tests/testthat/testbyIndv4Times.r
In briencj/growthPheno: Functional Analysis of Phenotypic Growth Data to Smooth and Extract Traits
cat("#### Test spline fitting using NCSS with leaf data when there are missing values\n")
test_that("leaf_growthPheno", {
skip_if_not_installed("growthPheno")
skip_on_cran()
library(dae)
library(ggplot2)
library(growthPheno)
# A small subset of Exp 270 leaf tracking data
data(testSpline)
#Set Days to NA to match xDays
test$Days[is.na(test$xDays)] <- NA
responses <- names(test)[5:ncol(test)]
##Test the fail options for NCSS
testthat::expect_error(byIndv4Times_SplinesGRs(data = test, response = "Area", times="Days",
individuals = "Snapshot.ID.Tag",
df = 4, na.x.action = "fail"))
testthat::expect_error(byIndv4Times_SplinesGRs(data = test, response = "Length.1",
individuals = "Snapshot.ID.Tag", times="Days",
df = 4, na.y.action = "fail"))
##Fit some splines - exclude y
leaf.dat <- test
testthat::expect_warning(
for (resp in responses)
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat, response = resp,
times="Days", df = 4),
regexp = "Need at least 4 distinct x values to fit a spline - all fitted values set to NA")
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.1)), 86)
testthat::expect_equal(sum(is.na(leaf.dat$sArea)), 3)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.3[13:24])), 4)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.3[49:60])), 0)
##trim
leaf.dat <- test
for (resp in responses)
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat, response = resp, times = "Days",
df = 4, na.y.action = "trim")
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.1)), 86)
testthat::expect_lt(abs(leaf.dat$sLength.1[57] - 11.067455), 1e-05)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.3[13:24])), 4)
##Test ltrimx
leaf.dat <- test
for (resp in responses)
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat, response = resp, times = "Days",
df = 4, na.y.action = "ltrim",
rates.method = "deriv",
suffices.rates = c("AGRdv", "RGRdv"))
testthat::expect_equal(length(lapply(responses,
function(resp, data)
{
resp <- paste0("s", resp)
testthat::expect_equal(sum(is.na(data[[resp]])),
sum(is.na(data[[paste(resp,"AGRdv",sep = ".")]])),
sum(is.na(data[[paste(resp,"RGRdv",sep = ".")]])))
}, data = leaf.dat)), 4)
testthat::expect_equal(nrow(leaf.dat), 96)
testthat::expect_equal(ncol(leaf.dat), 20)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.1)), 87)
testthat::expect_lt(abs(leaf.dat$sLength.1[57] - 11.067455), 1e-05)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.3[13:24])), 7)
leaf.dat.noC <- leaf.dat
##Test ltrimx with correctBoundaries
# - need to use xDays as Days causes correctBoundaries to go singular???
leaf.dat <- test
for (resp in responses)
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat, response = resp, times = "xDays",
df = 4, rates.method = "none",
na.y.action = "ltrim",
correctBoundaries = TRUE)
testthat::expect_equal(nrow(leaf.dat), 96)
testthat::expect_equal(ncol(leaf.dat), 12)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.1)), 87)
testthat::expect_lt(abs(leaf.dat$sLength.1[57] - 11.05895), 1e-05)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.3[13:24])), 7)
leaf.dat$sLength.1.noC <- leaf.dat.noC$sLength.1
leaf.dat$sLength.2.noC <- leaf.dat.noC$sLength.2
leaf.dat$sLength.3.noC <- leaf.dat.noC$sLength.3
ggplot(leaf.dat, aes(x = xDays, y = Length.1)) +
geom_line() + geom_line(aes(x = xDays, sLength.1), colour = "blue") +
geom_line(aes(x = xDays, sLength.1.noC), colour = "red") +
facet_wrap(~ Snapshot.ID.Tag)
##Test utrimx
leaf.dat <- test
for (resp in responses)
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat, response = resp, times = "Days",
df = 4, rates.method = "none",
na.y.action = "utrim")
testthat::expect_equal(nrow(leaf.dat), 96)
testthat::expect_equal(ncol(leaf.dat), 12)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.1)), 92)
testthat::expect_lt(abs(leaf.dat$sLength.1[57] - 11.067455), 1e-05)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.3[13:24])), 9)
##Test utrimx
leaf.dat <- test
for (resp in responses)
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat, response = resp, times = "Days",
df = 4, rates.method = "none",
na.y.action = "allx")
testthat::expect_equal(nrow(leaf.dat), 96)
testthat::expect_equal(ncol(leaf.dat), 12)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.1)), 93)
testthat::expect_lt(abs(leaf.dat$sLength.1[57] - 11.067455), 1e-05)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.3[13:24])), 12)
testthat::expect_equal(sum(is.na(leaf.dat$sLength.3[94:96])), 3)
##Test omit in smoothSpline - Length 3
leaf.dat <- test
carts <- levels(leaf.dat$Snapshot.ID.Tag)
fit <- vector(mode = "list", length = 0)
nrows <- vector(mode = "list", length = length(carts))
nrows <- list(6,4,5,3,2,6,1,1)
names(nrows) <- carts
for (cart in carts)
{
fit[[cart]] <- smoothSpline(subset(leaf.dat, Snapshot.ID.Tag == cart),
response = "Length.3", response.smoothed = "sLength.3",
x = "xDays",
df = 4, na.x.action = "omi", na.y.action = "omit",
rates = c("AGR", "RGR"),
suffices.rates=c("AGRdv", "RGRdv"))
testthat::expect_equal(nrows[[cart]], nrow(fit[[cart]]$predictions))
}
##Test omit in smoothSpline - Length 2 with a 0 length data.frame
fit <- vector(mode = "list", length = 0)
nrows <- list(11,12,12,12,9,12,0,9)
names(nrows) <- carts
for (cart in carts)
{
fit[[cart]] <- smoothSpline(subset(leaf.dat, Snapshot.ID.Tag == cart),
response = "Length.2", response.smoothed = "sLength.2",
x = "xDays",
df = 4, na.x.action = "omi", na.y.action = "omit",
rates = c("AGR", "RGR"),
suffices.rates=c("AGRdv", "RGRdv"))
testthat::expect_equal(nrows[[cart]], nrow(fit[[cart]]$predictions))
}
testthat::expect_equal(ncol(fit[[cart]]$predictions), 4)
##Test omit in byIndv4Times_SplinesGRs - get full data.frame because of merge in byIndv4Times_SplinesGRs
leaf.dat <- test
for (resp in responses)
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat, response = resp, times = "Days",
df = 4, rates.method = "none",
na.x.action = "omi", na.y.action = "omit")
testthat::expect_equal(nrow(leaf.dat), 96)
testthat::expect_equal(ncol(leaf.dat), 12)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.1)), 82)
leaf.dat <- test
for (resp in responses)
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat, response = resp, times = "Days",
df = 4, rates.method = "none", na.y.action = "omit")
##Test omit in smoothSpline - Length 2 with a 0 length data.frame
leaf.dat <- test
carts <- levels(leaf.dat$Snapshot.ID.Tag)
fit <- vector(mode = "list", length = 0)
nrows <- list(6,4,5,3,2,6,1,1)
names(nrows) <- carts
for (cart in carts)
{
fit[[cart]] <- smoothSpline(subset(leaf.dat, Snapshot.ID.Tag == cart),
response = "Length.3", response.smoothed = "sLength.3",
x="xDays", correctBoundaries = FALSE,
df = 4, na.x.action = "omit", na.y.action = "omit")
testthat::expect_equal(ncol(fit[[cart]]$predictions), 2)
testthat::expect_equal(nrow(fit[[cart]]$predictions), nrows[[cart]])
}
fitC <- vector(mode = "list", length = 0)
nrows <- list(6,4,5,3,2,6,1,1)
names(nrows) <- carts
for (cart in carts)
{
fitC[[cart]] <- smoothSpline(subset(leaf.dat, Snapshot.ID.Tag == cart),
response = "Length.3", response.smoothed = "sLength.3",
x="xDays", correctBoundaries = TRUE,
df = 4, na.x.action = "omit", na.y.action = "omit")
testthat::expect_equal(ncol(fitC[[cart]]$predictions), 2)
testthat::expect_equal(nrow(fitC[[cart]]$predictions), nrows[[cart]])
}
testthat::expect_true(all(abs(fit[["047162-C"]]$sLength.3 -
fitC[["047162-C"]]$sLength.3) > 0.01))
testthat::expect_true(all(abs(fit[["047164-S"]]$sLength.3 -
fitC[["047164-S"]]$sLength.3) < 1e-05))
})
cat("#### Test byIndv4Times_SplinesGRs using NCSS with leaf data for log-smoothing\n")
test_that("leaf_growthPheno", {
skip_if_not_installed("growthPheno")
skip_on_cran()
library(dae)
library(ggplot2)
library(growthPheno)
# A small subset of Exp 270 leaf tracking data
data(testSpline)
test$Days[is.na(test$xDays)] <- NA
##Smooth splines using identity and logarithm transformations - exclude y
leaf.dat <- test
leaf.dat$Area.log <- log(leaf.dat$Area)
#Investigate AGR and RGR calculations
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat, response="Area", times = "Days",
df = 4, smoothing.method = "log",
rates.method = "deriv",
suffices.rates = c("AGRdv", "RGRdv"),
na.y.action = "excl")
names(leaf.dat)[(match(c("sArea", "sArea.AGRdv","sArea.RGRdv"),
names(leaf.dat)))] <- paste(c("sArea", "sArea.AGRdv",
"sArea.RGRdv"), "log", sep = ".")
