Nothing
tests/testthat/testSplines.r
In growthPheno: Functional Analysis of Phenotypic Growth Data to Smooth and Extract Traits
#### This set of tests, including those involving fitSpline, can be removed when splitSplines is deprecated.
## splitSplines is the only function that calls fitSpline.
## All of these tests have been converted to use smoothSpline and byIndv4Times_SplinesGRs.
cat("#### Test fitSpline 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)
responses <- names(test)[5:ncol(test)]
##Test the fail options for NCSS
testthat::expect_error(splitSplines(test, response = "Area", x="xDays",
individuals = "Snapshot.ID.Tag",
df = 4, na.x.action = "fail"))
testthat::expect_error(splitSplines(test, response = "Length.1", x="xDays",
individuals = "Snapshot.ID.Tag",
df = 4, na.y.action = "fail"))
##Fit some splines - exclude y
leaf.dat <- test
testthat::expect_warning(
for (resp in responses)
leaf.dat <- splitSplines(leaf.dat, response = resp, x="xDays", 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$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1.smooth)), 82)
testthat::expect_equal(sum(is.na(leaf.dat$Area.smooth)), 3)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.3.smooth[13:24])), 4)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.3.smooth[49:60])), 0)
##trim
leaf.dat <- test
for (resp in responses)
leaf.dat <- splitSplines(leaf.dat, response = resp, x="xDays",
df = 4, na.y.action = "trim")
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1.smooth)), 86)
testthat::expect_lt(abs(leaf.dat$Length.1.smooth[57] - 11.067455), 1e-05)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.3.smooth[13:24])), 4)
##Test ltrimx
leaf.dat <- test
for (resp in responses)
leaf.dat <- splitSplines(leaf.dat, response = resp, x="xDays",
df = 4, na.y.action = "ltrim",
deriv=1, suffices.deriv="AGRdv",
extra.rate = c(RGRdv = "RGR"))
testthat::expect_equal(length(lapply(responses,
function(resp, data)
{
resp <- paste(resp,"smooth", sep = ".")
testthat::expect_equal(sum(is.na(data[[resp]])),
sum(is.na(data[[paste(resp,"AGRdv",sep = ".")]])),
sum(is.na(data[[paste(resp,"RGRdv",sep = ".")]])))
}, data = leaf.dat)), 4)
testthat::expect_equal(nrow(leaf.dat), 96)
testthat::expect_equal(ncol(leaf.dat), 20)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1.smooth)), 87)
testthat::expect_lt(abs(leaf.dat$Length.1.smooth[57] - 11.067455), 1e-05)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.3.smooth[13:24])), 7)
leaf.dat.noC <- leaf.dat
##Test ltrimx with correctBoundaries
leaf.dat <- test
for (resp in responses)
leaf.dat <- splitSplines(leaf.dat, response = resp, x="xDays",
df = 4, na.y.action = "ltrim",
correctBoundaries = TRUE)
testthat::expect_equal(nrow(leaf.dat), 96)
testthat::expect_equal(ncol(leaf.dat), 12)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1.smooth)), 87)
testthat::expect_lt(abs(leaf.dat$Length.1.smooth[57] - 11.05895), 1e-05)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.3.smooth[13:24])), 7)
leaf.dat$Length.1.smooth.noC <- leaf.dat.noC$Length.1.smooth
leaf.dat$Length.2.smooth.noC <- leaf.dat.noC$Length.2.smooth
leaf.dat$Length.3.smooth.noC <- leaf.dat.noC$Length.3.smooth
ggplot(leaf.dat, aes(x = xDays, y = Length.1)) +
geom_line() + geom_line(aes(x = xDays, Length.1.smooth), colour = "blue") +
geom_line(aes(x = xDays, Length.1.smooth.noC), colour = "red") +
facet_wrap(~ Snapshot.ID.Tag)
##Test utrimx
leaf.dat <- test
for (resp in responses)
leaf.dat <- splitSplines(leaf.dat, response = resp, x="xDays",
df = 4, na.y.action = "utrim")
testthat::expect_equal(nrow(leaf.dat), 96)
testthat::expect_equal(ncol(leaf.dat), 12)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1.smooth)), 92)
testthat::expect_lt(abs(leaf.dat$Length.1.smooth[57] - 11.067455), 1e-05)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.3.smooth[13:24])), 9)
