From 92ead3c543a753fb5cf7fad7e99f21291c49779a Mon Sep 17 00:00:00 2001 From: arcaldwell49 Date: Tue, 1 Aug 2023 14:03:05 -0400 Subject: [PATCH 1/4] Updated docs add lifecycle deprecation warnings. 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--- a/R/agree_coef.R +++ b/R/agree_coef.R @@ -1,5 +1,8 @@ -#' Agreeement Coefficents -#' @description agree_coef produces inter-rater reliability or "agreement coefficients" as described by Gwet. +#' @title Agreeement Coefficents +#' @description +#' `r lifecycle::badge('maturing')` +#' +#' agree_coef produces inter-rater reliability or "agreement coefficients" as described by Gwet. #' @param measure Name of column containing the measurement of interest. #' @param item Name of column containing the items. If this is an inter-rater reliability study then this would indicate the rater (e.g., rater1, rater2, rater3, etc). #' @param id Column with subject identifier. diff --git a/R/agree_nest.R b/R/agree_nest.R index 8b18012b..9484d716 100644 --- a/R/agree_nest.R +++ b/R/agree_nest.R @@ -56,7 +56,7 @@ agree_nest <- function(x, TOST = TRUE, prop_bias = FALSE, ccc = TRUE){ - + lifecycle::deprecate_soft("0.2.0", "agree_nest()", "agreement_limit()") agreeq = qnorm(1 - (1 - agree.level) / 2) agree_l = 1 - (1 - agree.level) / 2 agree_u = (1 - agree.level) / 2 diff --git a/R/agree_np.R b/R/agree_np.R index e27af0db..d9ca9cc2 100644 --- a/R/agree_np.R +++ b/R/agree_np.R @@ -1,4 +1,4 @@ -#' Nonparametric Test for Limits of Agreement +#' @title Nonparametric Test for Limits of Agreement #' #' @description #' diff --git a/R/agree_reps.R b/R/agree_reps.R index f9ef9f7f..5741e19d 100644 --- a/R/agree_reps.R +++ b/R/agree_reps.R @@ -48,6 +48,7 @@ agree_reps <- function(x, prop_bias = FALSE, TOST = TRUE, ccc = TRUE){ + lifecycle::deprecate_soft("0.2.0", "agree_reps()", "agreement_limit()") agreeq = qnorm(1 - (1 - agree.level) / 2) agree.l = 1 - (1 - agree.level) / 2 diff --git a/R/agree_test.R b/R/agree_test.R index db1d2371..e19ca49f 100644 --- a/R/agree_test.R +++ b/R/agree_test.R @@ -53,6 +53,7 @@ agree_test <- function(x, agree.level = .95, TOST = TRUE, prop_bias = FALSE) { + lifecycle::deprecate_soft("0.2.0", "agree_test()", "agreement_limit()") est <- lower.ci <- upper.ci <- NULL if (agree.level >= 1 || agree.level <= 0) { diff --git a/R/agreement_limit.R b/R/agreement_limit.R index b76aeed1..d9385c01 100644 --- a/R/agreement_limit.R +++ b/R/agreement_limit.R @@ -1,4 +1,4 @@ -#' Calculate the Limits of Agreement +#' @title Limits of Agreement #' #' @description #' `r lifecycle::badge('maturing')` diff --git a/R/blandPowerCurve.R b/R/blandPowerCurve.R index c4c22152..c913e187 100644 --- a/R/blandPowerCurve.R +++ b/R/blandPowerCurve.R @@ -1,6 +1,7 @@ -#' Estimate power curve for Bland-Altman limits of agreement +#' @title Power Curve for Bland-Altman Limits of Agreement #' #' @description +#' `r lifecycle::badge('maturing')` #' This function calculates the power for the Bland-Altman method under varying parameter settings and for a range of sample sizes. #' #' @param samplesizes vector of samples sizes at which to estimate power. diff --git a/R/dem_reg.R b/R/dem_reg.R index aa42a7d8..a35ec8e5 100644 --- a/R/dem_reg.R +++ b/R/dem_reg.R @@ -1,4 +1,4 @@ -#' Deming Regression +#' @title Deming Regression #' @description #' `r lifecycle::badge('stable')` #' diff --git a/R/loa_mixed.R b/R/loa_mixed.R index a503e818..65d9a1fa 100644 --- a/R/loa_mixed.R +++ b/R/loa_mixed.R @@ -1,4 +1,4 @@ -#' Mixed Effects Limits of Agreement +#' @title Mixed Effects Limits of Agreement #' #' @description #' `r lifecycle::badge('deprecated')` @@ -50,6 +50,7 @@ loa_mixed = function(diff, agree.level = .95, replicates = 1999, type = "bca"){ + lifecycle::deprecate_warn("0.2.0", "loa_mixed()", "loa_lme()") if (conf.level >= 1 || conf.level <= 0) { stop("conf.level must be a value between 0 and 1") } diff --git a/R/reli_stats.R b/R/reli_stats.R index ae9ee2cf..8a492c0b 100644 --- a/R/reli_stats.R +++ b/R/reli_stats.R @@ -1,4 +1,4 @@ -#' Reliability Statistics +#' @title Reliability Statistics #' #' @description #' diff --git a/R/tolerance_limit.R b/R/tolerance_limit.R index d843a4a8..a59533c8 100644 --- a/R/tolerance_limit.R +++ b/R/tolerance_limit.R @@ -1,10 +1,10 @@ -#' Tolerance Limits from an Agreement Study +#' @title Tolerance Limits from an Agreement Study #' #' @description `r lifecycle::badge('maturing')` #' #' A function for calculating tolerance limits for the difference between two measurements (difference = x-y). #' This is a procedure that should produce results similar to the Bland-Altman limits of agreement. -#' See `vignette("agreement_analysis")` for more details. +#' See vignettes for more details. #' #' @param data A data frame containing the variables. #' @param x Name of the column for the first measurement. diff --git a/docs/404.html b/docs/404.html index 048b287a..56077e7a 100644 --- a/docs/404.html +++ b/docs/404.html @@ -54,13 +54,13 @@