testthat::expect_equal(sum(is.na(leaf.dat$sArea.log)), 3)
testthat::expect_false(any(abs(leaf.dat$sArea.AGRdv.log[1:3] -
c(2.993617, 3.682534, 4.568932)) > 1e-03,
na.rm = TRUE))
testthat::expect_false(any(abs(leaf.dat$sArea.RGRdv.log[1:3] -
c(0.1878992, 0.1913271, 0.1955440)) > 1e-03,
na.rm = TRUE))
#Manual calculation of log smooth
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat, response = "Area.log", times = "Days",
df = 4, rates.method = "none")
leaf.dat$sArea.log <- exp(leaf.dat$sArea.log)
testthat::expect_false(any(abs(leaf.dat$sArea.log - leaf.dat$sArea.log) > 0.1,
na.rm = TRUE))
testthat::expect_equal(sum(is.na(leaf.dat$sArea.log)), 3)
#identity smoothing scale calculation of AGR and RGR
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat, response="Area", times = "Days",
df = 4, rates.method = "deriv",
suffices.rates = c("AGRdv", "RGRdv"))
testthat::expect_false(any(abs(leaf.dat$sArea[1:3] -
c(14.48536, 18.89667, 23.69953)) > 1e-03,
na.rm = TRUE))
testthat::expect_false(any(abs(leaf.dat$sArea.AGRdv[1:3] -
c(4.341943, 4.550298, 5.099377)) > 1e-03,
na.rm = TRUE))
testthat::expect_false(any(abs(leaf.dat$sArea.RGRdv[1:3] -
c(0.2997469, 0.2407990, 0.2151678)) > 1e-03,
na.rm = TRUE))
##Smooth splines using log-smoothing and rates.method = "deriv", with second deriv
leaf.dat <- test
#Investigate AGR and RGR calculations
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat, response="Area", times = "Days",
df = 4, smoothing.method = "log",
rates.method = "deriv",
suffices.rates = c("AGRdv", "RGRdv"),
extra.derivs = 2, suffices.extra.derivs = "Acc")
testthat::expect_equal(sum(is.na(leaf.dat$sArea)), 3)
testthat::expect_false(any(abs(leaf.dat$sArea.AGRdv[1:3] -
c(2.993617, 3.682534, 4.568932)) > 1e-03,
na.rm = TRUE))
testthat::expect_false(any(abs(leaf.dat$sArea.RGRdv[1:3] -
c(0.1878992, 0.1913271, 0.1955440)) > 1e-03,
na.rm = TRUE))
})
cat("#### Test correctBoundaries for NCSS in smoothSpline using a single plant from Rice germplasm\n")
test_that("area_correctBoundaries", {
skip_if_not_installed("growthPheno")
skip_on_cran()
library(dae)
library(ggplot2)
library(growthPheno)
data(area.dat)
fity <- smooth.spline(area.dat$xDays,area.dat$Area1,cv=FALSE)
fit <- as.data.frame(fity[1:2])
fit$AGR <- c(NA, diff(fit$y)/diff(fit$x))
fit$RGR <- c(NA, diff(log(fit$y))/diff(fit$x))
fit$yC <- smoothSpline(area.dat, x = "xDays",
response = "Area1", response.smoothed = "Area1.smooth",
correctBoundaries = TRUE)$predictions$Area1.smooth
ggplot(fit) + geom_line(aes(x=x, y=y)) + geom_line(aes(x=x, y=yC), colour = "red")
fit$AGRC <- c(NA, diff(fit$yC)/diff(fit$x))
fit$RGRC <- c(NA, diff(log(fit$yC))/diff(fit$x))
ggplot(fit) + geom_line(aes(x=x, y=AGR)) + geom_line(aes(x=x, y=AGRC), colour = "red")
ggplot(fit) + geom_line(aes(x=x, y=RGR)) + geom_line(aes(x=x, y=RGRC), colour = "red")
testthat::expect_true(abs(var(fit$yC) - 66391.75) < 1e-02)
testthat::expect_true(abs(var(fit$AGRC, na.rm = TRUE) - 153.9782) < 1e-03)
testthat::expect_true(abs(var(fit$RGRC, na.rm = TRUE) - 0.0009603766) < 1e-05)
#specify df
fit <- area.dat
fit$Area1.smooth <- smoothSpline(area.dat, x = "xDays",
response = "Area1", response.smoothed = "Area1.smooth",
df = 4,
correctBoundaries = FALSE)$predictions$Area1.smooth
ggplot(fit) + geom_line(aes(x=xDays, y=Area1)) + geom_line(aes(x=xDays, y=Area1.smooth),
colour = "blue")
fit$AGR <- c(NA, diff(fit$Area1.smooth)/diff(fit$xDays))
fit$RGR <- c(NA, diff(log(fit$Area1.smooth))/diff(fit$xDays))
ggplot(fit) + geom_line(aes(x=xDays, y=Area1.AGR)) + geom_line(aes(x=xDays, y=AGR),colour = "blue")
ggplot(fit) + geom_line(aes(x=xDays, y=Area1.RGR)) + geom_line(aes(x=xDays, y=RGR),colour = "blue")
testthat::expect_true(abs(var(fit$Area1.smooth) - 65264.71) < 1e-02)
testthat::expect_true(abs(var(fit$AGR, na.rm = TRUE) - 123.8462) < 1e-03)
testthat::expect_true(abs(var(fit$RGR, na.rm = TRUE) - 0.005474027) < 1e-03)
#Correct the boundaries
fit$Area1.smooth.C <- smoothSpline(area.dat, x = "xDays",
response = "Area1", response.smoothed = "Area1.smooth",
df = 4,
correctBoundaries = TRUE)$predictions$Area1.smooth
ggplot(fit) + geom_line(aes(x=xDays, y=Area1)) +
geom_line(aes(x=xDays, y=Area1.smooth),colour = "blue") +
geom_line(aes(x=xDays, y=Area1.smooth.C), colour = "red")
fit$AGRC <- c(NA, diff(fit$Area1.smooth.C)/diff(fit$xDays))
fit$RGRC <- c(NA, diff(log(fit$Area1.smooth.C))/diff(fit$xDays))
ggplot(fit) + geom_line(aes(x=xDays, y=Area1.AGR)) +
geom_line(aes(x=xDays, y=AGR), colour = "blue") +
geom_line(aes(x=xDays, y=AGRC), colour = "red")
ggplot(fit) + geom_line(aes(x=xDays, y=Area1.RGR)) +
geom_line(aes(x=xDays, y=RGR), colour = "blue") +
geom_line(aes(x=xDays, y=RGRC), colour = "red")
testthat::expect_true(abs(var(fit$Area1.smooth.C) - 66372.73) < 1e-02)
testthat::expect_true(abs(var(fit$AGRC, na.rm = TRUE) - 145.0717) < 1e-03)
testthat::expect_true(abs(var(fit$RGRC, na.rm = TRUE) - 0.000893429) < 1e-04)
})
cat("#### Test byIndv4Times_SplinesGRs using PS with leaf data when there are missing values\n")
test_that("leaf_growthPheno", {
skip_if_not_installed("growthPheno")
skip_on_cran()
library(dae)
library(ggplot2)
library(growthPheno)
# A small subset of Exp 270 leaf tracking data
data(testSpline)
test$Days[is.na(test$xDays)] <- NA
responses <- names(test)[5:ncol(test)]
##Test the fail options for PS
testthat::expect_error(byIndv4Times_SplinesGRs(data = test, response = "Area", times = "Days",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
rates.method = "none", na.x.action = "fail"))
testthat::expect_error(byIndv4Times_SplinesGRs(data = test, response = "Length.1", times = "Days",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
rates.method = "none", na.y.action = "fail"))
##Fit some splines - exclude y
leaf.dat <- test
resp <- responses[2]
testthat::expect_warning(
for (resp in responses)
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat,
response = resp, times = "Days",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
rates.method = "none", na.y.action = "exclude"),
regexp = "Need at least 4 distinct x values to fit a spline - all fitted values set to NA")
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.1)), 82)
testthat::expect_equal(sum(is.na(leaf.dat$sArea)), 3)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.3[13:24])), 4)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.3[49:60])), 0)
##trim
leaf.dat <- test
testthat::expect_warning(
for (resp in responses)
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat, response = resp, times = "Days",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
rates.method = "none", na.y.action = "trim"),
regexp = "Need at least 4 distinct x values to fit a spline - all fitted values set to NA")
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.1)), 86)
testthat::expect_lt(abs(leaf.dat$sLength.1[57] - 11.07072), 1e-05)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.3[13:24])), 4)
##Test ltrimx
leaf.dat <- test
for (resp in responses)
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat, response = resp, times = "Days",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
na.y.action = "ltrim",
rates.method = "deriv",
suffices.rates = c("AGRdv", "RGRdv"))
testthat::expect_equal(length(lapply(responses,
function(resp, data)
{
resp <- paste(resp,"smooth", sep = ".")
testthat::expect_equal(sum(is.na(data[[resp]])),
sum(is.na(data[[paste(resp,"AGRdv",sep = ".")]])),
sum(is.na(data[[paste(resp,"RGRdv",sep = ".")]])))
