inst/NEWS.md

In CenterForStatistics-UGent/RCM: Fit row-column association models with the negative binomial distribution for the microbiome

0.2.0

• Importance parameters (\psi) are no longer calculated when non-parametric response functions are used.

0.3.0

• Importance parameters (\psi) are enabled again when non-parametric response functions are used, but not used for plotting.
• 2D sample plots for constrained ordination with non-parametric response functions have been disabled, as they are not interpretable. Variable plots are the only 2D plots still allowed
• Explained deviance and inertia can be plotted on the axes rahter than the (\psi)’s using the “plotPsi” argument to the plot.RCM() function.
• Possibility to provide lower dimensional fits has been disabled. RCM is fast enough to fit the whole model.

1.0.0

• Release on BioConductor

1.0.1

• Bug fix in buildCovMat() to avoid false warning
• Check for alias structure in confounder and covariate matrices

1.2.0

• Missing values in count matrix are now allowed. They simply do not contribute to the parameter estimation, but the rest of the row (or column) is still used.

1.2.1

• Vertical reference line in residual plot
• Bug fix for problematic variable names

1.2.2

• Moving the online manual information to the vignette

1.2.3

• Rename a and b to rowExp and colExp to avoid partial matching
• Allow rowExp and colExp to be adapted for constrained correspondence analysis starting values as well

1.2.4

• Adding a new inflVar variable to disambiguate in the influence plotting
• More argument checking + tests for the plot.RCM function

1.5.2

• Avoid returning nulls for residualPlot

1.5.4

• A note in the vignette and in the help file of plot.RCM regarding limited number of combinations of constraining variables. Also a warning is now thrown

1.5.5

• Bug fix for higher dimension residualPlot function, and tests for this function

1.5.6

• Replace deprecated guides( =FALSE) by guides(=“none”)

1.5.7

• Update vignette to number table of contents

1.11.0

• Added FAQ section in vignette with first frequent question on number of samples not shown.
• Fixed bugs for plots of data with missing values, and added tests.

1.11.2

• Explicitly import stats::model.matrix, and only load necessary VGAM functions

1.11.3

• For the unconstrained models: fit feature models one by one and Gram-Schmidt orthogonalize and center afterwards, rather than using Lagrange multipliers and huge Jacobian matrices. This will use less memory and speed up computations, but may yield slightly different solutions. Nothing changes for the constrained models.

1.11.4

• Introduction of permanova testing for user-supplied groups using the permanova function.

CenterForStatistics-UGent/RCM documentation built on April 24, 2023, 8:26 p.m.