##Test utrimx
leaf.dat <- test
for (resp in responses)
leaf.dat <- splitSplines(leaf.dat, response = resp, x="xDays",
df = 4, na.y.action = "allx")
testthat::expect_equal(nrow(leaf.dat), 96)
testthat::expect_equal(ncol(leaf.dat), 12)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1.smooth)), 93)
testthat::expect_lt(abs(leaf.dat$Length.1.smooth[57] - 11.067455), 1e-05)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.3.smooth[13:24])), 12)
testthat::expect_equal(sum(is.na(leaf.dat$Length.3.smooth[94:96])), 3)
##Test omit in fitSpline - Length 3
leaf.dat <- test
carts <- levels(leaf.dat$Snapshot.ID.Tag)
fit <- vector(mode = "list", length = 0)
nrows <- vector(mode = "list", length = length(carts))
nrows <- list(6,4,5,3,2,6,1,1)
names(nrows) <- carts
for (cart in carts)
{
fit[[cart]] <- fitSpline(subset(leaf.dat, Snapshot.ID.Tag == cart),
response = "Length.3", response.smoothed = "sLength.3",
x="xDays",
df = 4, na.x.action = "omi", na.y.action = "omit",
deriv=1, suffices.deriv="AGRdv",
extra.rate = c(RGRdv = "RGR"))
testthat::expect_equal(nrows[[cart]], nrow(fit[[cart]]$predictions))
}
##Test omit in fitSpline - 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]] <- fitSpline(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",
deriv=1, suffices.deriv="AGRdv",
extra.rate = c(RGRdv = "RGR"))
testthat::expect_equal(nrows[[cart]], nrow(fit[[cart]]$predictions))
}
testthat::expect_equal(ncol(fit[[cart]]$predictions), 4)
##Test omit in splitSplines - get full data.frame because of merge in splitSplines
leaf.dat <- test
for (resp in responses)
leaf.dat <- splitSplines(leaf.dat, response = resp, x="xDays",
df = 4,
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$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1.smooth)), 82)
leaf.dat <- test
for (resp in responses)
leaf.dat <- splitSplines(leaf.dat, response = resp, x="xDays",
df = 4, na.y.action = "omit")
##Test omit in fitSpline - Length 2 with a 0 length data.frame
leaf.dat <- test
carts <- levels(leaf.dat$Snapshot.ID.Tag)
fit <- vector(mode = "list", length = 0)
nrows <- list(6,4,5,3,2,6,1,1)
names(nrows) <- carts
for (cart in carts)
{
fit[[cart]] <- fitSpline(subset(leaf.dat, Snapshot.ID.Tag == cart),
response = "Length.3", response.smoothed = "sLength.3",
x="xDays", correctBoundaries = FALSE,
df = 4, na.x.action = "omit", na.y.action = "omit")
testthat::expect_equal(ncol(fit[[cart]]$predictions), 2)
testthat::expect_equal(nrow(fit[[cart]]$predictions), nrows[[cart]])
}
fitC <- vector(mode = "list", length = 0)
nrows <- list(6,4,5,3,2,6,1,1)
names(nrows) <- carts
for (cart in carts)
{
fitC[[cart]] <- fitSpline(subset(leaf.dat, Snapshot.ID.Tag == cart),
response = "Length.3", response.smoothed = "sLength.3",
x="xDays", correctBoundaries = TRUE,
df = 4, na.x.action = "omit", na.y.action = "omit")
testthat::expect_equal(ncol(fitC[[cart]]$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"]]$sLength.3) < 1e-05))
})
cat("#### Test fitSpline using NCSS with leaf data for log-smoothing\n")
test_that("leaf_growthPheno", {
skip_if_not_installed("growthPheno")
skip_on_cran()
library(dae)
library(ggplot2)
library(growthPheno)
# A small subset of Exp 270 leaf tracking data
data(testSpline)
##Smooth splines using identity and logarithm transformations - exclude y
leaf.dat <- test
leaf.dat$Area.log <- log(leaf.dat$Area)
#Investigate AGR and RGR calculations
leaf.dat <- splitSplines(leaf.dat, response="Area", x="xDays",
df = 4, smoothing.method = "log",
deriv=1, suffices.deriv="RGRdv",
extra.rate = c(AGRdv = "AGR"))
names(leaf.dat)[(match(c("Area.smooth", "Area.smooth.AGRdv","Area.smooth.RGRdv"),
names(leaf.dat)))] <- paste(c("Area.smooth", "Area.smooth.AGRdv",
"Area.smooth.RGRdv"), "log", sep = ".")