}, data = leaf.dat)), 4)
testthat::expect_equal(nrow(leaf.dat), 96)
testthat::expect_equal(ncol(leaf.dat), 20)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.1)), 87)
testthat::expect_lt(abs(leaf.dat$sLength.1[57] - 11.07072), 1e-05)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.3[13:24])), 7)
leaf.dat.noC <- leaf.dat
##Test ltrimx with correctBoundaries (which is ignored)
leaf.dat <- test
for (resp in responses)
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat, response = resp, times = "Days",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
rates.method = "none", na.y.action = "ltrim",
correctBoundaries = TRUE)
testthat::expect_equal(nrow(leaf.dat), 96)
testthat::expect_equal(ncol(leaf.dat), 12)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.1)), 87)
testthat::expect_lt(abs(leaf.dat$sLength.1[57] - 11.07072), 1e-05)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.3[13:24])), 7)
##Test utrimx
leaf.dat <- test
for (resp in responses)
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat, response = resp, times = "Days",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
rates.method = "none", na.y.action = "utrim")
testthat::expect_equal(nrow(leaf.dat), 96)
testthat::expect_equal(ncol(leaf.dat), 12)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.1)), 92)
testthat::expect_lt(abs(leaf.dat$sLength.1[57] - 11.02593), 1e-05)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.3[13:24])), 9)
##Test utrimx
leaf.dat <- test
for (resp in responses)
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat, response = resp, times = "Days",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
rates.method = "none", na.y.action = "allx")
testthat::expect_equal(nrow(leaf.dat), 96)
testthat::expect_equal(ncol(leaf.dat), 12)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.1)), 93)
testthat::expect_lt(abs(leaf.dat$sLength.1[57] - 11.02593), 1e-05)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.3[13:24])), 12)
testthat::expect_equal(sum(is.na(leaf.dat$sLength.3[94:96])), 3)
##Test omit in smoothSpline - Length 3
leaf.dat <- test
carts <- levels(leaf.dat$Snapshot.ID.Tag)
fit <- vector(mode = "list", length = 0)
nrows <- vector(mode = "list", length = length(carts))
nrows <- list(6,4,5,3,2,6,1,1)
names(nrows) <- carts
for (cart in carts)
{
fit[[cart]] <- smoothSpline(subset(leaf.dat, Snapshot.ID.Tag == cart),
response = "Length.3", response.smoothed = "sLength.3",
x="xDays",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
na.x.action = "omi", na.y.action = "omit",
deriv=1, suffices.deriv="AGRdv",
extra.rate = c(RGRdv = "RGR"))
testthat::expect_equal(nrows[[cart]], nrow(fit[[cart]]$predictions))
}
##Test omit in smoothSpline - Length 2 with a 0 length data.frame
fit <- list()
nrows <- list(11,12,12,12,9,12,0,9)
names(nrows) <- carts
for (cart in carts)
{
fit[[cart]] <- smoothSpline(subset(leaf.dat, Snapshot.ID.Tag == cart),
response = "Length.2", response.smoothed = "sLength.2",
x="xDays",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
na.x.action = "omi", na.y.action = "omit",
rates = c("AGR", "RGR"),
suffices.rates = c("AGRdv", "RGRdv"))
testthat::expect_equal(nrows[[cart]], nrow(fit[[cart]]$predictions))
}
testthat::expect_equal(ncol(fit[[cart]]$predictions), 4)
##Test omit in byIndv4Times_SplinesGRs - get full data.frame because of merge in byIndv4Times_SplinesGRs
leaf.dat <- test
for (resp in responses)
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat, response = resp, times = "Days",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
rates.method = "none",
na.x.action = "omi", na.y.action = "omit")
testthat::expect_equal(nrow(leaf.dat), 96)
testthat::expect_equal(ncol(leaf.dat), 12)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.1)), 82)
leaf.dat <- test
for (resp in responses)
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat, response = resp, times = "Days",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
rates.method = "none", na.y.action = "omit")
##Test omit in smoothSpline - Length 2 with a 0 length data.frame
leaf.dat <- test
carts <- levels(leaf.dat$Snapshot.ID.Tag)
fit <- vector(mode = "list", length = 0)
nrows <- list(6,4,5,3,2,6,1,1)
names(nrows) <- carts
for (cart in carts)
{
fit[[cart]] <- smoothSpline(subset(leaf.dat, Snapshot.ID.Tag == cart),
response = "Length.3", response.smoothed = "sLength.3",
x="xDays", correctBoundaries = FALSE,
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
na.x.action = "omit", na.y.action = "omit")
testthat::expect_equal(ncol(fit[[cart]]$predictions), 2)
testthat::expect_equal(nrow(fit[[cart]]$predictions), nrows[[cart]])
}
fitC <- vector(mode = "list", length = 0)
nrows <- list(6,4,5,3,2,6,1,1)
names(nrows) <- carts
for (cart in carts)
{
fitC[[cart]] <- smoothSpline(subset(leaf.dat, Snapshot.ID.Tag == cart),
response = "Length.3", response.smoothed = "sLength.3",
x="xDays",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
na.x.action = "omit", na.y.action = "omit")
testthat::expect_equal(ncol(fitC[[cart]]$predictions), 2)
testthat::expect_equal(nrow(fitC[[cart]]$predictions), nrows[[cart]])
}
})
cat("#### Test byIndv4Times_SplinesGRs using PS with leaf data, including log-smoothing\n")
test_that("leaf_growthPheno", {
skip_if_not_installed("growthPheno")
skip_on_cran()
library(dae)
library(ggplot2)
library(growthPheno)
# A small subset of Exp 270 leaf tracking data
data(testSpline)
test$Days[is.na(test$xDays)] <- NA
##Smooth splines using identity and logarithm transformations - exclude y
leaf.dat <- test
leaf.dat$Area.log <- log(leaf.dat$Area)
#Investigate AGR and RGR calculations
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat,
response="Area", response.smoothed = "Area.smooth",
times = "Days",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
smoothing.method = "log",
rates.method = "deriv",
suffices.rates = c("AGRdv", "RGRdv"))
names(leaf.dat)[(match(c("Area.smooth", "Area.smooth.AGRdv","Area.smooth.RGRdv"),
names(leaf.dat)))] <- paste(c("Area.smooth", "Area.smooth.AGRdv",
"Area.smooth.RGRdv"), "log", sep = ".")
testthat::expect_equal(sum(is.na(leaf.dat$Area.smooth.log)), 3)
testthat::expect_false(any(abs(leaf.dat$Area.smooth.AGRdv.log[1:3] -
c(3.009742, 3.704214, 4.556166)) > 1e-03,
na.rm = TRUE))
testthat::expect_false(any(abs(leaf.dat$Area.smooth.RGRdv.log[1:3] -
c(0.1893088, 0.1924901, 0.1950459)) > 1e-03,
na.rm = TRUE))
#Manual calculation of log smooth
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat,
response = "Area.log", response.smoothed = "Area.log.smooth",
times = "Days",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
rates.method = "none")
leaf.dat$Area.log.smooth <- exp(leaf.dat$Area.log.smooth)
testthat::expect_false(any(abs(leaf.dat$Area.log.smooth - leaf.dat$Area.smooth.log) > 0.1,
na.rm = TRUE))
testthat::expect_equal(sum(is.na(leaf.dat$Area.log.smooth)), 3)
#identity smoothing scale calculation of AGR and RGR
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat,
response="Area", response.smoothed = "Area.smooth",
times = "Days",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
rates.method = "deriv",
suffices.rates = c("AGRdv", "RGRdv"))
testthat::expect_false(any(abs(leaf.dat$Area.smooth[1:3] -
c(14.89518, 18.97489, 23.57340)) > 1e-03,
na.rm = TRUE))
testthat::expect_false(any(abs(leaf.dat$Area.smooth.AGRdv[1:3] -
c(3.910074, 4.294226, 4.947678)) > 1e-03,
na.rm = TRUE))
testthat::expect_false(any(abs(leaf.dat$Area.smooth.RGRdv[1:3] -
c(0.2625059, 0.2263110, 0.2098839)) > 1e-03,
na.rm = TRUE))
#identity smoothing scale calculation of AGR and RGR - default calculation of npspline.segments
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat,
response="Area", response.smoothed = "Area.smooth",
times = "Days",
spline.type = "PS", lambda = 0.1,
rates.method = "deriv",
suffices.rates = c("AGRdv", "RGRdv"))
testthat::expect_false(any(abs(leaf.dat$Area.smooth[1:3] -
c(16.07077, 18.99996, 22.99637)) > 1e-03,
na.rm = TRUE))
testthat::expect_false(any(abs(leaf.dat$Area.smooth.AGRdv[1:3] -
c(2.599351, 3.367556, 4.687257)) > 1e-03,
na.rm = TRUE))
testthat::expect_false(any(abs(leaf.dat$Area.smooth.RGRdv[1:3] -
c(0.1617440, 0.1772402, 0.2038260)) > 1e-03,
na.rm = TRUE))
})
cat("#### Test smoothSpline using PS with leaf data when there are missing values\n")
test_that("leaf_growthPheno", {
skip_if_not_installed("growthPheno")
skip_on_cran()
library(dae)
library(ggplot2)
library(growthPheno)
# A small subset of Exp 270 leaf tracking data
data(testSpline)
