From eafee4c1925c372a78337f40ec50edd11db8cd9c Mon Sep 17 00:00:00 2001 From: Marlena Bannick Date: Mon, 18 Nov 2024 23:44:57 -0800 Subject: [PATCH] Updated gvcov to vcovG (#52) --- NAMESPACE | 2 +- R/robin_glm.R | 4 +- R/treatment_effect.R | 6 +- R/variance_anhecova.R | 2 +- man/robin_glm.Rd | 4 +- man/{gvcov.Rd => vcovG.Rd} | 6 +- tests/testthat/_snaps/bias.new.md | 608 ++++++++++++++++++++++ tests/testthat/_snaps/treatment_effect.md | 6 +- tests/testthat/_snaps/variance.md | 12 +- tests/testthat/test-variance.R | 12 +- 10 files changed, 635 insertions(+), 27 deletions(-) rename man/{gvcov.Rd => vcovG.Rd} (87%) create mode 100644 tests/testthat/_snaps/bias.new.md diff --git a/NAMESPACE b/NAMESPACE index c7697c3..05369f1 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -12,7 +12,6 @@ S3method(treatment_effect,prediction_cf) S3method(vcovHC,prediction_cf) export(bias) export(find_data) -export(gvcov) export(h_diff) export(h_jac_diff) export(h_jac_odds_ratio) @@ -22,6 +21,7 @@ export(h_ratio) export(predict_counterfactual) export(robin_glm) export(treatment_effect) +export(vcovG) import(checkmate) importFrom(MASS,negative.binomial) importFrom(numDeriv,jacobian) diff --git a/R/robin_glm.R b/R/robin_glm.R index 4601d7c..9cb4e41 100644 --- a/R/robin_glm.R +++ b/R/robin_glm.R @@ -8,7 +8,7 @@ #' @param contrast_jac (`function`) A function to calculate the Jacobian of the contrast function. Ignored if using #' default contrasts. #' @param vcov (`function`) A function to calculate the variance-covariance matrix of the treatment effect, -#' including `vcovHC` and `gvcov`. +#' including `vcovHC` and `vcovG`. #' @param family (`family`) A family object of the glm model. #' @param vcov_args (`list`) Additional arguments passed to `vcov`. #' @param ... Additional arguments passed to `glm` or `glm.nb`. @@ -23,7 +23,7 @@ #' ) robin_glm <- function( formula, data, treatment, contrast = "difference", - contrast_jac = NULL, vcov = "gvcov", family = gaussian(), vcov_args = list(), ...) { + contrast_jac = NULL, vcov = "vcovG", family = gaussian(), vcov_args = list(), ...) { attr(formula, ".Environment") <- environment() # check if using negative.binomial family with NA as theta. # If so, use MASS::glm.nb instead of glm. diff --git a/R/treatment_effect.R b/R/treatment_effect.R index 3bd35a3..cdd7306 100644 --- a/R/treatment_effect.R +++ b/R/treatment_effect.R @@ -16,7 +16,7 @@ treatment_effect <- function(object, pair, variance, eff_measure, eff_jacobian, #' @export treatment_effect.prediction_cf <- function( - object, pair = names(object), variance = "gvcov", eff_measure, eff_jacobian, vcov_args = list(), ...) { + object, pair = names(object), variance = "vcovG", eff_measure, eff_jacobian, vcov_args = list(), ...) { assert( test_string(variance), test_function(variance), @@ -75,7 +75,7 @@ treatment_effect.prediction_cf <- function( #' @export #' @inheritParams predict_counterfactual treatment_effect.lm <- function( - object, pair, variance = "gvcov", eff_measure, eff_jacobian, + object, pair, variance = "vcovG", eff_measure, eff_jacobian, vcov_args = list(), treatment, data = find_data(object), ...) { pc <- predict_counterfactual(object, data = data, treatment) treatment_effect(pc, pair = pair, variance = variance, eff_measure = eff_measure, eff_jacobian = eff_jacobian, ...) @@ -83,7 +83,7 @@ treatment_effect.lm <- function( #' @export treatment_effect.glm <- function( - object, pair, variance = "gvcov", eff_measure, eff_jacobian, + object, pair, variance = "vcovG", eff_measure, eff_jacobian, vcov_args = list(), treatment, data = find_data(object), ...) { pc <- predict_counterfactual(object, treatment, data) treatment_effect(pc, pair = pair, variance = variance, eff_measure = eff_measure, eff_jacobian = eff_jacobian, ...) diff --git a/R/variance_anhecova.R b/R/variance_anhecova.R index 99faa37..d93eb1c 100644 --- a/R/variance_anhecova.R +++ b/R/variance_anhecova.R @@ -6,7 +6,7 @@ #' #' @return Named covariance matrix. #' @export -gvcov <- function(x, decompose = TRUE, ...) { # nolint +vcovG <- function(x, decompose = TRUE, ...) { # nolint assert_class(x, "prediction_cf") assert_flag(decompose) resi <- attr(x, "residual") diff --git a/man/robin_glm.Rd b/man/robin_glm.Rd index 21e697b..4c5690f 100644 --- a/man/robin_glm.Rd +++ b/man/robin_glm.Rd @@ -10,7 +10,7 @@ robin_glm( treatment, contrast = "difference", contrast_jac = NULL, - vcov = "gvcov", + vcov = "vcovG", family = gaussian(), vcov_args = list(), ... @@ -31,7 +31,7 @@ or a string name of treatment assignment.} default contrasts.} \item{vcov}{(\code{function}) A function to calculate the variance-covariance matrix of the treatment effect, -including \code{vcovHC} and \code{gvcov}.} +including \code{vcovHC} and \code{vcovG}.} \item{family}{(\code{family}) A family object of the glm model.} diff --git a/man/gvcov.Rd b/man/vcovG.Rd similarity index 87% rename from man/gvcov.Rd rename to man/vcovG.Rd index b0ed059..eec27a2 100644 --- a/man/gvcov.Rd +++ b/man/vcovG.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/variance_anhecova.R -\name{gvcov} -\alias{gvcov} +\name{vcovG} +\alias{vcovG} \title{ANHECOVA Covariance} \usage{ -gvcov(x, decompose = TRUE, ...) +vcovG(x, decompose = TRUE, ...) } \arguments{ \item{x}{(\code{prediction_cf}) Counter-factual prediction.} diff --git a/tests/testthat/_snaps/bias.new.md b/tests/testthat/_snaps/bias.new.md new file mode 100644 index 0000000..39bbda3 --- /dev/null +++ b/tests/testthat/_snaps/bias.new.md @@ -0,0 +1,608 @@ +# bias works for guassian + + Code + bias(residuals(fit_glm), treatment = dummy_data$treatment, group_idx = list( + seq_len(nrow(dummy_data)))) + Output + [,1] [,2] [,3] + [1,] -5.604445e-16 -2.31077e-15 -9.578422e-16 + [2,] -5.604445e-16 -2.31077e-15 -9.578422e-16 + [3,] -5.604445e-16 -2.31077e-15 -9.578422e-16 + [4,] -5.604445e-16 -2.31077e-15 -9.578422e-16 + [5,] -5.604445e-16 -2.31077e-15 -9.578422e-16 + [6,] -5.604445e-16 -2.31077e-15 -9.578422e-16 + [7,] -5.604445e-16 -2.31077e-15 -9.578422e-16 + [8,] -5.604445e-16 -2.31077e-15 -9.578422e-16 + [9,] -5.604445e-16 -2.31077e-15 -9.578422e-16 + [10,] -5.604445e-16 -2.31077e-15 -9.578422e-16 + [11,] -5.604445e-16 -2.31077e-15 -9.578422e-16 + [12,] -5.604445e-16 -2.31077e-15 -9.578422e-16 + [13,] -5.604445e-16 -2.31077e-15 -9.578422e-16 + [14,] -5.604445e-16 -2.31077e-15 -9.578422e-16 + [15,] -5.604445e-16 -2.31077e-15 -9.578422e-16 + [16,] -5.604445e-16 -2.31077e-15 -9.578422e-16 + [17,] -5.604445e-16 -2.31077e-15 -9.578422e-16 + [18,] -5.604445e-16 -2.31077e-15 -9.578422e-16 + [19,] -5.604445e-16 -2.31077e-15 -9.578422e-16 + [20,] -5.604445e-16 -2.31077e-15 -9.578422e-16 + [21,] -5.604445e-16 -2.31077e-15 -9.578422e-16 + [22,] 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e91e990..07fc8e6 100644 --- a/tests/testthat/_snaps/treatment_effect.md +++ b/tests/testthat/_snaps/treatment_effect.md @@ -18,7 +18,7 @@ 0.03359913 0.03441801 0.03401864 - Variance Type: gvcov + Variance Type: vcovG Estimate Std.Err Z Value Pr(>|z|) trt1 - pbo 0.2246 0.0477 4.71 2.5e-06 *** trt2 - pbo 0.2653 0.0475 5.58 2.4e-08 *** @@ -47,7 +47,7 @@ 0.06768998 0.07592944 0.07654319 - Variance Type: gvcov + Variance Type: vcovG Estimate Std.Err Z Value Pr(>|z|) trt1 - pbo 0.564 0.101 5.60 2.2e-08 *** trt2 - pbo 0.771 0.101 7.61 2.8e-14 *** @@ -98,7 +98,7 @@ 0.03359913 0.03441801 - Variance Type: gvcov + Variance Type: vcovG Estimate Std.Err Z Value Pr(>|z|) trt1 - pbo 0.2246 0.0477 4.71 2.5e-06 *** --- diff --git a/tests/testthat/_snaps/variance.md b/tests/testthat/_snaps/variance.md index ef8bb18..ca741db 100644 --- a/tests/testthat/_snaps/variance.md +++ b/tests/testthat/_snaps/variance.md @@ -18,10 +18,10 @@ trt1 4.523445e-07 1.164889e-03 -7.709031e-07 trt2 -9.709004e-06 -7.709031e-07 1.170214e-03 -# gvcov works +# vcovG works Code - gvcov(pc) + vcovG(pc) Output pbo trt1 trt2 pbo 1.128902e-03 1.856234e-05 1.333885e-05 @@ -31,7 +31,7 @@ --- Code - gvcov(pc) + vcovG(pc) Output pbo trt1 trt2 pbo 1.128902e-03 1.856234e-05 1.333885e-05 @@ -41,7 +41,7 @@ --- Code - gvcov(pc) + vcovG(pc) Output pbo trt1 trt2 pbo 1.128902e-03 1.856234e-05 1.333885e-05 @@ -51,7 +51,7 @@ --- Code - gvcov(pc, decompose = FALSE) + vcovG(pc, decompose = FALSE) Output pbo trt1 trt2 pbo 1.127076e-03 1.856234e-05 1.333885e-05 @@ -61,7 +61,7 @@ --- Code - gvcov(pc) + vcovG(pc) Output pbo trt1 trt2 pbo 1.128902e-03 1.856234e-05 1.333885e-05 diff --git a/tests/testthat/test-variance.R b/tests/testthat/test-variance.R index 3a81b8f..f3c9d3a 100644 --- a/tests/testthat/test-variance.R +++ b/tests/testthat/test-variance.R @@ -9,24 +9,24 @@ test_that("vcovHC works", { ) }) -test_that("gvcov works", { +test_that("vcovG works", { pc <- predict_counterfactual(fit_binom, treatment ~ s1) expect_snapshot( - gvcov(pc) + vcovG(pc) ) pc <- predict_counterfactual(fit_binom, treatment ~ 1) expect_snapshot( - gvcov(pc) + vcovG(pc) ) pc <- predict_counterfactual(fit_binom, treatment ~ pb(s1)) expect_snapshot( - gvcov(pc) + vcovG(pc) ) expect_snapshot( - gvcov(pc, decompose = FALSE) + vcovG(pc, decompose = FALSE) ) pc <- predict_counterfactual(fit_binom, treatment ~ ps(s1)) expect_snapshot( - gvcov(pc) + vcovG(pc) ) })