:

(1) Fecundity or clonality in a stage from which there is no survival

If a given stage has positive fecundity or clonality but no survival, the previous version would zero out the sensitivities to fecundity/clonality as it pulled out the (nonexistent) survival component of those vital rates. This version retains those sensitivities — e.g. if there is fecundity but no survival in a given column, the 'full sensitivity' of a fecundity transition is attributed to the fecundity vital rate (and likewise for clonality).

(2) Age-based transition in matU (i.e. when a column of matU contains only 1 nonzero element)

The previous version would return nonzero sensitivites to growth for age-only models, because it effectively assumed that diagonal elements of matU were never structural zeros. This version treats all zeros as structural and assumes that, if a given column of matU has only 1 nonzero element, the only vital rate within that column is survival (no growth or shrinkage).

 
If an MPM doesn't have either of the above properties, this version of the fn gives the same result as the previous version. Here's an example that has both scenarios described above, with matching sensitivities from popbio for comparison:

# specify vital rates of survival and fecundity for age-only model
s1 <- 0.5
s2 <- 0.6
f <- 1.4

# specify matrices for Rage
matU <- rbind(c(0,  0,  0),
              c(s1, 0,  0),
              c(0,  s2, 0))

matF <- rbind(c(0,  0,  f),
              c(0,  0,  0),
              c(0,  0,  0))

# specify matA in expression form for popbio
matA_exp <- expression(
  0,   0,   f,
  s1,  0,   0,
  0,   s2,  0
)

# vital rate list for popbio
vital_rates_l <- list(s1 = s1, s2 = s2, f = f)

# perturbation with popbio
popbio::vitalsens(matA_exp, vital_rates_l)

# perturbation with new vitalRatePerturbation
vitalRatePerturbation(matU, matF)
# sensitivity to growth is zero, sensitivity to fecundity is positive
# with previous version, those are reversed

I don't mean to 'push through' changes that are still being debated. I'm happy to update the PR with recommended edits :)

[jonesor]

I will merge this pull request. I am in favour of implementing all these changes even though they may (will!) result in some backward compatibility issues. The changes could cause some headaches for workshops (take note @RobSalGo!) if we use existing materials, but since we plan on revamping the materials, and turning them into within-package vignettes I think we will cope.
Overall, the benefits of these improvements outweigh the minor headaches that might occur in my opinion.
If major problems DO emerge, then we can either roll back some specific changes, or adapt the code to cope with them perhaps. But fingers crossed that that is not necessary.

[RobSalGo]

dully noted and agreedo @jonesor & @patrickbarks