test$Days[is.na(test$xDays)] <- NA
responses <- names(test)[5:ncol(test)]
leaf.dat <- test
##Check the contents of the fit.spline object for PS
carts <- levels(leaf.dat$Snapshot.ID.Tag)
fit <- smoothSpline(subset(leaf.dat, Snapshot.ID.Tag == carts),
response = "Length.2", response.smoothed = "Length.2.smooth",
x="xDays",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
na.x.action = "exclude", na.y.action = "allx",
rates = c("AGR", "RGR"),
suffices.rates = c("AGRdv", "RGRdv"))
testthat::expect_true(all(c(fit$fit.spline$lambda, fit$fit.spline$uncorrected.fit$lambda) == 0.1))
testthat::expect_true(all(c(fit$fit.spline$npspline.segments, fit$fit.spline$uncorrected.fit$npspline.segments) == 4))
testthat::expect_true(all((c(fit$fit.spline$df, fit$fit.spline$uncorrected.fit$effdim) -3.816562) < 1e-04))
testthat::expect_equal(length(subset(leaf.dat, Snapshot.ID.Tag == carts)$Length.2) -
length(fit$fit.spline$x) , 1)
testthat::expect_equal(length(subset(leaf.dat, Snapshot.ID.Tag == carts)$Length.2) -
length(fit$fit.spline$uncorrected.fit$xgrid) , 1)
})
cat("#### Test byIndv4Times_SplinesGRs with small example\n")
test_that("exampleData_byIndv4Times_SplinesGRs", {
skip_if_not_installed("growthPheno")
skip_on_cran()
library(growthPheno)
data(exampleData)
#Segmented smoothing
t <- byIndv4Times_SplinesGRs(data = longi.dat,
response = "PSA", response.smoothed = "sPSA",
times = "DAP",
smoothing.segments = list(c(28,34), c(35,42)),
df = 5, rates.method = "none")
testthat::expect_equal(nrow(t), 280)
testthat::expect_equal(ncol(t), 37)
testthat::expect_true(all(unique(t$DAP) == c(28, 30:42)))
testthat::expect_false(all(abs(t$sPSA-longi.dat$sPSA) < 1e-04))
testthat::expect_silent(
plotProfiles(t, x = "DAP", response = "sPSA",
facet.y = "Treatment.1", alpha = 0.75,
y.title = "sPSA (kpixels)",
ggplotFuncs = list(ggplot2::geom_vline(xintercept=35, linetype="longdash",
alpha = 0.5, size=0.75, colour = "blue"))))
#smooth = direct, rates.methods = "none
dat <- longi.dat[,-match(c("sPSA.AGR", "sPSA.RGR"), names(longi.dat))]
testthat::expect_silent(
t <- byIndv4Times_SplinesGRs(data = dat, response="sPSA",
times = "DAP",
rates.method = "none", df = 4))
testthat::expect_equal(nrow(t), 280)
testthat::expect_equal(ncol(t), 36)
#smooth = direct, rates.methods = "deriv", which.rates = AGR & RGR
testthat::expect_silent(
all.rates <- byIndv4Times_SplinesGRs(data = dat, response="PSA",
times = "DAP",
rates.method = "deriv", which.rates = c("AGR","RGR"),
df = 4))
testthat::expect_equal(nrow(all.rates), 280)
testthat::expect_equal(ncol(all.rates), 37)
testthat::expect_true(any(abs(all.rates$sPSA.AGR[1:3] -
c(17.78304, 19.16926, 20.99404)) < 1e-03))
testthat::expect_true(any(abs(all.rates$sPSA.RGR[1:3] -
c(0.3474298, 0.2186439, 0.1949627)) < 1e-05))
#smooth = direct, rates.methods = "deriv", which.rates = AGR
testthat::expect_silent(
t <- byIndv4Times_SplinesGRs(data = dat, response="PSA",
times = "DAP",
rates.method = "deriv", which.rates = "AGR",
df = 4))
testthat::expect_equal(nrow(t), 280)
testthat::expect_equal(ncol(t), 36)
testthat::expect_true(any(abs(t$sPSA.AGR - all.rates$sPSA.AGR) < 1e-05))
#smooth = direct, rates.methods = "deriv", which.rates = RGR
testthat::expect_silent(
t <- byIndv4Times_SplinesGRs(data = dat, response="PSA",
times = "DAP",
rates.method = "deriv", which.rates = "RGR",
df = 4))
testthat::expect_equal(nrow(t), 280)
testthat::expect_equal(ncol(t), 36)
testthat::expect_true(any(abs(t$sPSA.RGR - all.rates$sPSA.RGR) < 1e-05))
#smooth = log, rates.methods = "none
dat <- longi.dat[,-match(c("sPSA.AGR", "sPSA.RGR"), names(longi.dat))]
testthat::expect_silent(
t <- byIndv4Times_SplinesGRs(data = dat, response="PSA",
times = "DAP",
rates.method = "none",
smoothing.method = "log", df = 4))
testthat::expect_equal(nrow(t), 280)
testthat::expect_equal(ncol(t), 35)
#smooth = log, rates.methods = "deriv", which.rates = AGR & RGR
dat <- longi.dat[,-match(c("sPSA.AGR", "sPSA.RGR"), names(longi.dat))]
testthat::expect_silent(
all.rates <- byIndv4Times_SplinesGRs(data = dat, response="PSA",
times = "DAP",
rates.method = "deriv", which.rates = c("AGR","RGR"),
smoothing.method = "log", df = 4))
testthat::expect_equal(nrow(all.rates), 280)
testthat::expect_equal(ncol(all.rates), 37)
testthat::expect_true(any(abs(all.rates$sPSA.AGR[1:3] -
c(11.65445, 16.87781, 19.97875)) < 1e-03))
testthat::expect_true(any(abs(all.rates$sPSA.RGR[1:3] -
c(0.1986342, 0.1939544, 0.1895384)) < 1e-05))
#smooth = log, rates.methods = "deriv", which.rates = AGR
testthat::expect_silent(
t <- byIndv4Times_SplinesGRs(data = dat, response="PSA",
times = "DAP",
rates.method = "deriv", which.rates = "AGR",
smoothing.method = "log", df = 4))
testthat::expect_equal(nrow(t), 280)
testthat::expect_equal(ncol(t), 36)
testthat::expect_true(any(abs(t$sPSA.AGR - all.rates$sPSA.AGR) < 1e-05))
#smooth = log, rates.methods = "deriv", which.rates = RGR
testthat::expect_silent(
t <- byIndv4Times_SplinesGRs(data = dat, response="PSA",
times = "DAP",
rates.method = "deriv", which.rates = "RGR",
smoothing.method = "log", df = 4))
testthat::expect_equal(nrow(t), 280)
testthat::expect_equal(ncol(t), 36)
testthat::expect_true(any(abs(t$sPSA.RGR - all.rates$sPSA.RGR) < 1e-05))
#smooth = direct, rates.methods = "deriv", which.rates = AGR & RGR, P-splines
testthat::expect_silent(
all.rates <- byIndv4Times_SplinesGRs(data = dat, response="PSA",
times = "DAP",
rates.method = "deriv", which.rates = c("AGR","RGR"),
spline.type = "PS", lambda = 1))
testthat::expect_equal(nrow(all.rates), 280)
testthat::expect_equal(ncol(all.rates), 37)
testthat::expect_true(any(abs(all.rates$sPSA.AGR[1:3] -
c(15.77705, 18.01763, 20.59344)) < 1e-03))
testthat::expect_true(any(abs(all.rates$sPSA.RGR[1:3] -
c(0.2886963, 0.2051182, 0.1923348)) < 1e-05))
#smooth = direct, rates.methods = "deriv", which.rates = AGR, P-splines
testthat::expect_silent(
t <- byIndv4Times_SplinesGRs(data = dat, response="PSA",
times = "DAP",
rates.method = "deriv", which.rates = "AGR",
spline.type = "PS", lambda = 1))
testthat::expect_equal(nrow(t), 280)
testthat::expect_equal(ncol(t), 36)
testthat::expect_true(any(abs(t$sPSA.AGR - all.rates$sPSA.AGR) < 1e-05))
#smooth = direct, rates.methods = "deriv", which.rates = RGR
testthat::expect_silent(
t <- byIndv4Times_SplinesGRs(data = dat, response="PSA",
times = "DAP",
rates.method = "deriv", which.rates = "RGR",
spline.type = "PS", lambda = 1))
testthat::expect_equal(nrow(t), 280)
testthat::expect_equal(ncol(t), 36)
testthat::expect_true(any(abs(t$sPSA.RGR - all.rates$sPSA.RGR) < 1e-05))
#Fitting an extra.derivs
testthat::expect_silent(
t <- byIndv4Times_SplinesGRs(data = longi.dat, response="PSA",
times = "DAP",
rates.method = "deriv", df = 4,
extra.derivs = 2, suffices.extra.derivs = "Accel"))
testthat::expect_equal(nrow(t), 280)
testthat::expect_equal(ncol(t), 38)
testthat::expect_true(all(c("sPSA","sPSA.AGR","sPSA.RGR",
"sPSA.Accel") %in% names(t)))
testthat::expect_true(any(abs(t$sPSA.AGR[1:3] -
c(17.78304, 19.16926, 20.99404)) < 1e-03))
testthat::expect_true(any(abs(t$sPSA.RGR[1:3] -
c(0.3474298, 0.2186439, 0.1949627)) < 1e-05))
testthat::expect_true(any(abs(t$sPSA.Accel[1:3] -
c(-0.002044201, 1.388259633, 2.261297448)) < 1e-05))
#Calculate 2nd deriv by differencing the AGR and compare with deriv =2 using r
t <- byIndv4Times_GRsDiff(data = t, response="sPSA.AGR", times = "DAP",
which.rates = "AGR", suffices.rates = "Acc",
ntimes2span = 3)
testthat::expect_true(abs(cor(na.omit(t[c("sPSA.Accel", "sPSA.AGR.Acc")]))[1,2] -
0.9965408) < 1e-05)
#Calculate 2nd deriv using PS to compare with NCSS
#Fitting an extra.derivs
testthat::expect_silent(
PS <- byIndv4Times_SplinesGRs(data = longi.dat, response="PSA",
times = "DAP",
spline.type = "PS", lambda = 1,
rates.method = "deriv",
extra.derivs = 2, suffices.extra.derivs = "Accel"))
testthat::expect_equal(nrow(PS), 280)
testthat::expect_equal(ncol(PS), 38)
testthat::expect_true(all(c("sPSA","sPSA.AGR","sPSA.RGR",
"sPSA.Accel") %in% names(t)))
testthat::expect_true(any(abs(PS$sPSA.AGR[1:3] -
c(15.77705, 18.01763, 20.59344)) < 1e-03))
testthat::expect_true(any(abs(PS$sPSA.RGR[1:3] -
c(0.2886963, 0.2051182, 0.1923348)) < 1e-05))
testthat::expect_true(any(abs(PS$sPSA.Accel[1:3] -
c(0.2378153, 2.0798768, 2.8410223)) < 1e-05))
testthat::expect_true(abs(
cor(na.omit(data.frame(NCSS = t$sPSA.Accel, PS = PS$sPSA.Accel)))[1,2] - 0.9721318) < 1e-05)
})
briencj/growthPheno documentation built on April 14, 2025, 6:17 p.m.
