diff --git a/404.html b/404.html index b3b62e2..e505bfe 100644 --- a/404.html +++ b/404.html @@ -32,7 +32,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/authors.html b/authors.html index dbb76a3..f7d0c87 100644 --- a/authors.html +++ b/authors.html @@ -17,7 +17,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/index.html b/index.html index a51e588..3ff7a44 100644 --- a/index.html +++ b/index.html @@ -33,7 +33,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/pkgdown.yml b/pkgdown.yml index 9237946..c790b46 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -2,4 +2,4 @@ pandoc: 3.1.11 pkgdown: 2.1.1 pkgdown_sha: ~ articles: {} -last_built: 2024-09-29T17:13Z +last_built: 2024-10-02T13:54Z diff --git a/reference/argnames.html b/reference/argnames.html index 43f7568..4e05881 100644 --- a/reference/argnames.html +++ b/reference/argnames.html @@ -23,7 +23,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/reference/asr-bisse.html b/reference/asr-bisse.html index a16c9fd..8a4c475 100644 --- a/reference/asr-bisse.html +++ b/reference/asr-bisse.html @@ -20,7 +20,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/reference/asr-mkn.html b/reference/asr-mkn.html index 0dc3ff5..06de893 100644 --- a/reference/asr-mkn.html +++ b/reference/asr-mkn.html @@ -20,7 +20,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/reference/asr.html b/reference/asr.html index 182bc5e..8c28b64 100644 --- a/reference/asr.html +++ b/reference/asr.html @@ -20,7 +20,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/reference/big.brother.html b/reference/big.brother.html index de9c53d..983b932 100644 --- a/reference/big.brother.html +++ b/reference/big.brother.html @@ -20,7 +20,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/reference/check.html b/reference/check.html index 2abebe5..7a27cad 100644 --- a/reference/check.html +++ b/reference/check.html @@ -18,7 +18,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/reference/combine.html b/reference/combine.html index 4e9855e..16b7056 100644 --- a/reference/combine.html +++ b/reference/combine.html @@ -20,7 +20,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/reference/constants.html b/reference/constants.html index 09db884..41211c1 100644 --- a/reference/constants.html +++ b/reference/constants.html @@ -19,7 +19,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/reference/constrain.html b/reference/constrain.html index 081a74d..55d3f3e 100644 --- a/reference/constrain.html +++ b/reference/constrain.html @@ -23,7 +23,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/reference/diversitree-deprecated.html b/reference/diversitree-deprecated.html index 15263e0..43f0c41 100644 --- a/reference/diversitree-deprecated.html +++ b/reference/diversitree-deprecated.html @@ -19,7 +19,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/reference/diversitree-package.html b/reference/diversitree-package.html index 8d0ea5b..fd19df8 100644 --- a/reference/diversitree-package.html +++ b/reference/diversitree-package.html @@ -24,7 +24,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/reference/find.mle.html b/reference/find.mle.html index 06b0db8..8384b76 100644 --- a/reference/find.mle.html +++ b/reference/find.mle.html @@ -19,7 +19,7 @@ diversitree - 0.10-0 + 0.10-1 @@ -125,17 +125,17 @@

Details

(see the Examples).

Different method arguments take different arguments passed through ... to control their behaviour:

-

method="optim": Uses R's optim function for the +

method="optim": Uses R's optim function for the optimisation. This allows access to a variety of general purpose optimisation algorithms. The method within optim can be chosen via the argument optim.method, which is set to "L-BFGS-B" by default (box constrained quasi-Newton optimisation). This should be suitable for most uses. See the method argument - of optim for other possibilities. If "L-BFGS-B" + of optim for other possibilities. If "L-BFGS-B" is used, then upper and lower bounds may be specified by the arguments lower and upper. The argument control can be used to specify other control parameters for the algorithms - see - optim for details. Most of the optim algorithms + optim for details. Most of the optim algorithms require finite values be returned at every evaluated point. This is often not possible (extreme values of parameters or particular combinations may have zero likelihood and therefore -Inf @@ -153,7 +153,7 @@

Details

subplex for details). The argument fail.value can be used as in method="optim", but by default -Inf will be used on failure to evaluate, which is generally appropriate.

-

method="nlminb": Uses the function nlminb for +

method="nlminb": Uses the function nlminb for optimisation, so that optimising a Mk2/Mkn likelihood function behaves as similarly as possible to ape's ace function. As for method="optim", lower and upper bounds on parameters may @@ -163,7 +163,7 @@

Details

cases. Additional control parameters may be passed via control - see link{nlminb} for details. This function is not generally recommended for use.

-

method="nlm": Uses the function nlm for +

method="nlm": Uses the function nlm for optimisation, so that optimising a birth-death likelihood function behaves as similarly as possible to ape's birthdeath function. Takes the same additional @@ -172,13 +172,13 @@

Details

this is not recommended for general use.

code and logLik methods exist for fit.mle objects so that parameters and log-likelihoods may be extracted. This also - allows use with AIC.

