From 4f0848e30e77fa73be16e8a4cb4c0452409b7949 Mon Sep 17 00:00:00 2001 From: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> Date: Fri, 2 Aug 2024 15:09:16 +0200 Subject: [PATCH 1/9] Restore missing if lost in 567e9957ad7ffca1b300264bda953626926a4f78. --- R/sensmodel.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/R/sensmodel.R b/R/sensmodel.R index 9403cd60..a82a13b8 100644 --- a/R/sensmodel.R +++ b/R/sensmodel.R @@ -81,8 +81,8 @@ sensmodel <- function(peaksens, range = c(300, 700), lambdacut = NULL, Bmid = NU if (!is.null(lambdacut) && !is.null(oiltype) && length(lambdacut) != length(oiltype)) { stop("lambdacut and oiltype must be of same length", call. = FALSE) } - if (!is.null(lambdacut) && !is.null(Bmid)) { - + if (!is.null(lambdacut) && !is.null(Bmid) && length(lambdacut) != length(Bmid)) { + stop("lambdacut and Bmid must be of same length") } sensecurves <- matrix(ncol = length(peaksens), nrow = (range[2] - range[1] + 1)) From 80859a679e45a46ff118fd25abbffc44d8c0bf43 Mon Sep 17 00:00:00 2001 From: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> Date: Fri, 2 Aug 2024 15:15:06 +0200 Subject: [PATCH 2/9] Move integration out of the loop --- R/sensmodel.R | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/R/sensmodel.R b/R/sensmodel.R index a82a13b8..d377f9c2 100644 --- a/R/sensmodel.R +++ b/R/sensmodel.R @@ -128,11 +128,6 @@ sensmodel <- function(peaksens, range = c(300, 700), lambdacut = NULL, Bmid = NU peak <- peak * T.oil } - # Apply integration - if (integrate) { - peak <- peak / sum(peak) - } - # Apply ocular media transmission correction if (!is.null(om)) { @@ -154,6 +149,11 @@ sensmodel <- function(peaksens, range = c(300, 700), lambdacut = NULL, Bmid = NU sensecurves[, i] <- peak } + # Apply integration + if (integrate) { + sensecurves <- sensecurves / colSums(sensecurves) + } + sensecurves <- as.data.frame(sensecurves) if (length(sensnames) != length(sensecurves)) { From 03f6208d467b44ca3bcb3f87886ef06bed827b83 Mon Sep 17 00:00:00 2001 From: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> Date: Fri, 2 Aug 2024 15:18:25 +0200 Subject: [PATCH 3/9] Simplify successive ifs --- R/sensmodel.R | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/R/sensmodel.R b/R/sensmodel.R index d377f9c2..50857e82 100644 --- a/R/sensmodel.R +++ b/R/sensmodel.R @@ -131,15 +131,13 @@ sensmodel <- function(peaksens, range = c(300, 700), lambdacut = NULL, Bmid = NU # Apply ocular media transmission correction if (!is.null(om)) { - if (length(om) == 1) { - if (om == "bird") { + if (identical(om, "bird")) { T.e <- log(8.928 * 10^-13 * wl^5 - 2.595 * 10^-9 * wl^4 + 3.006 * 10^-6 * wl^3 - 0.001736 * wl^2 + 0.5013 * wl - 55.56) T.e[which(T.e < 0)] <- 0 peak <- peak * T.e - } } else { T.e <- om peak <- peak * T.e From c7161845f31b95955f2b10987df3c8519859ca30 Mon Sep 17 00:00:00 2001 From: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> Date: Fri, 2 Aug 2024 15:19:20 +0200 Subject: [PATCH 4/9] Move T.e multiplication outside of the if else --- R/sensmodel.R | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/R/sensmodel.R