testthat::expect_equal(sum(is.na(leaf.dat$Area.smooth.log)), 3)
testthat::expect_false(any(abs(leaf.dat$Area.smooth.AGRdv.log[1:3] -
c(2.993617, 3.682534, 4.568932)) > 1e-03,
na.rm = TRUE))
testthat::expect_false(any(abs(leaf.dat$Area.smooth.RGRdv.log[1:3] -
c(0.1878992, 0.1913271, 0.1955440)) > 1e-03,
na.rm = TRUE))
#Manual calculation of log smooth
leaf.dat <- splitSplines(leaf.dat, response = "Area.log", x="xDays",
df = 4)
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$Area.log.smooth)), 3)
#identity smoothing scale calculation of AGR and RGR
leaf.dat <- splitSplines(leaf.dat, response="Area", x="xDays",
df = 4, deriv=1, suffices.deriv="AGRdv",
extra.rate = c(RGRdv = "RGR"))
testthat::expect_false(any(abs(leaf.dat$Area.smooth[1:3] -
c(14.48536, 18.89667, 23.69953)) > 1e-03,
na.rm = TRUE))
testthat::expect_false(any(abs(leaf.dat$Area.smooth.AGRdv[1:3] -
c(4.341943, 4.550298, 5.099377)) > 1e-03,
na.rm = TRUE))
testthat::expect_false(any(abs(leaf.dat$Area.smooth.RGRdv[1:3] -
c(0.2997469, 0.2407990, 0.2151678)) > 1e-03,
na.rm = TRUE))
})
cat("#### Test correctBoundaries for NCSS in fitSpline 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$yC <- fitSpline(area.dat, x = "xDays",
response = "Area1", response.smoothed = "Area1.smooth",
correctBoundaries = TRUE)$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$Area1.smooth <- fitSpline(area.dat, x = "xDays",
response = "Area1", response.smoothed = "Area1.smooth",
df = 4,
correctBoundaries = FALSE)$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$Area1.smooth.C <- fitSpline(area.dat, x = "xDays",
response = "Area1", response.smoothed = "Area1.smooth",
df = 4,
correctBoundaries = TRUE)$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 fitSpline 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)
responses <- names(test)[5:ncol(test)]
##Test the fail options for PS
testthat::expect_error(splitSplines(test, response = "Area", x="xDays",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
na.x.action = "fail"))
testthat::expect_error(splitSplines(test, response = "Length.1", x="xDays",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
na.y.action = "fail"))
##Fit some splines - exclude y
leaf.dat <- test
resp <- responses[2]
testthat::expect_warning(
for (resp in responses)
leaf.dat <- splitSplines(leaf.dat, response = resp, x="xDays",
spline.type = "PS", lambda = 0.1, npspline.segments = 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$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1.smooth)), 82)
testthat::expect_equal(sum(is.na(leaf.dat$Area.smooth)), 3)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.3.smooth[13:24])), 4)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.3.smooth[49:60])), 0)
##trim
leaf.dat <- test
testthat::expect_warning(
for (resp in responses)
leaf.dat <- splitSplines(leaf.dat, response = resp, x="xDays",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
na.y.action = "trim"),
regexp = "Need at least 4 distinct x values to fit a spline - all fitted values set to NA")
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1.smooth)), 86)
testthat::expect_lt(abs(leaf.dat$Length.1.smooth[57] - 11.07072), 1e-05)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.3.smooth[13:24])), 4)
##Test ltrimx
leaf.dat <- test
for (resp in responses)
leaf.dat <- splitSplines(leaf.dat, response = resp, x="xDays",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
na.y.action = "ltrim",
deriv=1, suffices.deriv="AGRdv",
extra.rate = c(RGRdv = "RGR"))
testthat::expect_equal(length(lapply(responses,
function(resp, data)
{
resp <- paste(resp,"smooth", sep = ".")