+ allows use with AIC.

Simple model comparison by way of likelihood ratio tests can be - performed with anova. See Examples for usage.

+ performed with anova. See Examples for usage.

Model comparison

-

The anova function carries out likelihood ratio tests. +

The anova function carries out likelihood ratio tests. There are a few possible configurations.

First, the first fit provided could be the focal fit, and all other fits are either special cases of it (every additional model is nested @@ -190,7 +190,7 @@

Model comparison

increasing in parameters (A nested in B, B nested in C, ...) or strictly decreasing in parameters (D nested in C, C nested in B, ...).

In both cases, nestedness is checked. First, the "class" of the - fitted object must match. Second, the argnames of the + fitted object must match. Second, the argnames of the likelihood function of a sub model must all appear in the argnames of the parent model. There are some cases where this second condition may not be satisfied and yet the comparison is valid @@ -250,14 +250,14 @@

Examples

logLik(fit) # -659.93 AIC(fit) # 1331.86 -## find.mle works with constrained models (see \link{constrain}). Here +## find.mle works with constrained models (see constrain). Here ## the two speciation rates are constrained to be the same as each ## other. lik.l <- constrain(lik, lambda0 ~ lambda1) fit.l <- find.mle(lik.l, pars[-2]) logLik(fit.l) # 663.41 -## Compare the models with \link{anova} - this shows that the more +## Compare the models with anova - this shows that the more ## complicated model with two separate speciation rates fits ## significantly better than the simpler model with equal rates ## (p=0.008). diff --git a/reference/history.from.sim.html b/reference/history.from.sim.html index 77ebb2e..3fcce97 100644 --- a/reference/history.from.sim.html +++ b/reference/history.from.sim.html @@ -18,7 +18,7 @@ diversitree - 0.10-0 + 0.10-1
diff --git a/reference/index.html b/reference/index.html index 35c424f..da74d4e 100644 --- a/reference/index.html +++ b/reference/index.html @@ -17,7 +17,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/reference/make.bd.html b/reference/make.bd.html index 8af4b8c..4a4f939 100644 --- a/reference/make.bd.html +++ b/reference/make.bd.html @@ -24,7 +24,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/reference/make.bd.split.html b/reference/make.bd.split.html index ce173e0..5f3dde4 100644 --- a/reference/make.bd.split.html +++ b/reference/make.bd.split.html @@ -18,7 +18,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/reference/make.bd.t.html b/reference/make.bd.t.html index 7047109..ca817cf 100644 --- a/reference/make.bd.t.html +++ b/reference/make.bd.t.html @@ -18,7 +18,7 @@ diversitree - 0.10-0 + 0.10-1 @@ -149,7 +149,7 @@

Examples

#> 0.001 0.000 0.001 system.time(lik.t2(pars2)) # ~ 0.003 #> user system elapsed -#> 0.002 0.000 0.002 +#> 0.002 0.001 0.002 if (FALSE) { # \dontrun{ fit <- find.mle(lik.direct, pars) diff --git a/reference/make.bisse.html b/reference/make.bisse.html index 4363727..523971e 100644 --- a/reference/make.bisse.html +++ b/reference/make.bisse.html @@ -21,7 +21,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/reference/make.bisse.split.html b/reference/make.bisse.split.html index 1729818..eec1062 100644 --- a/reference/make.bisse.split.html +++ b/reference/make.bisse.split.html @@ -20,7 +20,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/reference/make.bisse.td.html b/reference/make.bisse.td.html index 7e20c1a..fb6051d 100644 --- a/reference/make.bisse.td.html +++ b/reference/make.bisse.td.html @@ -19,7 +19,7 @@ diversitree - 0.10-0 + 0.10-1 @@ -279,7 +279,7 @@

Examples

## heavily paid for the time-chunk case: system.time(lik.b(pars)) #> user system elapsed -#> 0.003 0.000 0.002 +#> 0.002 0.000 0.002 system.time(lik.td2(p.td)) # 1.9x slower than plain BiSSE #> user system elapsed #> 0.004 0.000 0.004 diff --git a/reference/make.bisseness.html b/reference/make.bisseness.html index 4413550..77b97c3 100644 --- a/reference/make.bisseness.html +++ b/reference/make.bisseness.html @@ -21,7 +21,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/reference/make.bm.html b/reference/make.bm.html index afa582e..c036933 100644 --- a/reference/make.bm.html +++ b/reference/make.bm.html @@ -22,7 +22,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/reference/make.clade.tree.html b/reference/make.clade.tree.html index eea97b4..1089391 100644 --- a/reference/make.clade.tree.html +++ b/reference/make.clade.tree.html @@ -20,7 +20,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/reference/make.classe.html b/reference/make.classe.html index 8015f1c..987b5f9 100644 --- a/reference/make.classe.html +++ b/reference/make.classe.html @@ -21,7 +21,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/reference/make.geosse.html b/reference/make.geosse.html index 8d66d21..435514a 100644 --- a/reference/make.geosse.html +++ b/reference/make.geosse.html @@ -21,7 +21,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/reference/make.geosse.split.html b/reference/make.geosse.split.html index 50fff49..61dc976 100644 --- a/reference/make.geosse.split.html +++ b/reference/make.geosse.split.html @@ -18,7 +18,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/reference/make.geosse.t.html b/reference/make.geosse.t.html index 58f273f..cd01ce9 100644 --- a/reference/make.geosse.t.html +++ b/reference/make.geosse.t.html @@ -21,7 +21,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/reference/make.mkn.html b/reference/make.mkn.html index 3cc1e16..c8500fa 100644 --- a/reference/make.mkn.html +++ b/reference/make.mkn.html @@ -25,7 +25,7 @@ diversitree - 0.10-0 + 0.10-1 @@ -201,7 +201,7 @@

