From 26f41388d36781d892ed005365a7f2348171990e Mon Sep 17 00:00:00 2001
From: Sebastian Henz <sebastian.henz@ufz.de>
Date: Mon, 16 Mar 2020 15:04:50 +0100
Subject: [PATCH] Rename the mixture_effect column to effect
---
R/predict_mixture.R | 14 +++++++-------
man/predict_mixture.Rd | 6 +++---
tests/testthat/test-predict_mixture.R | 10 +++++-----
3 files changed, 15 insertions(+), 15 deletions(-)
diff --git a/R/predict_mixture.R b/R/predict_mixture.R
index c79582c..52da740 100644
--- a/R/predict_mixture.R
+++ b/R/predict_mixture.R
@@ -63,9 +63,9 @@
#' conc_a <- c(0, 0.03, 0.3, 3)
#' conc_b <- rep(5.5, 4)
#' prop_ca <- 0.75
-#' effect_a <- predict_mixture(toxicant_a , toxicant_b , conc_a, conc_b, prop_ca)
-#' effect_b <- predict_mixture(toxicant_b , toxicant_a , conc_b, conc_a, prop_ca)
-#' identical(effect_a$mixture_effect, effect_b$mixture_effect)
+#' mix_a <- predict_mixture(toxicant_a , toxicant_b , conc_a, conc_b, prop_ca)
+#' mix_b <- predict_mixture(toxicant_b , toxicant_a , conc_b, conc_a, prop_ca)
+#' identical(mix_a$effect, mix_b$effect)
#'
#' @export
predict_mixture <- function(model_a,
@@ -129,11 +129,11 @@ predict_mixture <- function(model_a,
proportion_sam <- 1 - proportion_ca
stress_tox_total <- stress_tox_ca * proportion_ca + stress_tox_sam * proportion_sam
stress_total <- stress_tox_total + sys_total
- mixture_effect <- stress_to_effect(stress_total) * effect_max
+ effect <- stress_to_effect(stress_total) * effect_max
- # unname() to remove the name when concentration_a is a single number.
- mixture_effect <- unname(mixture_effect)
- data.frame(concentration_a, concentration_b, mixture_effect)
+ # Setting row.names to NULL to prevent row names when one of the
+ # concentrations is a single number.
+ data.frame(concentration_a, concentration_b, effect, row.names = NULL)
}
diff --git a/man/predict_mixture.Rd b/man/predict_mixture.Rd
index 297c291..98c1573 100644
--- a/man/predict_mixture.Rd
+++ b/man/predict_mixture.Rd
@@ -65,8 +65,8 @@ predict_mixture(
conc_a <- c(0, 0.03, 0.3, 3)
conc_b <- rep(5.5, 4)
prop_ca <- 0.75
-effect_a <- predict_mixture(toxicant_a , toxicant_b , conc_a, conc_b, prop_ca)
-effect_b <- predict_mixture(toxicant_b , toxicant_a , conc_b, conc_a, prop_ca)
-identical(effect_a$mixture_effect, effect_b$mixture_effect)
+mix_a <- predict_mixture(toxicant_a , toxicant_b , conc_a, conc_b, prop_ca)
+mix_b <- predict_mixture(toxicant_b , toxicant_a , conc_b, conc_a, prop_ca)
+identical(mix_a$effect, mix_b$effect)
}
diff --git a/tests/testthat/test-predict_mixture.R b/tests/testthat/test-predict_mixture.R
index 2ad99b6..0e94dfa 100644
--- a/tests/testthat/test-predict_mixture.R
+++ b/tests/testthat/test-predict_mixture.R
@@ -40,7 +40,7 @@ test_that("results have not changed", {
c(0, 0.01, 0.1, 1, 7, 15),
rep(5, 6),
0.3
- )$mixture_effect
+ )$effect
reference <- c(88.574578, 84.361552, 80.633762, 56.730550, 2.882718, 0)
expect_equal(new, reference, tolerance = 1e-5)
@@ -51,7 +51,7 @@ test_that("results have not changed", {
c(0, 0.01, 0.1, 1, 7, 15),
c(0, 0.02, 0.2, 2, 14, 30),
0.3
- )$mixture_effect
+ )$effect
reference <- c(88.2698383, 79.9617127, 78.1574808, 65.7999834, 0.3861678, 0)
expect_equal(new, reference, tolerance = 1e-5)
@@ -63,7 +63,7 @@ test_that("results have not changed", {
c(0, 0.02, 0.2, 2, 14, 30),
0.3,
42
- )$mixture_effect
+ )$effect
reference <- c(88.2698383, 79.9617127, 78.1574808, 65.7999834, 0.3861678, 0) * 0.42
expect_equal(new, reference, tolerance = 1e-5)
})
@@ -73,8 +73,8 @@ test_that("predictions are symmetric", {
conc_a <- c(0, 10^seq(log10(0.001), log10(40), length.out = 50))
conc_b <- rep(3.5, length(conc_a))
prop_ca <- 0.8
- effect_12 <- predict_mixture(model_a, model_b, conc_a, conc_b, prop_ca)$mixture_effect
- effect_21 <- predict_mixture(model_b, model_a, conc_b, conc_a, prop_ca)$mixture_effect
+ effect_12 <- predict_mixture(model_a, model_b, conc_a, conc_b, prop_ca)$effect
+ effect_21 <- predict_mixture(model_b, model_a, conc_b, conc_a, prop_ca)$effect
expect_equal(effect_12, effect_21)
})
--
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