* using log directory 'd:/Rcompile/CRANpkg/local/4.4/hisse.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'hisse/DESCRIPTION' ... OK * this is package 'hisse' version '2.1.11' * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'hisse' can be installed ... OK * used C compiler: 'gcc.exe (GCC) 13.3.0' * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... 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[1s] NOTE checkRd: (-1) generateMiSSEGreedyCombinations.Rd:25: Lost braces 25 | Estimating extinction rates is hard. This affects all diversification models (even if all you want and look at is speciation rate, extinction rate estimates still affect what this is as they affect the likelihood). It is most noticeable in MiSSE with eps, the extinction fraction (extinction rate divided by speciation rate). One option, following Magallon & Sanderson (2001), is to set extinction fraction at set values. By default, we use theirs, 0 (meaning a Yule model - no extinction) or 0.9 (a lot of extinction, though still less than paleontoligists find). You can set your own in \code{fixed.eps.tries}. If you only want to use fixed values, and not estimate, get rid of the NA, as well. However, don't \dQuote{cheat} -- if you use a range of values for fixed.eps, it's basically doing a search for this, though the default AICc calculation doesn't dQuote{know} this to penalize it for another parameter. | ^ checkRd: (-1) generateMiSSEGreedyCombinations.Rd:27: Lost braces 27 | HiSSE and thus MiSSE assume that a taxon has a particular hidden state (though they recognize that there can be uncertainty in which state it actually has). Thus, they're written to assume that we dQuote{paint} these states on the tree and a given state affects both turnover and eps. So if turnover has four hidden states, eps has four hidden states. They can be constrained: the easiest way is to have, say, turnover having an independent rate for each hidden state and eps having the same rate for all the hidden states. If \code{vary.both} is set to FALSE, all models are of this sort: if turnover varies, eps is constant across all hidden states, or vice versa. Jeremy Beaulieu prefers this. If \code{vary.both} is set to TRUE, both can vary: for example, there could be five hidden states for both turnover and eps, but turnover lets each of these have a different rate, but eps only allows three values (so that eps_A and eps_D might be forced to be equal, and eps_B and eps_E might be forced to be equal). Brian O'Meara would consider allowing this, while cautioning you about the risks of too many parameters. | ^ * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking pragmas in C/C++ headers and code ... OK * checking compiled code ... OK * checking sizes of PDF files under 'inst/doc' ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... [6s] OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... [7s] OK Running 'testthat.R' [6s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [199s] OK * checking PDF version of manual ... [23s] OK * checking HTML version of manual ... [10s] OK * DONE Status: 1 NOTE