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Changelog

Source: NEWS.md

phylosem 2.0.0

  • Adding error check for factors in data (which are not supported)
  • Switching to a sparseMatrix construction and GMRF for the conditional distribution, to allow estimation with larger number (J>>10) of variables
  • Fit error in as_fitted_DAG occurring when getsd=FALSE, resulting in an uniformative error message … now adding branching logic for output (h/t Jack Oyston)
  • Adding option for moderator variables for one-headed path coefficients, including latent variables representing varying slopes
  • Adding argument estimate_xbar to allow user specification of whether to estimate mean xbar for each column of data, i.e., for use when estimating the mean for a latent variable representing a varying path
  • Add experiments argument to allow user-specified experiment-level data that then estimates species-specific trait values
  • Change family argument to allow fixed(), gaussian(), etc as named list (BREAKS BACKWARDS COMPATIBILITY)
  • Add categorical(group = [string]) family option, using a multivariate logit-link across levels of [string] for categorical traits
  • start model-description vignette, add phylosem_citations.bib, and scratch/citations/readme.md

phylosem 1.1.4

CRAN release: 2024-04-02

  • removing checkDepPackageVersion(dep_pkg="Matrix", this_pkg="TMB") from .onLoad() as requested by K. Kristensen

phylosem 1.1.3

CRAN release: 2024-02-01

  • Removing fit_tmb to simplify code and remove unnecessary warnings
  • Adding codecov and extra tests
  • Fixing R-CMD-check to force build Matrix/TMB from source

phylosem 1.1.2

CRAN release: 2023-12-20

  • Adding new functions to provide warning if Matrix version doesn’t match what’s expected by TMB

phylosem 1.1.1

CRAN release: 2023-11-26

  • Re-adding phylosignal as SUGGESTS
  • Re-adding phylosignal to Fisheries vignette
  • adding arguemnt what to as_phylo4d to allow easy extraction of standard errors

phylosem 1.1.0

CRAN release: 2023-10-06

  • Adding new S3 generic functions: logLik and vcov
  • Adding vignette “fisheries” associated with paper “Trees for fishes: The neglected role for phylogenetic comparative methods in fisheries science” accepted at Fish and Fisheries

phylosem 1.0.2

CRAN release: 2023-09-22

  • Fixed bug arising when data are missing for observations in the earliest tips and for the first inputted variable
  • Updating vignette to show confidence intervals on alpha/kappa/lambda as well as lnalppha/lnkappa/logitlambda

phylosem 1.0.1

CRAN release: 2023-09-19

  • Address request from CRAN to use Suggests packages conditionally in examples
  • Continuing to use Suggests packages unconditionally in vignettes based on Wickham guidance online

phylosem 1.0.0

CRAN release: 2023-08-25

  • Attempting to fix warnings