testthat::expect_equal(sum(is.na(data[[resp]])),
sum(is.na(data[[paste(resp,"AGRdv",sep = ".")]])),
sum(is.na(data[[paste(resp,"RGRdv",sep = ".")]])))
}, data = leaf.dat)), 4)
testthat::expect_equal(nrow(leaf.dat), 96)
testthat::expect_equal(ncol(leaf.dat), 20)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1.smooth)), 87)
testthat::expect_lt(abs(leaf.dat$Length.1.smooth[57] - 11.07072), 1e-05)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.3.smooth[13:24])), 7)
leaf.dat.noC <- leaf.dat
##Test ltrimx with correctBoundaries (which is ignored)
leaf.dat <- test
for (resp in responses)
leaf.dat <- splitSplines(leaf.dat, response = resp, x="xDays",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
na.y.action = "ltrim",
correctBoundaries = TRUE)
testthat::expect_equal(nrow(leaf.dat), 96)
testthat::expect_equal(ncol(leaf.dat), 12)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1.smooth)), 87)
testthat::expect_lt(abs(leaf.dat$Length.1.smooth[57] - 11.07072), 1e-05)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.3.smooth[13:24])), 7)
##Test utrimx
leaf.dat <- test
for (resp in responses)
leaf.dat <- splitSplines(leaf.dat, response = resp, x="xDays",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
na.y.action = "utrim")
testthat::expect_equal(nrow(leaf.dat), 96)
testthat::expect_equal(ncol(leaf.dat), 12)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1.smooth)), 92)
testthat::expect_lt(abs(leaf.dat$Length.1.smooth[57] - 11.02593), 1e-05)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.3.smooth[13:24])), 9)
##Test utrimx
leaf.dat <- test
for (resp in responses)
leaf.dat <- splitSplines(leaf.dat, response = resp, x="xDays",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
na.y.action = "allx")
testthat::expect_equal(nrow(leaf.dat), 96)
testthat::expect_equal(ncol(leaf.dat), 12)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1.smooth)), 93)
testthat::expect_lt(abs(leaf.dat$Length.1.smooth[57] - 11.02593), 1e-05)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.3.smooth[13:24])), 12)
testthat::expect_equal(sum(is.na(leaf.dat$Length.3.smooth[94:96])), 3)
##Test omit in fitSpline - Length 3
leaf.dat <- test
carts <- levels(leaf.dat$Snapshot.ID.Tag)
fit <- vector(mode = "list", length = 0)
nrows <- vector(mode = "list", length = length(carts))
nrows <- list(6,4,5,3,2,6,1,1)
names(nrows) <- carts
for (cart in carts)
{
fit[[cart]] <- fitSpline(subset(leaf.dat, Snapshot.ID.Tag == cart),
response = "Length.3", response.smoothed = "sLength.3",
x="xDays",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
na.x.action = "omi", na.y.action = "omit",
deriv=1, suffices.deriv="AGRdv",
extra.rate = c(RGRdv = "RGR"))
testthat::expect_equal(nrows[[cart]], nrow(fit[[cart]]$predictions))
}
##Test omit in fitSpline - 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]] <- fitSpline(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",
deriv=1, suffices.deriv="AGRdv",
extra.rate = c(RGRdv = "RGR"))
testthat::expect_equal(nrows[[cart]], nrow(fit[[cart]]$predictions))
}
testthat::expect_equal(ncol(fit[[cart]]$predictions), 4)
##Test omit in splitSplines - get full data.frame because of merge in splitSplines
leaf.dat <- test
for (resp in responses)
leaf.dat <- splitSplines(leaf.dat, response = resp, x="xDays",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
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$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1.smooth)), 82)