Examples

## These are the same (except for the naming of arguments) all.equal(fit.mkn[-7], fit.mk2[-7], check.attr=FALSE, tolerance=1e-7) -## Equivalence to ape's \link{ace} function: +## Equivalence to ape's ace function: model <- matrix(c(0, 2, 1, 0), 2) fit.ape <- ace(phy$tip.state, phy, "discrete", model=model, ip=p) diff --git a/reference/make.musse.html b/reference/make.musse.html index 03599a3..4f1ec73 100644 --- a/reference/make.musse.html +++ b/reference/make.musse.html @@ -29,7 +29,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/reference/make.musse.multitrait.html b/reference/make.musse.multitrait.html index d9877b0..267f412 100644 --- a/reference/make.musse.multitrait.html +++ b/reference/make.musse.multitrait.html @@ -25,7 +25,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/reference/make.musse.split.html b/reference/make.musse.split.html index 8a369c1..0742fac 100644 --- a/reference/make.musse.split.html +++ b/reference/make.musse.split.html @@ -18,7 +18,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/reference/make.musse.td.html b/reference/make.musse.td.html index 9d9e013..0a1c201 100644 --- a/reference/make.musse.td.html +++ b/reference/make.musse.td.html @@ -19,7 +19,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/reference/make.pgls.html b/reference/make.pgls.html index 46d5123..8bd2411 100644 --- a/reference/make.pgls.html +++ b/reference/make.pgls.html @@ -20,7 +20,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/reference/make.prior.html b/reference/make.prior.html index 2e18cd5..7a36f94 100644 --- a/reference/make.prior.html +++ b/reference/make.prior.html @@ -18,7 +18,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/reference/make.quasse.html b/reference/make.quasse.html index 9ddd9ce..bf43cd9 100644 --- a/reference/make.quasse.html +++ b/reference/make.quasse.html @@ -21,7 +21,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/reference/make.quasse.split.html b/reference/make.quasse.split.html index e50341d..4ceea23 100644 --- a/reference/make.quasse.split.html +++ b/reference/make.quasse.split.html @@ -18,7 +18,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/reference/mcmc.html b/reference/mcmc.html index 0e31597..5ff4f46 100644 --- a/reference/mcmc.html +++ b/reference/mcmc.html @@ -18,7 +18,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/reference/plot.history.html b/reference/plot.history.html index e3edc74..559c211 100644 --- a/reference/plot.history.html +++ b/reference/plot.history.html @@ -18,7 +18,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/reference/profiles.plot.html b/reference/profiles.plot.html index 93bfb46..16a5afa 100644 --- a/reference/profiles.plot.html +++ b/reference/profiles.plot.html @@ -18,7 +18,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/reference/protect.html b/reference/protect.html index 67e207d..2880565 100644 --- a/reference/protect.html +++ b/reference/protect.html @@ -18,7 +18,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/reference/quasse-common.html b/reference/quasse-common.html index e3aa0f9..aa26abc 100644 --- a/reference/quasse-common.html +++ b/reference/quasse-common.html @@ -21,7 +21,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/reference/set.defaults.html b/reference/set.defaults.html index 693d570..913232b 100644 --- a/reference/set.defaults.html +++ b/reference/set.defaults.html @@ -17,7 +17,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/reference/sim.character.html b/reference/sim.character.html index 043bf5d..dfc1c84 100644 --- a/reference/sim.character.html +++ b/reference/sim.character.html @@ -20,7 +20,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/reference/simulate.html b/reference/simulate.html index 00cee36..1c02c41 100644 --- a/reference/simulate.html +++ b/reference/simulate.html @@ -24,7 +24,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/reference/trait.plot.html b/reference/trait.plot.html index 86ef1a8..f66c07b 100644 --- a/reference/trait.plot.html +++ b/reference/trait.plot.html @@ -19,7 +19,7 @@ diversitree - 0.10-0 + 0.10-1 diff --git a/reference/utils.html b/reference/utils.html index 2894c9f..aeb1d1c 100644 --- a/reference/utils.html +++ b/reference/utils.html @@ -21,7 +21,7 @@ diversitree - 0.10-0 + 0.10-1