R Package Documentation
Browse R Packages
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
cat("#### Test spline fitting using NCSS with leaf data when there are missing values\n")
test_that("leaf_growthPheno", {
skip_if_not_installed("growthPheno")
skip_on_cran()
library(dae)
library(ggplot2)
library(growthPheno)
# A small subset of Exp 270 leaf tracking data
data(testSpline)
#Set Days to NA to match xDays
test$Days[is.na(test$xDays)] <- NA
responses <- names(test)[5:ncol(test)]
##Test the fail options for NCSS
testthat::expect_error(byIndv4Times_SplinesGRs(data = test, response = "Area", times="Days",
individuals = "Snapshot.ID.Tag",
df = 4, na.x.action = "fail"))
testthat::expect_error(byIndv4Times_SplinesGRs(data = test, response = "Length.1",
individuals = "Snapshot.ID.Tag", times="Days",
df = 4, na.y.action = "fail"))
##Fit some splines - exclude y
leaf.dat <- test
testthat::expect_warning(
for (resp in responses)
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat, response = resp,
times="Days", df = 4),
regexp = "Need at least 4 distinct x values to fit a spline - all fitted values set to NA")
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.1)), 86)
testthat::expect_equal(sum(is.na(leaf.dat$sArea)), 3)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.3[13:24])), 4)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.3[49:60])), 0)
##trim
leaf.dat <- test
for (resp in responses)
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat, response = resp, times = "Days",
df = 4, na.y.action = "trim")
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.1)), 86)
testthat::expect_lt(abs(leaf.dat$sLength.1[57] - 11.067455), 1e-05)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.3[13:24])), 4)
##Test ltrimx
leaf.dat <- test
for (resp in responses)
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat, response = resp, times = "Days",
df = 4, na.y.action = "ltrim",
rates.method = "deriv",
suffices.rates = c("AGRdv", "RGRdv"))
testthat::expect_equal(length(lapply(responses,
function(resp, data)
{
resp <- paste0("s", resp)
testthat::expect_equal(sum(is.na(data[[resp]])),
sum(is.na(data[[paste(resp,"AGRdv",sep = ".")]])),
sum(is.na(data[[paste(resp,"RGRdv",sep = ".")]])))
}, data = leaf.dat)), 4)
testthat::expect_equal(nrow(leaf.dat), 96)
testthat::expect_equal(ncol(leaf.dat), 20)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.1)), 87)
testthat::expect_lt(abs(leaf.dat$sLength.1[57] - 11.067455), 1e-05)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.3[13:24])), 7)
leaf.dat.noC <- leaf.dat
##Test ltrimx with correctBoundaries
# - need to use xDays as Days causes correctBoundaries to go singular???
leaf.dat <- test
for (resp in responses)
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat, response = resp, times = "xDays",
df = 4, rates.method = "none",
na.y.action = "ltrim",
correctBoundaries = TRUE)
testthat::expect_equal(nrow(leaf.dat), 96)
testthat::expect_equal(ncol(leaf.dat), 12)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.1)), 87)
testthat::expect_lt(abs(leaf.dat$sLength.1[57] - 11.05895), 1e-05)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.3[13:24])), 7)
leaf.dat$sLength.1.noC <- leaf.dat.noC$sLength.1
leaf.dat$sLength.2.noC <- leaf.dat.noC$sLength.2
leaf.dat$sLength.3.noC <- leaf.dat.noC$sLength.3
ggplot(leaf.dat, aes(x = xDays, y = Length.1)) +
geom_line() + geom_line(aes(x = xDays, sLength.1), colour = "blue") +
geom_line(aes(x = xDays, sLength.1.noC), colour = "red") +
facet_wrap(~ Snapshot.ID.Tag)
##Test utrimx
leaf.dat <- test
for (resp in responses)
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat, response = resp, times = "Days",
df = 4, rates.method = "none",
na.y.action = "utrim")
testthat::expect_equal(nrow(leaf.dat), 96)
testthat::expect_equal(ncol(leaf.dat), 12)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.1)), 92)
testthat::expect_lt(abs(leaf.dat$sLength.1[57] - 11.067455), 1e-05)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.3[13:24])), 9)
##Test utrimx
leaf.dat <- test
for (resp in responses)
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat, response = resp, times = "Days",
df = 4, rates.method = "none",
na.y.action = "allx")
testthat::expect_equal(nrow(leaf.dat), 96)
testthat::expect_equal(ncol(leaf.dat), 12)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.1)), 93)
testthat::expect_lt(abs(leaf.dat$sLength.1[57] - 11.067455), 1e-05)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.3[13:24])), 12)
testthat::expect_equal(sum(is.na(leaf.dat$sLength.3[94:96])), 3)
##Test omit in smoothSpline - Length 3
leaf.dat <- test
carts <- levels(leaf.dat$Snapshot.ID.Tag)
fit <- vector(mode = "list", length = 0)
nrows <- vector(mode = "list", length = length(carts))
nrows <- list(6,4,5,3,2,6,1,1)
names(nrows) <- carts
for (cart in carts)
{
fit[[cart]] <- smoothSpline(subset(leaf.dat, Snapshot.ID.Tag == cart),
response = "Length.3", response.smoothed = "sLength.3",
x = "xDays",
df = 4, na.x.action = "omi", na.y.action = "omit",
rates = c("AGR", "RGR"),
suffices.rates=c("AGRdv", "RGRdv"))
testthat::expect_equal(nrows[[cart]], nrow(fit[[cart]]$predictions))
}
##Test omit in smoothSpline - Length 2 with a 0 length data.frame
fit <- vector(mode = "list", length = 0)
nrows <- list(11,12,12,12,9,12,0,9)
names(nrows) <- carts
for (cart in carts)
{
fit[[cart]] <- smoothSpline(subset(leaf.dat, Snapshot.ID.Tag == cart),
response = "Length.2", response.smoothed = "sLength.2",
x = "xDays",
df = 4, na.x.action = "omi", na.y.action = "omit",
rates = c("AGR", "RGR"),
suffices.rates=c("AGRdv", "RGRdv"))
testthat::expect_equal(nrows[[cart]], nrow(fit[[cart]]$predictions))
}
testthat::expect_equal(ncol(fit[[cart]]$predictions), 4)
##Test omit in byIndv4Times_SplinesGRs - get full data.frame because of merge in byIndv4Times_SplinesGRs
leaf.dat <- test
for (resp in responses)
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat, response = resp, times = "Days",
df = 4, rates.method = "none",
na.x.action = "omi", na.y.action = "omit")
testthat::expect_equal(nrow(leaf.dat), 96)
testthat::expect_equal(ncol(leaf.dat), 12)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.1)), 82)
leaf.dat <- test
for (resp in responses)
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat, response = resp, times = "Days",
df = 4, rates.method = "none", na.y.action = "omit")
##Test omit in smoothSpline - Length 2 with a 0 length data.frame
leaf.dat <- test
carts <- levels(leaf.dat$Snapshot.ID.Tag)
fit <- vector(mode = "list", length = 0)
nrows <- list(6,4,5,3,2,6,1,1)
names(nrows) <- carts
for (cart in carts)
{
fit[[cart]] <- smoothSpline(subset(leaf.dat, Snapshot.ID.Tag == cart),
response = "Length.3", response.smoothed = "sLength.3",
x="xDays", correctBoundaries = FALSE,
df = 4, na.x.action = "omit", na.y.action = "omit")
testthat::expect_equal(ncol(fit[[cart]]$predictions), 2)
testthat::expect_equal(nrow(fit[[cart]]$predictions), nrows[[cart]])
}
fitC <- vector(mode = "list", length = 0)
nrows <- list(6,4,5,3,2,6,1,1)
names(nrows) <- carts
for (cart in carts)
{
fitC[[cart]] <- smoothSpline(subset(leaf.dat, Snapshot.ID.Tag == cart),
response = "Length.3", response.smoothed = "sLength.3",
x="xDays", correctBoundaries = TRUE,
df = 4, na.x.action = "omit", na.y.action = "omit")
testthat::expect_equal(ncol(fitC[[cart]]$predictions), 2)
testthat::expect_equal(nrow(fitC[[cart]]$predictions), nrows[[cart]])
}
testthat::expect_true(all(abs(fit[["047162-C"]]$sLength.3 -
fitC[["047162-C"]]$sLength.3) > 0.01))
testthat::expect_true(all(abs(fit[["047164-S"]]$sLength.3 -
fitC[["047164-S"]]$sLength.3) < 1e-05))
})
cat("#### Test byIndv4Times_SplinesGRs using NCSS with leaf data for log-smoothing\n")
test_that("leaf_growthPheno", {
skip_if_not_installed("growthPheno")
skip_on_cran()
library(dae)
library(ggplot2)
library(growthPheno)
# A small subset of Exp 270 leaf tracking data
data(testSpline)
test$Days[is.na(test$xDays)] <- NA
##Smooth splines using identity and logarithm transformations - exclude y
leaf.dat <- test
leaf.dat$Area.log <- log(leaf.dat$Area)
#Investigate AGR and RGR calculations
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat, response="Area", times = "Days",
df = 4, smoothing.method = "log",
rates.method = "deriv",
suffices.rates = c("AGRdv", "RGRdv"),
na.y.action = "excl")
names(leaf.dat)[(match(c("sArea", "sArea.AGRdv","sArea.RGRdv"),
names(leaf.dat)))] <- paste(c("sArea", "sArea.AGRdv",
"sArea.RGRdv"), "log", sep = ".")
