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NEWS.md

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Version 2.0.

  • Added VA implementation of Tweedie

Version 2.0

  • For CRAN release 2.0 see updates for versions 1.4.4 - 1.4.9

Version 1.4.9

  • Row.eff can now be used for community-level (species-common) effect
  • Both fixed and random at the same time (i.e., a mixed effects formula)
    • Does not allow for a single random intercept
    • Does not yet allow for between random effect correlation
  • New formula interface for phylogenetic model adapted to trait model too
  • New phyplot.gllvm function for plotting the phylogenetic random effects
  • Minor adjustment in the behavior of 'caption' in plot.gllvm

Version 1.4.8

  • Added functionality for correlated random canonical coefficients
  • Changed "site.index" argument in getResidualCov.gllvm to "x", in line with getEnvironCov.gllvm
  • New vignette for the correlation structures of random effects and latent variables.

Bug Fixes

  • Bug fixed for calculating residual covariances of quadratic concurrent ordination

Version 1.4.7

  • Added "fungi" dataset by Abrego et al. 2022
  • Added "kelpforest" dataset by Reed and Miller 2023
  • New vignette for phylogenetic random effects
  • New vignette for percent cover data analysis
  • Function for calculating and plotting variance partitioning (varPartitioning.gllvm and plotVP)

Version 1.4.6

  • Added a 'getLoadings' function for retrieving species' loadings
  • Added 'fac.center' argument in ordiplot to plot canonical coefficients of binary variables as points
  • Added a simple plotting function for the gllvm summary
  • Improved scaling for ordiplot with quadratic model and with biplot = FALSE
  • optima.gllvm and tolerances.gllvm for num.lv now correctly provide tolerances w.r.t. the scaled LV
  • Improved starting values for models with 'randomB'
  • 'which.Xcoef' in coefplot.gllvm now also works for fourth-corner models
  • Added intercept if beta0com=TRUE to coefplot.gllvm for fourth-corner models

Bug Fixes

  • Bug fixed that prevented increasing he point size of sites in ordiplot with symbols = TRUE
  • Bug fixed in optima.gllvm for models with a single LV

Version 1.4.5

  • Separated "n.init" functionality into gllvm.iter.R
    • Prep for parallelisation
    • Enabled parallelisation (see TMB::openmp)
  • Largely vectorized "residuals.gllvm", and residuals in "gllvm.aux"
  • Added covariance of random effects to summary
  • In preparation of emmeans support: moved the design matrix in "lv.X" to "lv.X.design". "lv.X" now stores the original supplied data.frame

Bug Fixes

  • Bug in ZINB fixed

Version 1.4.4

  • Removed "dependent.row" feature
  • Added possibility for multiple random row intercepts
  • Added possibility for (correlated) random species random effects
    • Can be plotted with "randomCoefPlot"
  • Added possibility to Phylogenetically structure the random species effects
    • Phylogenetic signal parameter is included as object$params$rho.sp
    • Can be covariate specific
  • num.RR and num.lv.c can now be larger than the number of predictors if randomB!=FALSE
  • Added "iid" option for "randomB"
  • Added a "getEnvironCov" function to extract species associations due to random covariate effects

Version 1.4.3

  • For CRAN release 1.4.3 see updates for versions 1.4.2 and 1.4.3

Bug Fixes

  • Bug in correlated row effects fixed
  • Bug in getPredictErr for models fitted with LA fixed, and it returns now prediction errors for random slopes of X covariates as well
  • Bug in randomCoefplot fixed

Version 1.4.2

New Features

  • Added a correction factor to the second partial derivatives of the canonical coefficients for concurrent and constrained ordination
  • Added randomCoefPlot functionality of constrained and concurrent ordination models with random slopes. Currently not supported for models with quadratic responses
  • Summary now provides the possibility to calculate wald statistics across LVs or predictors for concurrent and constrained ordination
  • coef now renames parameter estimates with more intuitive names and allows to subset the parameter list with names
  • Tweedie power parameter is estimated now if set to NULL in `gllvm.
  • VA support for Zero-inflated poisson distribution
  • Zero-inflated negative-binomial distribution added
  • Binomial (Ntrials>1) support added (previously only Bernoulli)
  • Now allowed to have (some) NAs in the response data

Bug Fixes

  • Fixed an issue with structured row-effects in concurrent and constrained ordination
  • Fixed a bug that prevented plotting prediction regions for constrained ordination with structured row-effects
  • No standard errors should be returned by optima.gllvm and tolerances.gllvm with randomB != FALSE
  • Species names were in the original order with order = TRUE in RandomCoefPlot
  • Fixed an issue that arose when {0,1} bounded parameters reached the bounds
  • Various bug fixes for constrained/concurrent ordination with random intercepts and random slopes
  • Bug in predictions with structured row intercepts was fixed, see issue #86

Version 1.4.1

New Features

  • Computational stability of random slopes for constr. and concr. ordination significantly improved
  • Computational stability of quadratic model significantly improved
  • Unstructured VA covariance matrix for quadratic models with random intercepts
  • Added example for se.gllvm

