From 9792c176c5dbeb463b97ee5f4c90cee0a660e6a1 Mon Sep 17 00:00:00 2001
From: Sebastian Henz <sebastian.henz@ufz.de>
Date: Wed, 29 Apr 2020 18:09:25 +0200
Subject: [PATCH] Rename predict_mixture() to multi_tox()
---
NAMESPACE | 2 +-
NEWS.md | 1 +
R/predict_mixture.R | 18 +++++++++---------
man/{predict_mixture.Rd => multi_tox.Rd} | 12 ++++++------
tests/testthat/test-predict_mixture.R | 10 +++++-----
5 files changed, 22 insertions(+), 21 deletions(-)
rename man/{predict_mixture.Rd => multi_tox.Rd} (90%)
diff --git a/NAMESPACE b/NAMESPACE
index f2c5e8c..36d0c1d 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -2,10 +2,10 @@
export(ecxsys)
export(lc)
+export(multi_tox)
export(plot_stress)
export(plot_survival)
export(predict_ecxsys)
-export(predict_mixture)
export(stress_to_survival)
export(survival_to_stress)
import(grDevices)
diff --git a/NEWS.md b/NEWS.md
index 07a6145..17d92ed 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -2,6 +2,7 @@
* Rename all instances of "effect" to "survival".
* Rename all instances of "ec" to "lc".
+* Rename `predict_mixture()` to `multi_tox()`.
# stressaddition 2.7.0
diff --git a/R/predict_mixture.R b/R/predict_mixture.R
index a275ece..3a9bab1 100644
--- a/R/predict_mixture.R
+++ b/R/predict_mixture.R
@@ -54,7 +54,7 @@
#' survival_tox_observed = c(26, 25, 24, 27, 5, 0),
#' survival_max = 30
#' )
-#' predict_mixture(
+#' multi_tox(
#' toxicant_a ,
#' toxicant_b ,
#' c(0, 0.02, 0.2, 2, 20),
@@ -65,17 +65,17 @@
#' conc_a <- c(0, 0.03, 0.3, 3)
#' conc_b <- 5.5
#' prop_ca <- 0.75
-#' 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)
+#' mix_a <- multi_tox(toxicant_a , toxicant_b , conc_a, conc_b, prop_ca)
+#' mix_b <- multi_tox(toxicant_b , toxicant_a , conc_b, conc_a, prop_ca)
#' identical(mix_a$survival, mix_b$survival)
#'
#' @export
-predict_mixture <- function(model_a,
- model_b,
- concentration_a,
- concentration_b,
- proportion_ca = 0.5,
- survival_max = 100) {
+multi_tox <- function(model_a,
+ model_b,
+ concentration_a,
+ concentration_b,
+ proportion_ca = 0.5,
+ survival_max = 100) {
stopifnot(
inherits(model_a, "ecxsys"),
inherits(model_b, "ecxsys"),
diff --git a/man/predict_mixture.Rd b/man/multi_tox.Rd
similarity index 90%
rename from man/predict_mixture.Rd
rename to man/multi_tox.Rd
index b15f7f1..f518529 100644
--- a/man/predict_mixture.Rd
+++ b/man/multi_tox.Rd
@@ -1,10 +1,10 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/predict_mixture.R
-\name{predict_mixture}
-\alias{predict_mixture}
+\name{multi_tox}
+\alias{multi_tox}
\title{Predict the survival of a mixture of two toxicants}
\usage{
-predict_mixture(
+multi_tox(
model_a,
model_b,
concentration_a,
@@ -56,7 +56,7 @@ toxicant_b <- ecxsys(
survival_tox_observed = c(26, 25, 24, 27, 5, 0),
survival_max = 30
)
-predict_mixture(
+multi_tox(
toxicant_a ,
toxicant_b ,
c(0, 0.02, 0.2, 2, 20),
@@ -67,8 +67,8 @@ predict_mixture(
conc_a <- c(0, 0.03, 0.3, 3)
conc_b <- 5.5
prop_ca <- 0.75
-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)
+mix_a <- multi_tox(toxicant_a , toxicant_b , conc_a, conc_b, prop_ca)
+mix_b <- multi_tox(toxicant_b , toxicant_a , conc_b, conc_a, prop_ca)
identical(mix_a$survival, mix_b$survival)
}
diff --git a/tests/testthat/test-predict_mixture.R b/tests/testthat/test-predict_mixture.R
index cbc035a..77bf217 100644
--- a/tests/testthat/test-predict_mixture.R
+++ b/tests/testthat/test-predict_mixture.R
@@ -34,7 +34,7 @@ model_b <- ecxsys(
test_that("results have not changed", {
# one concentration_b
- new <- predict_mixture(
+ new <- multi_tox(
model_a,
model_b,
c(0, 0.01, 0.1, 1, 7, 15),
@@ -54,7 +54,7 @@ test_that("results have not changed", {
expect_equal(new, reference, tolerance = 1e-5)
# diverse concentration_b
- new <- predict_mixture(
+ new <- multi_tox(
model_a,
model_b,
c(0, 0.01, 0.1, 1, 7, 15),
@@ -74,7 +74,7 @@ test_that("results have not changed", {
expect_equal(new, reference, tolerance = 1e-5)
# diverse concentration_b and custom survival_max
- new <- predict_mixture(
+ new <- multi_tox(
model_a,
model_b,
c(0, 0.01, 0.1, 1, 7, 15),
@@ -100,8 +100,8 @@ test_that("predictions are symmetric", {
conc_a <- c(0, 10^seq(log10(0.001), log10(40), length.out = 50))
conc_b <- 3.5
prop_ca <- 0.8
- survival_12 <- predict_mixture(model_a, model_b, conc_a, conc_b, prop_ca)$survival
- survival_21 <- predict_mixture(model_b, model_a, conc_b, conc_a, prop_ca)$survival
+ survival_12 <- multi_tox(model_a, model_b, conc_a, conc_b, prop_ca)$survival
+ survival_21 <- multi_tox(model_b, model_a, conc_b, conc_a, prop_ca)$survival
expect_equal(survival_12, survival_21)
})
--
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