testthat::expect_equal(sum(is.na(leaf.dat$sArea.log)), 3)
testthat::expect_false(any(abs(leaf.dat$sArea.AGRdv.log[1:3] -
c(2.993617, 3.682534, 4.568932)) > 1e-03,
na.rm = TRUE))
testthat::expect_false(any(abs(leaf.dat$sArea.RGRdv.log[1:3] -
c(0.1878992, 0.1913271, 0.1955440)) > 1e-03,
na.rm = TRUE))
#Manual calculation of log smooth
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat, response = "Area.log", times = "Days",
df = 4, rates.method = "none")
leaf.dat$sArea.log <- exp(leaf.dat$sArea.log)
testthat::expect_false(any(abs(leaf.dat$sArea.log - leaf.dat$sArea.log) > 0.1,
na.rm = TRUE))
testthat::expect_equal(sum(is.na(leaf.dat$sArea.log)), 3)
#identity smoothing scale calculation of AGR and RGR
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat, response="Area", times = "Days",
df = 4, rates.method = "deriv",
suffices.rates = c("AGRdv", "RGRdv"))
testthat::expect_false(any(abs(leaf.dat$sArea[1:3] -
c(14.48536, 18.89667, 23.69953)) > 1e-03,
na.rm = TRUE))
testthat::expect_false(any(abs(leaf.dat$sArea.AGRdv[1:3] -
c(4.341943, 4.550298, 5.099377)) > 1e-03,
na.rm = TRUE))
testthat::expect_false(any(abs(leaf.dat$sArea.RGRdv[1:3] -
c(0.2997469, 0.2407990, 0.2151678)) > 1e-03,
na.rm = TRUE))
##Smooth splines using log-smoothing and rates.method = "deriv", with second deriv
leaf.dat <- test
#Investigate AGR and RGR calculations
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat, response="Area", times = "Days",
df = 4, smoothing.method = "log",
rates.method = "deriv",
suffices.rates = c("AGRdv", "RGRdv"),
extra.derivs = 2, suffices.extra.derivs = "Acc")
testthat::expect_equal(sum(is.na(leaf.dat$sArea)), 3)
testthat::expect_false(any(abs(leaf.dat$sArea.AGRdv[1:3] -
c(2.993617, 3.682534, 4.568932)) > 1e-03,
na.rm = TRUE))
testthat::expect_false(any(abs(leaf.dat$sArea.RGRdv[1:3] -
c(0.1878992, 0.1913271, 0.1955440)) > 1e-03,
na.rm = TRUE))
})
cat("#### Test correctBoundaries for NCSS in smoothSpline using a single plant from Rice germplasm\n")
test_that("area_correctBoundaries", {
skip_if_not_installed("growthPheno")
skip_on_cran()
library(dae)
library(ggplot2)
library(growthPheno)
data(area.dat)
fity <- smooth.spline(area.dat$xDays,area.dat$Area1,cv=FALSE)
fit <- as.data.frame(fity[1:2])
fit$AGR <- c(NA, diff(fit$y)/diff(fit$x))
fit$RGR <- c(NA, diff(log(fit$y))/diff(fit$x))
fit$yC <- smoothSpline(area.dat, x = "xDays",
response = "Area1", response.smoothed = "Area1.smooth",
correctBoundaries = TRUE)$predictions$Area1.smooth
ggplot(fit) + geom_line(aes(x=x, y=y)) + geom_line(aes(x=x, y=yC), colour = "red")
fit$AGRC <- c(NA, diff(fit$yC)/diff(fit$x))
fit$RGRC <- c(NA, diff(log(fit$yC))/diff(fit$x))
ggplot(fit) + geom_line(aes(x=x, y=AGR)) + geom_line(aes(x=x, y=AGRC), colour = "red")
ggplot(fit) + geom_line(aes(x=x, y=RGR)) + geom_line(aes(x=x, y=RGRC), colour = "red")
testthat::expect_true(abs(var(fit$yC) - 66391.75) < 1e-02)
testthat::expect_true(abs(var(fit$AGRC, na.rm = TRUE) - 153.9782) < 1e-03)
testthat::expect_true(abs(var(fit$RGRC, na.rm = TRUE) - 0.0009603766) < 1e-05)
#specify df
fit <- area.dat
fit$Area1.smooth <- smoothSpline(area.dat, x = "xDays",
response = "Area1", response.smoothed = "Area1.smooth",
df = 4,
correctBoundaries = FALSE)$predictions$Area1.smooth
ggplot(fit) + geom_line(aes(x=xDays, y=Area1)) + geom_line(aes(x=xDays, y=Area1.smooth),
colour = "blue")
fit$AGR <- c(NA, diff(fit$Area1.smooth)/diff(fit$xDays))
fit$RGR <- c(NA, diff(log(fit$Area1.smooth))/diff(fit$xDays))
ggplot(fit) + geom_line(aes(x=xDays, y=Area1.AGR)) + geom_line(aes(x=xDays, y=AGR),colour = "blue")
ggplot(fit) + geom_line(aes(x=xDays, y=Area1.RGR)) + geom_line(aes(x=xDays, y=RGR),colour = "blue")
testthat::expect_true(abs(var(fit$Area1.smooth) - 65264.71) < 1e-02)
testthat::expect_true(abs(var(fit$AGR, na.rm = TRUE) - 123.8462) < 1e-03)
testthat::expect_true(abs(var(fit$RGR, na.rm = TRUE) - 0.005474027) < 1e-03)
#Correct the boundaries
fit$Area1.smooth.C <- smoothSpline(area.dat, x = "xDays",
response = "Area1", response.smoothed = "Area1.smooth",
df = 4,
correctBoundaries = TRUE)$predictions$Area1.smooth
ggplot(fit) + geom_line(aes(x=xDays, y=Area1)) +
geom_line(aes(x=xDays, y=Area1.smooth),colour = "blue") +
geom_line(aes(x=xDays, y=Area1.smooth.C), colour = "red")
fit$AGRC <- c(NA, diff(fit$Area1.smooth.C)/diff(fit$xDays))
fit$RGRC <- c(NA, diff(log(fit$Area1.smooth.C))/diff(fit$xDays))
ggplot(fit) + geom_line(aes(x=xDays, y=Area1.AGR)) +
geom_line(aes(x=xDays, y=AGR), colour = "blue") +
geom_line(aes(x=xDays, y=AGRC), colour = "red")
ggplot(fit) + geom_line(aes(x=xDays, y=Area1.RGR)) +
geom_line(aes(x=xDays, y=RGR), colour = "blue") +
geom_line(aes(x=xDays, y=RGRC), colour = "red")
testthat::expect_true(abs(var(fit$Area1.smooth.C) - 66372.73) < 1e-02)
testthat::expect_true(abs(var(fit$AGRC, na.rm = TRUE) - 145.0717) < 1e-03)
testthat::expect_true(abs(var(fit$RGRC, na.rm = TRUE) - 0.000893429) < 1e-04)
})
cat("#### Test byIndv4Times_SplinesGRs using PS with leaf data when there are missing values\n")
test_that("leaf_growthPheno", {
skip_if_not_installed("growthPheno")
skip_on_cran()
library(dae)
library(ggplot2)
library(growthPheno)
# A small subset of Exp 270 leaf tracking data
data(testSpline)
test$Days[is.na(test$xDays)] <- NA
responses <- names(test)[5:ncol(test)]
##Test the fail options for PS
testthat::expect_error(byIndv4Times_SplinesGRs(data = test, response = "Area", times = "Days",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
rates.method = "none", na.x.action = "fail"))
testthat::expect_error(byIndv4Times_SplinesGRs(data = test, response = "Length.1", times = "Days",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
rates.method = "none", na.y.action = "fail"))
##Fit some splines - exclude y
leaf.dat <- test
resp <- responses[2]
testthat::expect_warning(
for (resp in responses)
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat,
response = resp, times = "Days",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
rates.method = "none", na.y.action = "exclude"),
regexp = "Need at least 4 distinct x values to fit a spline - all fitted values set to NA")
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.1)), 82)
testthat::expect_equal(sum(is.na(leaf.dat$sArea)), 3)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.3[13:24])), 4)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.3[49:60])), 0)
##trim
leaf.dat <- test
testthat::expect_warning(
for (resp in responses)
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat, response = resp, times = "Days",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
rates.method = "none", na.y.action = "trim"),
regexp = "Need at least 4 distinct x values to fit a spline - all fitted values set to NA")
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.1)), 86)
testthat::expect_lt(abs(leaf.dat$sLength.1[57] - 11.07072), 1e-05)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.3[13:24])), 4)
##Test ltrimx
leaf.dat <- test
for (resp in responses)
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat, response = resp, times = "Days",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
na.y.action = "ltrim",
rates.method = "deriv",
suffices.rates = c("AGRdv", "RGRdv"))
testthat::expect_equal(length(lapply(responses,
function(resp, data)
{
resp <- paste(resp,"smooth", sep = ".")
testthat::expect_equal(sum(is.na(data[[resp]])),
sum(is.na(data[[paste(resp,"AGRdv",sep = ".")]])),
sum(is.na(data[[paste(resp,"RGRdv",sep = ".")]])))
