Changelog

Source: NEWS.md

lukesRlib 0.2.10 (6th June 2024)

Changes

• Change URL to reflect my GitHub username change from lukepilling to lcpilling to be more consistent between different logins, websites, and social media
• https://lcpilling.github.io/lukesRlib
• https://github.com/lcpilling/lukesRlib
• get_assoc()
• Add options to Winsorize the exposure or outcome
• Remove beep
• Improved verbose reporting

lukesRlib 0.2.9 (28th Feb 2024)

Bug fixes

• get_assoc() - Fix fit_stat_se if missing
• get_assoc() - Fix covariate checking if interaction included in formula. Resolving issue #1

lukesRlib 0.2.8 (19th Feb 2024)

• get_assoc()
  • add interacts_with argument. Default is ““. User can provide a variable name (string) to also get interaction terms
  • Fixed bug in return_all_terms when exposure was factor
  • Include SE for C-statistic if returning fit_stat for coxph() models

lukesRlib 0.2.7 (29th Jan 2024)

• get_assoc() - add return_all_terms argument. Default is false. If TRUE, adds a new col terms and returns the estimates for all independent variables in the models.
• get_assoc() - remove subset_d argument
• get_assoc() - fixed if exposure or outcome needs to be protected by backticks (previously failed if variable was something like “bmi-1”)
• get_assoc() - fixed problem where covariate estimates were also included in certain situations (e.g., if x=“age” do not get covariate “percentage”)
• Update examples for many functions

lukesRlib 0.2.6 (13 Nov 2023)

• get_assoc() - fixed if no covariates provided
• get_assoc() - if x and y are the same, skip (useful if providing same list of variables twice for pairwise analysis)
• get_assoc() - added verbose option for bug checking
• get_assoc() - added beep option for beeping when finished
• tidy_ci() - add some functionality for summarizing fixed-effects from lme4::lmer()
• Add example_data object for examples. Contains ~5,000 participants from Framingham Heart Study

lukesRlib 0.2.5 (25 Aug 2023)

• get_assoc() now expects the data as first argument, if not defined. Brings it more into the tidyverse. For instance, one can now:
  • data |> filter(age>60) |> get_assoc(x="BMI", y="diabetes", z="sex")
• Add theme theme_minimal_modified for ggplots
• Moves most dependencies to “Imports” - this is the preferred way to use existing packages https://r-pkgs.org/dependencies-mindset-background.html#sec-dependencies-namespace
• Fix -log10p calculation

lukesRlib 0.2.4 (30 Jun 2023)

• Add option “get_fit” to get_assoc() to also get model fit statistic when PheWASing. For each model type the fit_stat is:
  • lm = R-squared
  • logistic = McFadden’s pseudo-R2
  • coxph = Harrell’s c-statistic
• Fix error if user does not want to provide any covariates to get_assoc()
• tidy_ci() now returns the C-statistic for CoxPH models by default

lukesRlib 0.2.3 (7 Jun 2023)

• Decided to remove genetics-related functions to instead have them in a separate package, as the dependencies were getting out of hand
  • See https://github.com/lukepilling/gwasRtools
• Add annotate_textp() function for use in ggplot2 plots for adding easy text annotation geoms
• Moved some functions to be internal only to tidy up the namespace
• Fix get_p_extreme if NaN is passed rather than NA

lukesRlib 0.2.2

• Decided to remove doCoxSplinePlot() because it is so much easier to do in {ggplot2} that a whole function is no longer necessary
  • Therefore the {pspline} dependency can be removed
• Set extreme_ps default to FALSE in get_assoc()

lukesRlib 0.2.1

• Added p-value threshold option to get_loci()
• Fix problem getting n in get_assoc() when model="coxph"

lukesRlib 0.2.0 (5 May 2023)

• get_assoc() can now perform coxph() models from the {survival} package. The user provides strings depicting the survival object as the outcome e.g., “Surv(time, event)”
• Added two genetics-related functions: lambda_gc() (to calculate Lambda GC!) and get_loci() (to crudely determine independent loci in GWAS summary stats)
• General improvements/clarifications throughout code and documentation

lukesRlib 0.1.9

• Added dependency {rlang} >= v1.0.0 so that the sym() function can be used - i.e., using provided variable name strings in dplyr::mutate() etc
• get_assoc() now allows options inv_norm_x and inv_norm_y

lukesRlib 0.1.8

• Changed get_assoc() so that x and y can be vectors - i.e., multiple exposures/outcomes can be provided. Then uses {purrr} function map2() to iterate over combinations
• • This package now depends on {purrr} >= v1.0.0 & {stringr} >= v1.5.0
• • Added functions xv() and yv() to improve ease of using {purrr} function map2() with get_assoc() for PheWAS of multiple exposures and outcomes in one analysis

lukesRlib 0.1.7

• Calculate R^2 in tidy_ci() if glm() is linear regression
• Tidy up tidy_ci() parameter documentation

lukesRlib 0.1.6

• fixes to get_assoc() (when no events in exposure group, or when two factor variables included)
• add scale options for exposure and outcome to get_assoc()
• in tidy_ci() tidy variable names with “scale()”

lukesRlib 0.1.5

• tidy_ci() now tidies up terms included as categorical variables. “as.factor(x_var)1” is replaced with “x_var-1”. Can be disabled with tidy_factors=FALSE
• addition of “Plotting” category of functions, starting with doCoxSplinePlot() that nicely plots the output of a spline term in a CoxPH model
• Minor fix to tidy_ci() to avoid breaks due to missing p-values in model summary statistics

lukesRlib 0.1.4

• Add new function get_assoc() to easily run PheWAS-like analysis using tidy_ci()

lukesRlib 0.1.3

• Updates to tidy_ci()
• Add get_se() from CIs function – very simple but adds to collection of related functions
• General improvements

lukesRlib 0.1.2

• Updated method for -log10 p-value calculation. One just uses Z. Other uses Z and N.

lukesRlib 0.1.1

• Added two new p-value related functions – very simple but nice to have available

lukesRlib 0.1.0 (26 Jan 2023)

• Added a NEWS.md file to track changes to the package.