• Added cloglog link for binomial, ZIB and ZNIB.

Bugfixes

  • Bugfix in VP for random effects in formula
  • For CRAN release 2.0.5 see updates for versions 2.0.3 - 2.0.5
  • num.RR and num.lv with lvCor can now be combined
  • lvCor can be used with multiple (iid) terms
  • New start.optimizer and start.optim.method arguments for changing the optimizers for generating starting values, related to #229.
  • cex.spp in ordiplot.gllvm can now be a vector
  • Added zero-inflated binomial distribution
  • Added zero-n-inflated binomial distribution

Bugfixes

  • Bug fixed in VP for mixed effects formula
  • Bug fixed for num.lv.c = 1 models
  • Bug fixed that crashed ordinal models with num.lv>0 and species-specific random effects
  • Bug fixed in residuals for ZIP and ZINB models
  • Logit and cumulative logit models with method = “VA”
  • Add option for scaling in getEnvironCor
  • Added logistic GLLVM with VA via polya-gamma augmentation (see Polson et al. 2012)
  • Added residual variance term in getResidualCov.gllvm for ordinal models
  • Boundary check for cumulative probit model
  • New ‘ind.spp’ argument for coefplot and RandomCoefPlot to possibly plot for fewer species
  • Implemented predict for species-specific random effects
  • Improved handling of provided ‘start.fit’

Bugfixes

  • Fixed a bug that caused phyloplot.gllvm to fail with trait models
  • Ensured that update.gllvm also adopts non-formula arguments
  • Default optimizer for random canonical coefficients was not set right for Tweedie
  • Bugfix for showing categorical ordination effects as centroids
  • Bugfix for getPredictErr and trait model
  • Bugfix for phylogenetic model with traits; the phylogenetic matrix was not passed on to the output
  • Bugfix for predict with constrained ordination and randomB
  • Fixed a rare bug that caused a warning message in starting value generation with square response matrices
  • Bugfix for starting values of family = “ordinal” and zeta.struc = “species”
  • Bug fixed for partial constrained/concurrent ordination with more than one conditioning variable

Bugfixes

  • Fixed a bug that caused model failure when starting values for row effects could not be calculated
  • Fixed a bug that caused issues when using ‘randomCoefPlot’ in combination with lme4-type formula for the 4th corner model
  • Fixed a bug in the prediction error calculation of the 4th corner model fitted with method = “LA”
  • Fixed a bug in the starting values random reduced rank models when the design matrix is of reduced rank
  • Fixed a bug that occurred with ‘starting.values = “zero”’ for random reduced rank models with correlation parameters
  • Fixed a bug in the calculation of starting values for concurrent ordination with ordinal species responses and common cut-off parameters
  • Fixed a bug that caused the variance parameter of a second row effect to be fixed to the variance of the first
  • Fixed a bug that increased the duration for calculating starting values of some Tweedie models significantly
  • Added VA implementation of Tweedie
  • Added “band matrix” as a sparsity pattern for phylogenetic models, as alternative to the NNGP
  • Added ‘tick.length’ argument for phyplot.gllvm to control the tick length in the species-specific random effects plot
  • Improvement for the starting values of concurrent ordination
  • Added correlation canonical coefficients option for randomB=“LV”
  • Added additional (LV-specific) variance parameters for randomB=“P”
  • Default for rel.tol changed to 1e-10
  • Default for NN changed to 10
  • A Matern smoothness parameter changed to fixed value given by user by default

Bug Fixes

  • Fixed a bug in the calculation of standard errors for models involving traits and a ZIP/ZINB response distribution. See #204.
  • Fixed a bug that prevented from incorporating correlated random effects via “formula”
  • Fixed a bug that prevented successfully incorporating phylogenetic random effects with traits
  • Fixed a bug in the confidence level of phyloplot.gllvm
  • Fixed a bug in residuals.gllvm
  • Fixed a bug in starting value generation
  • Fixed a bug in the number of parameters by logLik.gllvm for ‘randomB’ models with correlation parameters
  • Fixed a bug in the normalization constant for randomB=“LV”
  • Fixed a bug in the variance partitioning for models with species random effects
  • Fixed a bug in extracting fourth corner coefficients, see #214 and #215
  • Fixed a bug in standard errors involving row.eff = “random”
  • Fixed a bug that prevented using getEnvironCov with the fourth corner model
  • Fixed a bug in gllvm:::RRse
  • Fixed a bug which occurred when correlated latent variables are included and Variational covariance was anything else that diagonal
  • For CRAN release 2.0 see updates for versions 1.4.4 - 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
  • 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
  • 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)
  • 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
  • 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
  • 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 objectparamsparamsrho.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
  • 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

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

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

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

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

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

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.

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.

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.

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.