}, data = leaf.dat)), 4)
testthat::expect_equal(nrow(leaf.dat), 96)
testthat::expect_equal(ncol(leaf.dat), 20)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.1)), 87)
testthat::expect_lt(abs(leaf.dat$sLength.1[57] - 11.07072), 1e-05)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.3[13:24])), 7)
leaf.dat.noC <- leaf.dat
##Test ltrimx with correctBoundaries (which is ignored)
leaf.dat <- test
for (resp in responses)
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat, response = resp, times = "Days",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
rates.method = "none", na.y.action = "ltrim",
correctBoundaries = TRUE)
testthat::expect_equal(nrow(leaf.dat), 96)
testthat::expect_equal(ncol(leaf.dat), 12)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.1)), 87)
testthat::expect_lt(abs(leaf.dat$sLength.1[57] - 11.07072), 1e-05)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.3[13:24])), 7)
##Test utrimx
leaf.dat <- test
for (resp in responses)
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat, response = resp, times = "Days",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
rates.method = "none", na.y.action = "utrim")
testthat::expect_equal(nrow(leaf.dat), 96)
testthat::expect_equal(ncol(leaf.dat), 12)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.1)), 92)
testthat::expect_lt(abs(leaf.dat$sLength.1[57] - 11.02593), 1e-05)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.3[13:24])), 9)
##Test utrimx
leaf.dat <- test
for (resp in responses)
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat, response = resp, times = "Days",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
rates.method = "none", na.y.action = "allx")
testthat::expect_equal(nrow(leaf.dat), 96)
testthat::expect_equal(ncol(leaf.dat), 12)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.1)), 93)
testthat::expect_lt(abs(leaf.dat$sLength.1[57] - 11.02593), 1e-05)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.3[13:24])), 12)
testthat::expect_equal(sum(is.na(leaf.dat$sLength.3[94:96])), 3)
##Test omit in smoothSpline - Length 3
leaf.dat <- test
carts <- levels(leaf.dat$Snapshot.ID.Tag)
fit <- vector(mode = "list", length = 0)
nrows <- vector(mode = "list", length = length(carts))
nrows <- list(6,4,5,3,2,6,1,1)
names(nrows) <- carts
for (cart in carts)
{
fit[[cart]] <- smoothSpline(subset(leaf.dat, Snapshot.ID.Tag == cart),
response = "Length.3", response.smoothed = "sLength.3",
x="xDays",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
na.x.action = "omi", na.y.action = "omit",
deriv=1, suffices.deriv="AGRdv",
extra.rate = c(RGRdv = "RGR"))
testthat::expect_equal(nrows[[cart]], nrow(fit[[cart]]$predictions))
}
##Test omit in smoothSpline - Length 2 with a 0 length data.frame
fit <- list()
nrows <- list(11,12,12,12,9,12,0,9)
names(nrows) <- carts
for (cart in carts)
{
fit[[cart]] <- smoothSpline(subset(leaf.dat, Snapshot.ID.Tag == cart),
response = "Length.2", response.smoothed = "sLength.2",
x="xDays",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
na.x.action = "omi", na.y.action = "omit",
rates = c("AGR", "RGR"),
suffices.rates = c("AGRdv", "RGRdv"))
testthat::expect_equal(nrows[[cart]], nrow(fit[[cart]]$predictions))
}
testthat::expect_equal(ncol(fit[[cart]]$predictions), 4)
##Test omit in byIndv4Times_SplinesGRs - get full data.frame because of merge in byIndv4Times_SplinesGRs
leaf.dat <- test
for (resp in responses)
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat, response = resp, times = "Days",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
rates.method = "none",
na.x.action = "omi", na.y.action = "omit")
testthat::expect_equal(nrow(leaf.dat), 96)
testthat::expect_equal(ncol(leaf.dat), 12)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$sLength.1)), 82)
leaf.dat <- test
for (resp in responses)
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat, response = resp, times = "Days",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
rates.method = "none", na.y.action = "omit")
##Test omit in smoothSpline - Length 2 with a 0 length data.frame
leaf.dat <- test
carts <- levels(leaf.dat$Snapshot.ID.Tag)
fit <- vector(mode = "list", length = 0)
nrows <- list(6,4,5,3,2,6,1,1)
names(nrows) <- carts
for (cart in carts)
{
fit[[cart]] <- smoothSpline(subset(leaf.dat, Snapshot.ID.Tag == cart),
response = "Length.3", response.smoothed = "sLength.3",
x="xDays", correctBoundaries = FALSE,
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
na.x.action = "omit", na.y.action = "omit")
testthat::expect_equal(ncol(fit[[cart]]$predictions), 2)
testthat::expect_equal(nrow(fit[[cart]]$predictions), nrows[[cart]])
}
fitC <- vector(mode = "list", length = 0)
nrows <- list(6,4,5,3,2,6,1,1)
names(nrows) <- carts
for (cart in carts)
{
fitC[[cart]] <- smoothSpline(subset(leaf.dat, Snapshot.ID.Tag == cart),
response = "Length.3", response.smoothed = "sLength.3",
x="xDays",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
na.x.action = "omit", na.y.action = "omit")
testthat::expect_equal(ncol(fitC[[cart]]$predictions), 2)
testthat::expect_equal(nrow(fitC[[cart]]$predictions), nrows[[cart]])
}
})
cat("#### Test byIndv4Times_SplinesGRs using PS with leaf data, including log-smoothing\n")
test_that("leaf_growthPheno", {
skip_if_not_installed("growthPheno")
skip_on_cran()
library(dae)
library(ggplot2)
library(growthPheno)
# A small subset of Exp 270 leaf tracking data
data(testSpline)
test$Days[is.na(test$xDays)] <- NA
##Smooth splines using identity and logarithm transformations - exclude y
leaf.dat <- test
leaf.dat$Area.log <- log(leaf.dat$Area)
#Investigate AGR and RGR calculations
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat,
response="Area", response.smoothed = "Area.smooth",
times = "Days",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
smoothing.method = "log",
rates.method = "deriv",
suffices.rates = c("AGRdv", "RGRdv"))
names(leaf.dat)[(match(c("Area.smooth", "Area.smooth.AGRdv","Area.smooth.RGRdv"),
names(leaf.dat)))] <- paste(c("Area.smooth", "Area.smooth.AGRdv",
"Area.smooth.RGRdv"), "log", sep = ".")
testthat::expect_equal(sum(is.na(leaf.dat$Area.smooth.log)), 3)
testthat::expect_false(any(abs(leaf.dat$Area.smooth.AGRdv.log[1:3] -
c(3.009742, 3.704214, 4.556166)) > 1e-03,
na.rm = TRUE))
testthat::expect_false(any(abs(leaf.dat$Area.smooth.RGRdv.log[1:3] -
c(0.1893088, 0.1924901, 0.1950459)) > 1e-03,
na.rm = TRUE))
#Manual calculation of log smooth
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat,
response = "Area.log", response.smoothed = "Area.log.smooth",
times = "Days",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
rates.method = "none")
leaf.dat$Area.log.smooth <- exp(leaf.dat$Area.log.smooth)
testthat::expect_false(any(abs(leaf.dat$Area.log.smooth - leaf.dat$Area.smooth.log) > 0.1,
na.rm = TRUE))
testthat::expect_equal(sum(is.na(leaf.dat$Area.log.smooth)), 3)
#identity smoothing scale calculation of AGR and RGR
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat,
response="Area", response.smoothed = "Area.smooth",
times = "Days",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
rates.method = "deriv",
suffices.rates = c("AGRdv", "RGRdv"))
testthat::expect_false(any(abs(leaf.dat$Area.smooth[1:3] -
c(14.89518, 18.97489, 23.57340)) > 1e-03,
na.rm = TRUE))
testthat::expect_false(any(abs(leaf.dat$Area.smooth.AGRdv[1:3] -
c(3.910074, 4.294226, 4.947678)) > 1e-03,
na.rm = TRUE))
testthat::expect_false(any(abs(leaf.dat$Area.smooth.RGRdv[1:3] -
c(0.2625059, 0.2263110, 0.2098839)) > 1e-03,
na.rm = TRUE))
#identity smoothing scale calculation of AGR and RGR - default calculation of npspline.segments
leaf.dat <- byIndv4Times_SplinesGRs(data = leaf.dat,
response="Area", response.smoothed = "Area.smooth",
times = "Days",
spline.type = "PS", lambda = 0.1,
rates.method = "deriv",
suffices.rates = c("AGRdv", "RGRdv"))
testthat::expect_false(any(abs(leaf.dat$Area.smooth[1:3] -
c(16.07077, 18.99996, 22.99637)) > 1e-03,
na.rm = TRUE))
testthat::expect_false(any(abs(leaf.dat$Area.smooth.AGRdv[1:3] -
c(2.599351, 3.367556, 4.687257)) > 1e-03,
na.rm = TRUE))
testthat::expect_false(any(abs(leaf.dat$Area.smooth.RGRdv[1:3] -
c(0.1617440, 0.1772402, 0.2038260)) > 1e-03,
na.rm = TRUE))
})
cat("#### Test smoothSpline using PS with leaf data when there are missing values\n")
test_that("leaf_growthPheno", {
skip_if_not_installed("growthPheno")
skip_on_cran()
library(dae)
library(ggplot2)
library(growthPheno)