b/R/sensmodel.R index 50857e82..c4b01b65 100644 --- a/R/sensmodel.R +++ b/R/sensmodel.R @@ -137,11 +137,10 @@ sensmodel <- function(peaksens, range = c(300, 700), lambdacut = NULL, Bmid = NU wl^3 - 0.001736 * wl^2 + 0.5013 * wl - 55.56) T.e[which(T.e < 0)] <- 0 - peak <- peak * T.e } else { T.e <- om - peak <- peak * T.e } + peak <- peak * T.e } sensecurves[, i] <- peak From b15535b575246c9540f70e4a3b8111904634ae84 Mon Sep 17 00:00:00 2001 From: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> Date: Fri, 2 Aug 2024 15:22:50 +0200 Subject: [PATCH 5/9] Move ocular media transmission effect outside of the loop --- R/sensmodel.R | 28 +++++++++++++--------------- 1 file changed, 13 insertions(+), 15 deletions(-) diff --git a/R/sensmodel.R b/R/sensmodel.R index c4b01b65..56de0021 100644 --- a/R/sensmodel.R +++ b/R/sensmodel.R @@ -128,27 +128,25 @@ sensmodel <- function(peaksens, range = c(300, 700), lambdacut = NULL, Bmid = NU peak <- peak * T.oil } - # Apply ocular media transmission correction - - if (!is.null(om)) { - if (identical(om, "bird")) { - T.e <- log(8.928 * 10^-13 * wl^5 - 2.595 * 10^-9 * - wl^4 + 3.006 * 10^-6 * - wl^3 - 0.001736 * wl^2 + 0.5013 * - wl - 55.56) - T.e[which(T.e < 0)] <- 0 - } else { - T.e <- om - } - peak <- peak * T.e - } - sensecurves[, i] <- peak } # Apply integration if (integrate) { sensecurves <- sensecurves / colSums(sensecurves) + + # Apply ocular media transmission correction + if (!is.null(om)) { + if (identical(om, "bird")) { + T.e <- log(8.928 * 10^-13 * wl^5 - 2.595 * 10^-9 * + wl^4 + 3.006 * 10^-6 * + wl^3 - 0.001736 * wl^2 + 0.5013 * + wl - 55.56) + T.e[which(T.e < 0)] <- 0 + } else { + T.e <- om + } + sensecurves <- sensecurves * T.e } sensecurves <- as.data.frame(sensecurves) From 7bb9c32685a2cb04fa65f6a844597c4c85e01a6c Mon Sep 17 00:00:00 2001 From: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> Date: Fri, 2 Aug 2024 15:23:12 +0200 Subject: [PATCH 6/9] integration --- R/sensmodel.R | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/R/sensmodel.R b/R/sensmodel.R index 56de0021..58e1ea64 100644 --- a/R/sensmodel.R +++ b/R/sensmodel.R @@ -133,7 +133,8 @@ sensmodel <- function(peaksens, range = c(300, 700), lambdacut = NULL, Bmid = NU # Apply integration if (integrate) { - sensecurves <- sensecurves / colSums(sensecurves) + sensecurves <- t(t(sensecurves) / colSums(sensecurves)) + } # Apply ocular media transmission correction if (!is.null(om)) { From e0e634c851d13427f6ad7b51f331168c1d73dcae Mon Sep 17 00:00:00 2001 From: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> Date: Sat, 31 Aug 2024 15:57:56 +0200 Subject: [PATCH 7/9] Add stricter tests --- tests/testthat/_snaps/sensmodel.md | 155 +++++++++++++++++++++++++++++ tests/testthat/test-sensmodel.R | 19 +++- 2 files changed, 169 insertions(+), 5 deletions(-) create mode 100644 tests/testthat/_snaps/sensmodel.md diff --git a/tests/testthat/_snaps/sensmodel.md b/tests/testthat/_snaps/sensmodel.md new file mode 100644 index 00000000..1145a284 --- /dev/null +++ b/tests/testthat/_snaps/sensmodel.md @@ -0,0 +1,155 @@ +# sensmodel() values + + { + "type": "list", + "attributes": { + "names": { + "type": "character", + "attributes": {}, + "value": ["wl", "lmax300", "lmax400", "lmax500"] + }, + "class": { + "type": "character", + "attributes": {}, + "value": ["sensmod", "rspec", "data.frame"] + }, + "row.names": { + "type": "integer", + "attributes": {}, + "value": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 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} + ] + } + diff --git a/tests/testthat/test-sensmodel.R b/tests/testthat/test-sensmodel.R index 916efe09..e181ad0a 100644 --- a/tests/testthat/test-sensmodel.R +++ b/tests/testthat/test-sensmodel.R @@ -1,9 +1,18 @@ test_that("sensmodel() values", { - expect_equal(colSums(sensmodel(c(300, 400, 500), lambdacut = c(350, 450, 550), oiltype = c("C", "Y", "R"))[, -1]), c(1, 1, 1), ignore_attr = TRUE) - expect_equal( - round(sum(sensmodel(c(300, 400, 500), lambdacut = c(350, 450, 550), oiltype = c("C", "T", "P"), beta = FALSE, integrate = FALSE, om = "bird")[, -1]), 4), - 68.271, - ignore_attr = TRUE + expect_snapshot_value( + sensmodel(c(300, 400, 500), lambdacut = c(350, 450, 550), oiltype = c("C", "Y", "R")), + style = "json2", tolerance = 1e-5 + ) + + expect_snapshot_value( + sensmodel(c(300, 400, 500), lambdacut = c(350, 450, 550), oiltype = c("C", "T", "P"), beta = FALSE, integrate = FALSE, om = "bird"), + style = "json2", tolerance = 5e-5 + ) + + expect_snapshot_value( + # Danio aequipinnatus based on Govardovskii et al. (2000) + sensmodel(c(357, 411, 477, 569)), + style = "json2", tolerance = 1e-5 ) # Custom names From 67cce519a5fc38b1f805bbbf4cdfcba9845291b8 Mon Sep 17 00:00:00 2001 From: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> Date: Sun, 1 Sep 2024 14:00:53 +0200 Subject: [PATCH 8/9] Refactor sensmodel() without loop --- R/sensmodel.R | 57 ++++++++++++++++++++++----------------------------- 1 file changed, 25 insertions(+), 32 deletions(-) diff --git a/R/sensmodel.R b/R/sensmodel.R index 58e1ea64..141f5e64 100644 --- a/R/sensmodel.R +++ b/R/sensmodel.R @@ -85,32 +85,28 @@ sensmodel <- function(peaksens, range = c(300, 700), lambdacut = NULL, Bmid = NU stop("lambdacut and Bmid must be of same length") } - sensecurves <- matrix(ncol = length(peaksens), nrow = (range[2] - range[1] + 1)) - wl <- range[1]:range[2] - for (i in seq_along(peaksens)) { - # Sensitivities w/o oil droplets - peak <- 1 / (exp(69.7 * (0.8795 + 0.0459 * exp(-(peaksens[i] - range[1])^2 / 11940) - (peaksens[i] / wl))) - + exp(28 * (0.922 - peaksens[i] / wl)) + exp(-14.9 * (1.104 - (peaksens[i] / wl))) + 0.674) + sensecurves <- matrix(wl, ncol = length(wl), nrow = length(peaksens), byrow = TRUE) - if (beta) { - betaband <- 0.26 * exp(-((wl - (189 + 0.315 * peaksens[i])) / (-40.5 + 0.195 * peaksens[i]))^2) - peak <- peak + betaband - } + peaks <- 1 / (exp(69.7 * (0.8795 + 0.0459 * exp(-(peaksens - range[1])^2 / 11940) - (peaksens / sensecurves))) + + exp(28 * (0.922 - peaksens / sensecurves)) + exp(-14.9 * (1.104 - (peaksens / sensecurves))) + 0.674) - peak <- peak / max(peak) + if (beta) { + betabands <- 0.26 * exp(-((sensecurves - (189 + 0.315 * peaksens)) / (-40.5 + 0.195 * peaksens))^2) + peaks <- peaks + betabands + } + + peaks <- peaks / apply(peaks, 1, max) + + # FIXME: re-add handling of NA + if (!is.null(lambdacut) && !is.null(Bmid)) { + T.oil <- exp(-exp(-2.89 * Bmid * (sensecurves - lambdacut) + 1.08)) + peaks <- peaks * T.oil + } - if (!is.null(lambdacut) && !is.null(Bmid)) { - if (is.na(lambdacut[i]) && !is.na(Bmid[i])) { - warning("NA in lambdacut not paired with NA in Bmid, value of Bmid omitted", call. = FALSE) - T.oil <- 1 - } else { - T.oil <- exp(-exp(-2.89 * Bmid[i] * (wl - lambdacut[i]) + 1.08)) - peak <- peak * T.oil - } - } + for (i in seq_along(peaksens)) { if (!is.null(lambdacut) && !is.null(oiltype)) { if (oiltype[i] == "T") { T.oil <- 1 @@ -122,35 +118,32 @@ sensmodel <- function(peaksens, range = c(300, 700), lambdacut = NULL, Bmid = NU # Oil droplet transmission from Hart and Vorobyev (2005) T.oil <- exp(-exp(-2.89 * (0.5 / ((oil[1] * lambdacut[i] + oil[2]) - lambdacut[i])) * - (wl - lambdacut[i]) + 1.08)) + (sensecurves[i, ] - lambdacut[i]) + 1.08)) } - - peak <- peak * T.oil + peaks[i, ] <- peaks[i, ] * T.oil } - - sensecurves[, i] <- peak } # Apply integration if (integrate) { - sensecurves <- t(t(sensecurves) / colSums(sensecurves)) + peaks <- peaks / rowSums(peaks) } # Apply ocular media transmission correction if (!is.null(om)) { if (identical(om, "bird")) { - T.e <- log(8.928 * 10^-13 * wl^5 - 2.595 * 10^-9 * - wl^4 + 3.006 * 10^-6 * - wl^3 - 0.001736 * wl^2 + 0.5013 * - wl - 55.56) + T.e <- log(8.928 * 10^-13 * sensecurves^5 - 2.595 * 10^-9 * + sensecurves^4 + 3.006 * 10^-6 * + sensecurves^3 - 0.001736 * sensecurves^2 + 0.5013 * + sensecurves - 55.56) T.e[which(T.e < 0)] <- 0 } else { T.e <- om } - sensecurves <- sensecurves * T.e + peaks <- peaks * T.e } - sensecurves <- as.data.frame(sensecurves) + sensecurves <- as.data.frame(t(peaks)) if (length(sensnames) != length(sensecurves)) { message("The length of argument 'sensnames' does not equal the number of curves specified by 'peaksens'. Reverting to default names.") From ee8d21eebb575baaa0fa3c84b12af8a3ec8b0c68 Mon Sep 17 00:00:00 2001 From: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> Date: Fri, 6 Sep 2024 14:08:02 +0200 Subject: [PATCH 9/9] Restore NA handling in T.oil --- R/sensmodel.R | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/R/sensmodel.R b/R/sensmodel.R index 141f5e64..79fa7aaa 100644 --- a/R/sensmodel.R +++ b/R/sensmodel.R @@ -99,13 +99,15 @@ sensmodel <- function(peaksens, range = c(300, 700), lambdacut = NULL, Bmid = NU peaks <- peaks / apply(peaks, 1, max) - # FIXME: re-add handling of NA if (!is.null(lambdacut) && !is.null(Bmid)) { T.oil <- exp(-exp(-2.89 * Bmid * (sensecurves - lambdacut) + 1.08)) + if (!identical(is.na(lambdacut), is.na(Bmid))) { + warning("NA in lambdacut not paired with NA in Bmid, value of Bmid omitted", call. = FALSE) + T.oil[is.na(lambdacut)] <- 1 + } peaks <- peaks * T.oil } - for (i in seq_along(peaksens)) { if (!is.null(lambdacut) && !is.null(oiltype)) { if (oiltype[i] == "T") {