Bug Fixes

  • Bugfix in random slopes for concr. ordination with LV-specific variances and random row intercepts
  • Bugfix for quadratic model with Poisson, NB, gamma, or exponential responses
  • Bugfix in starting values for constrained and concurrent quadratic model

Bug Fixes

  • Valgrind error fixed

Version 1.4.0

New Features

  • For CRAN release 1.4.0's new features see features described for versions 1.3.2-1.3.3

Bug Fixes

  • For bug fixes to CRAN release 1.4.0 see versions 1.3.2-1.3.3

Version 1.3.3

New Features

  • The n.init option has been improved, so that it stops if no improved fit has been found after n.init.max (defaults to 10) iterations.
  • Row names from the data now carry over to the site scores, so that they can be displayed in ordiplot

Bug Fixes

  • Memory allocation problem in development version fixed

  • Diagonal elements of loading matrix 'theta' fixed for fourth corner model

  • Bug in 'predict' for random slopes fixed, occurred when new x-covariate values were given

Version 1.3.2

New Features

  • Ordination with predictors (num.RR,num.lv.c) is now implemented with constrained optimization routines (alabama,nloptr) as long as the canonical coefficients are treated as fixed-effects. This follows from the necessary identifiability constraints.

  • The reduced-rank approximated predictor slopes of a multivariate regression can now be plotted (with confidence intervals) using coefplot. Not available yet for quadratic effects.

  • Separate checks are put in place to warn users if the constraints on the canonical coefficients (orthogonality of the columns) have not converged.

  • Separate checks are put in place to warn users if the coefficients of a quadratic model have not converged

  • Canonical coefficients in ordination with predictors (num.RR,num.lv.c) can now be treated as random-effects using the 'randomB' argument. For the moment, all need to be either random or fixed, no mixing. Prediction intervals can be retrieved with the getPredictErr function.

  • An extended version of the spider dataset has been made available

  • Added an option to magnify the x-axis labels in coefplot

  • Site names present as row labels in the response data are now shown in the ordination plot

Bug Fixes

  • The order of the quadratic coefficients was wrong when num.RR, num.lv, and num.lv.c were all used in the same model.

  • Fixed a bug in the calculation of starting values for constrained ordination (num.RR) where the residuals were not re-calculated if num.lv.c>0

  • Fixed a bug in coefplot for when only one predictor was included in the model

  • Fixed a bug that would prevent using a gllvm with quadratic response model as starting values for another model

  • Changed import/export of various functions as requested in github issue #65

  • Various minor tweaks to the summary function

Version 1.3.1

New Features

  • Structured row parameters are implemented, including a possibility for between or within group correlations for random row effects.

  • Constrained ordination model is implemented.

  • NB and binomial (with probit and logit) response model implemented using extended variational approximation method.

Bug Fixes

  • Vignettes are removed from the CRAN version of the package, can be seen at the package's website only.

Version 1.3.0

New Features

  • Quadratic latent variables allowed, that is term - u_i'D_j u_i can be included in the model using 'quadratic = TRUE'. In addition, functions 'optima()', 'tolerances()' and 'gradient.length()' included.

  • Beta response distribution implemented using Laplace approximation and extended variational approximation method.

  • Tweedie response model implemented using extended variational approximation method.

  • Ordinal model works now for 'num.lv=0'.

  • Residual covariance adjustment added for gaussian family.

Bug Fixes

  • Estimation of the variances of random slopes of the X covariates didn't work properly when 'row.eff = FALSE' or 'row.eff = "fixed"'.

  • Problems occurred in calculation of the starting values for ordinal model.

  • Problems occurred in predict() and residuals(), when random slopes for X covariates were included.

  • Problems occurred in predict() when new X covariates were given.

  • Problems occurred in predictLVs() for fourth corner models.

Version 1.3.1

New Features

  • Structured row parameters are implemented, including a possibility for between or within group correlations for random row effects.

  • Constrained ordination model is implemented.

  • NB and binomial (with probit and logit) response model implemented using extended variational approximation method.

Bug Fixes

  • Vignettes are removed from the CRAN version of the package, can be seen at the package's website only.

Version 1.3.0

New Features

  • Quadratic latent variables allowed, that is term - u_i'D_j u_i can be included in the model using 'quadratic = TRUE'. In addition, functions 'optima()', 'tolerances()' and 'gradient.length()' included.

  • Beta response distribution implemented using Laplace approximation and extended variational approximation method.

  • Tweedie response model implemented using extended variational approximation method.

  • Ordinal model works now for 'num.lv=0'.

  • Residual covariance adjustment added for gaussian family.

Bug Fixes

  • Estimation of the variances of random slopes of the X covariates didn't work properly when 'row.eff = FALSE' or 'row.eff = "fixed"'.

  • Problems occurred in calculation of the starting values for ordinal model.

  • Problems occurred in predict() and residuals(), when random slopes for X covariates were included.

  • Problems occurred in predict() when new X covariates were given.

  • Problems occurred in predictLVs() for fourth corner models.