# A small subset of Exp 270 leaf tracking data
data(testSpline)
test$Days[is.na(test$xDays)] <- NA
responses <- names(test)[5:ncol(test)]
leaf.dat <- test
##Check the contents of the fit.spline object for PS
carts <- levels(leaf.dat$Snapshot.ID.Tag)
fit <- smoothSpline(subset(leaf.dat, Snapshot.ID.Tag == carts),
response = "Length.2", response.smoothed = "Length.2.smooth",
x="xDays",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
na.x.action = "exclude", na.y.action = "allx",
rates = c("AGR", "RGR"),
suffices.rates = c("AGRdv", "RGRdv"))
testthat::expect_true(all(c(fit$fit.spline$lambda, fit$fit.spline$uncorrected.fit$lambda) == 0.1))
testthat::expect_true(all(c(fit$fit.spline$npspline.segments, fit$fit.spline$uncorrected.fit$npspline.segments) == 4))
testthat::expect_true(all((c(fit$fit.spline$df, fit$fit.spline$uncorrected.fit$effdim) -3.816562) < 1e-04))
testthat::expect_equal(length(subset(leaf.dat, Snapshot.ID.Tag == carts)$Length.2) -
length(fit$fit.spline$x) , 1)
testthat::expect_equal(length(subset(leaf.dat, Snapshot.ID.Tag == carts)$Length.2) -
length(fit$fit.spline$uncorrected.fit$xgrid) , 1)
})
cat("#### Test byIndv4Times_SplinesGRs with small example\n")
test_that("exampleData_byIndv4Times_SplinesGRs", {
skip_if_not_installed("growthPheno")
skip_on_cran()
library(growthPheno)
data(exampleData)
#Segmented smoothing
t <- byIndv4Times_SplinesGRs(data = longi.dat,
response = "PSA", response.smoothed = "sPSA",
times = "DAP",
smoothing.segments = list(c(28,34), c(35,42)),
df = 5, rates.method = "none")
testthat::expect_equal(nrow(t), 280)
testthat::expect_equal(ncol(t), 37)
testthat::expect_true(all(unique(t$DAP) == c(28, 30:42)))
testthat::expect_false(all(abs(t$sPSA-longi.dat$sPSA) < 1e-04))
testthat::expect_silent(
plotProfiles(t, x = "DAP", response = "sPSA",
facet.y = "Treatment.1", alpha = 0.75,
y.title = "sPSA (kpixels)",
ggplotFuncs = list(ggplot2::geom_vline(xintercept=35, linetype="longdash",
alpha = 0.5, size=0.75, colour = "blue"))))
#smooth = direct, rates.methods = "none
dat <- longi.dat[,-match(c("sPSA.AGR", "sPSA.RGR"), names(longi.dat))]
testthat::expect_silent(
t <- byIndv4Times_SplinesGRs(data = dat, response="sPSA",
times = "DAP",
rates.method = "none", df = 4))
testthat::expect_equal(nrow(t), 280)
testthat::expect_equal(ncol(t), 36)
#smooth = direct, rates.methods = "deriv", which.rates = AGR & RGR
testthat::expect_silent(
all.rates <- byIndv4Times_SplinesGRs(data = dat, response="PSA",
times = "DAP",
rates.method = "deriv", which.rates = c("AGR","RGR"),
df = 4))
testthat::expect_equal(nrow(all.rates), 280)
testthat::expect_equal(ncol(all.rates), 37)
testthat::expect_true(any(abs(all.rates$sPSA.AGR[1:3] -
c(17.78304, 19.16926, 20.99404)) < 1e-03))
testthat::expect_true(any(abs(all.rates$sPSA.RGR[1:3] -
c(0.3474298, 0.2186439, 0.1949627)) < 1e-05))
#smooth = direct, rates.methods = "deriv", which.rates = AGR
testthat::expect_silent(
t <- byIndv4Times_SplinesGRs(data = dat, response="PSA",
times = "DAP",
rates.method = "deriv", which.rates = "AGR",
df = 4))
testthat::expect_equal(nrow(t), 280)
testthat::expect_equal(ncol(t), 36)
testthat::expect_true(any(abs(t$sPSA.AGR - all.rates$sPSA.AGR) < 1e-05))
#smooth = direct, rates.methods = "deriv", which.rates = RGR
testthat::expect_silent(
t <- byIndv4Times_SplinesGRs(data = dat, response="PSA",
times = "DAP",
rates.method = "deriv", which.rates = "RGR",
df = 4))
testthat::expect_equal(nrow(t), 280)
testthat::expect_equal(ncol(t), 36)
testthat::expect_true(any(abs(t$sPSA.RGR - all.rates$sPSA.RGR) < 1e-05))
#smooth = log, rates.methods = "none
dat <- longi.dat[,-match(c("sPSA.AGR", "sPSA.RGR"), names(longi.dat))]
testthat::expect_silent(
t <- byIndv4Times_SplinesGRs(data = dat, response="PSA",
times = "DAP",
rates.method = "none",
smoothing.method = "log", df = 4))
testthat::expect_equal(nrow(t), 280)
testthat::expect_equal(ncol(t), 35)
#smooth = log, rates.methods = "deriv", which.rates = AGR & RGR
dat <- longi.dat[,-match(c("sPSA.AGR", "sPSA.RGR"), names(longi.dat))]
testthat::expect_silent(
all.rates <- byIndv4Times_SplinesGRs(data = dat, response="PSA",
times = "DAP",
rates.method = "deriv", which.rates = c("AGR","RGR"),
smoothing.method = "log", df = 4))
testthat::expect_equal(nrow(all.rates), 280)
testthat::expect_equal(ncol(all.rates), 37)
testthat::expect_true(any(abs(all.rates$sPSA.AGR[1:3] -
c(11.65445, 16.87781, 19.97875)) < 1e-03))
testthat::expect_true(any(abs(all.rates$sPSA.RGR[1:3] -
c(0.1986342, 0.1939544, 0.1895384)) < 1e-05))
#smooth = log, rates.methods = "deriv", which.rates = AGR
testthat::expect_silent(
t <- byIndv4Times_SplinesGRs(data = dat, response="PSA",
times = "DAP",
rates.method = "deriv", which.rates = "AGR",
smoothing.method = "log", df = 4))
testthat::expect_equal(nrow(t), 280)
testthat::expect_equal(ncol(t), 36)
testthat::expect_true(any(abs(t$sPSA.AGR - all.rates$sPSA.AGR) < 1e-05))
#smooth = log, rates.methods = "deriv", which.rates = RGR
testthat::expect_silent(
t <- byIndv4Times_SplinesGRs(data = dat, response="PSA",
times = "DAP",
rates.method = "deriv", which.rates = "RGR",
smoothing.method = "log", df = 4))
testthat::expect_equal(nrow(t), 280)
testthat::expect_equal(ncol(t), 36)
testthat::expect_true(any(abs(t$sPSA.RGR - all.rates$sPSA.RGR) < 1e-05))
#smooth = direct, rates.methods = "deriv", which.rates = AGR & RGR, P-splines
testthat::expect_silent(
all.rates <- byIndv4Times_SplinesGRs(data = dat, response="PSA",
times = "DAP",
rates.method = "deriv", which.rates = c("AGR","RGR"),
spline.type = "PS", lambda = 1))
testthat::expect_equal(nrow(all.rates), 280)
testthat::expect_equal(ncol(all.rates), 37)
testthat::expect_true(any(abs(all.rates$sPSA.AGR[1:3] -
c(15.77705, 18.01763, 20.59344)) < 1e-03))
testthat::expect_true(any(abs(all.rates$sPSA.RGR[1:3] -
c(0.2886963, 0.2051182, 0.1923348)) < 1e-05))
#smooth = direct, rates.methods = "deriv", which.rates = AGR, P-splines
testthat::expect_silent(
t <- byIndv4Times_SplinesGRs(data = dat, response="PSA",
times = "DAP",
rates.method = "deriv", which.rates = "AGR",
spline.type = "PS", lambda = 1))
testthat::expect_equal(nrow(t), 280)
testthat::expect_equal(ncol(t), 36)
testthat::expect_true(any(abs(t$sPSA.AGR - all.rates$sPSA.AGR) < 1e-05))
#smooth = direct, rates.methods = "deriv", which.rates = RGR
testthat::expect_silent(
t <- byIndv4Times_SplinesGRs(data = dat, response="PSA",
times = "DAP",
rates.method = "deriv", which.rates = "RGR",
spline.type = "PS", lambda = 1))
testthat::expect_equal(nrow(t), 280)
testthat::expect_equal(ncol(t), 36)
testthat::expect_true(any(abs(t$sPSA.RGR - all.rates$sPSA.RGR) < 1e-05))
#Fitting an extra.derivs
testthat::expect_silent(
t <- byIndv4Times_SplinesGRs(data = longi.dat, response="PSA",
times = "DAP",
rates.method = "deriv", df = 4,
extra.derivs = 2, suffices.extra.derivs = "Accel"))
testthat::expect_equal(nrow(t), 280)
testthat::expect_equal(ncol(t), 38)
testthat::expect_true(all(c("sPSA","sPSA.AGR","sPSA.RGR",
"sPSA.Accel") %in% names(t)))
testthat::expect_true(any(abs(t$sPSA.AGR[1:3] -
c(17.78304, 19.16926, 20.99404)) < 1e-03))
testthat::expect_true(any(abs(t$sPSA.RGR[1:3] -
c(0.3474298, 0.2186439, 0.1949627)) < 1e-05))
testthat::expect_true(any(abs(t$sPSA.Accel[1:3] -
c(-0.002044201, 1.388259633, 2.261297448)) < 1e-05))
#Calculate 2nd deriv by differencing the AGR and compare with deriv =2 using r
t <- byIndv4Times_GRsDiff(data = t, response="sPSA.AGR", times = "DAP",
which.rates = "AGR", suffices.rates = "Acc",
ntimes2span = 3)
testthat::expect_true(abs(cor(na.omit(t[c("sPSA.Accel", "sPSA.AGR.Acc")]))[1,2] -
0.9965408) < 1e-05)
#Calculate 2nd deriv using PS to compare with NCSS
#Fitting an extra.derivs
testthat::expect_silent(
PS <- byIndv4Times_SplinesGRs(data = longi.dat, response="PSA",
times = "DAP",
spline.type = "PS", lambda = 1,
rates.method = "deriv",
extra.derivs = 2, suffices.extra.derivs = "Accel"))
testthat::expect_equal(nrow(PS), 280)
testthat::expect_equal(ncol(PS), 38)
testthat::expect_true(all(c("sPSA","sPSA.AGR","sPSA.RGR",
"sPSA.Accel") %in% names(t)))
testthat::expect_true(any(abs(PS$sPSA.AGR[1:3] -
c(15.77705, 18.01763, 20.59344)) < 1e-03))
testthat::expect_true(any(abs(PS$sPSA.RGR[1:3] -
c(0.2886963, 0.2051182, 0.1923348)) < 1e-05))
testthat::expect_true(any(abs(PS$sPSA.Accel[1:3] -
c(0.2378153, 2.0798768, 2.8410223)) < 1e-05))
testthat::expect_true(abs(
cor(na.omit(data.frame(NCSS = t$sPSA.Accel, PS = PS$sPSA.Accel)))[1,2] - 0.9721318) < 1e-05)
})
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