NEWS.md

In pfh/weitrix: Tools for matrices with precision weights, test and explore weighted or sparse data

weitrix 1.13.1

• Use read.csv rather than read_csv in vignettes, as read_csv was causing a hard-to-reproduce error when building vignettes.

weitrix 1.11.1

• Don't import colSums, rowSums, which have disappeared from BiocGenerics.

weitrix 1.7.1

• counts_shifts and counts_proportions now have a "typecast" argument, allowing use of memory-efficient matrix types.

weitrix 1.5.1

• weitrix_sd_confects now has an option to drop the assumption of normally distributed weighted residuals.

weitrix 1.1.10

• Fix bug with weitrix_confects due to [[ ]] <- NULL deleting elements from a list instead of storing NULL in the list.

weitrix 1.1.9

• Peaks were sometimes in reverse order in APA example, data file updated.
• Try to get rid of an odd new build error about stack usage by using serial processing in vignettes.

weitrix 1.1.8

• Use geom_bin2d in weitrix_calplot scatterplots.

weitrix 1.1.7

• Add mu_min, mu_max arguments to weitrix_calibrate_all.

weitrix 1.1.6

• Use glm2, which is less prone to optimization failure.
• Auto-disable parallel processing if X11 device is open.
• Add SLAM-Seq vignette.

weitrix 1.1.5

• well_knotted_spline for natural splines with good choice of knots.

weitrix 1.1.4

• weitrix_confects for differential testing.
• weitrix_rms_confects now called weitrix_sd_confects.
• weitrix_calplot now shows mean trend and mean +/- standard deviation trend.

weitrix 1.1.3

• weitrix_calibrate_all now includes a simple scaling factor to account for residuals from a fitted model being smaller than residuals from the true model.
• weitrix_calplot blue guidelines are similarly adjusted.
• Add weitrix_rms_confects to find rows with confidently excessive variation.

weitrix 1.1.2

• Vignettes use weitrix_calibrate_all, demonstrate weitrix_calplot.
• weitrix_calplot now uses sqrt(weight)*residual on y axis.

weitrix 1.1.1

• Switch calibration from linear model on log dispersions to using a gamma GLM.
• Add weitrix_calibrate_all function for very flexible calibration.
• Add weitrix_calplot to examine quality of weights.

weitrix 0.99.2

• Automatic package builder wants package to depend on R version 4.0.

weitrix 0.99.1

• weitrix now uses the BiocParallel default parallel processing, rather than the DelayedArray default. (DelayedArray does not use parallel processing by default as of version 0.14.0.)

weitrix 0.99.0

• Bioconductor submission.

weitrix 0.1.0

• Initial version.

pfh/weitrix documentation built on Aug. 29, 2024, 1:46 a.m.