leaf.dat <- test
for (resp in responses)
leaf.dat <- splitSplines(leaf.dat, response = resp, x="xDays",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
na.y.action = "omit")
##Test omit in fitSpline - Length 2 with a 0 length data.frame
leaf.dat <- test
carts <- levels(leaf.dat$Snapshot.ID.Tag)
fit <- vector(mode = "list", length = 0)
nrows <- list(6,4,5,3,2,6,1,1)
names(nrows) <- carts
for (cart in carts)
{
fit[[cart]] <- fitSpline(subset(leaf.dat, Snapshot.ID.Tag == cart),
response = "Length.3", response.smoothed = "sLength.3",
x="xDays", correctBoundaries = FALSE,
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
na.x.action = "omit", na.y.action = "omit")
testthat::expect_equal(ncol(fit[[cart]]$predictions), 2)
testthat::expect_equal(nrow(fit[[cart]]$predictions), nrows[[cart]])
}
fitC <- vector(mode = "list", length = 0)
nrows <- list(6,4,5,3,2,6,1,1)
names(nrows) <- carts
for (cart in carts)
{
fitC[[cart]] <- fitSpline(subset(leaf.dat, Snapshot.ID.Tag == cart),
response = "Length.3", response.smoothed = "sLength.3",
x="xDays",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
na.x.action = "omit", na.y.action = "omit")
testthat::expect_equal(ncol(fitC[[cart]]$predictions), 2)
testthat::expect_equal(nrow(fitC[[cart]]$predictions), nrows[[cart]])
}
})
cat("#### Test splitSplines using PS with leaf data, including log-smoothing\n")
test_that("leaf_growthPheno", {
skip_if_not_installed("growthPheno")
skip_on_cran()
library(dae)
library(ggplot2)
library(growthPheno)
# A small subset of Exp 270 leaf tracking data
data(testSpline)
##Smooth splines using identity and logarithm transformations - exclude y
leaf.dat <- test
leaf.dat$Area.log <- log(leaf.dat$Area)
#Investigate AGR and RGR calculations
leaf.dat <- splitSplines(leaf.dat, response="Area", x="xDays",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
smoothing.method = "log",
deriv=1, suffices.deriv="RGRdv",
extra.rate = c(AGRdv = "AGR"))
names(leaf.dat)[(match(c("Area.smooth", "Area.smooth.AGRdv","Area.smooth.RGRdv"),
names(leaf.dat)))] <- paste(c("Area.smooth", "Area.smooth.AGRdv",
"Area.smooth.RGRdv"), "log", sep = ".")
testthat::expect_equal(sum(is.na(leaf.dat$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 <- splitSplines(leaf.dat, response = "Area.log", x="xDays",
spline.type = "PS", lambda = 0.1, npspline.segments = 4)
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$Area.log.smooth)), 3)
#identity smoothing scale calculation of AGR and RGR
leaf.dat <- splitSplines(leaf.dat, response="Area", x="xDays",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
deriv=1, suffices.deriv="AGRdv",
extra.rate = c(RGRdv = "RGR"))
testthat::expect_false(any(abs(leaf.dat$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 <- splitSplines(leaf.dat, response="Area", x="xDays",
spline.type = "PS", lambda = 0.1,
deriv=1, suffices.deriv="AGRdv",
extra.rate = c(RGRdv = "RGR"))
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$Area.smooth.RGRdv[1:3] -
c(0.1617440, 0.1772402, 0.2038260)) > 1e-03,
na.rm = TRUE))
})
cat("#### Test fitSpline using PS with leaf data when there are missing values\n")
test_that("leaf_growthPheno", {
skip_if_not_installed("growthPheno")
skip_on_cran()
library(dae)
library(ggplot2)
library(growthPheno)
# A small subset of Exp 270 leaf tracking data
data(testSpline)
responses <- names(test)[5:ncol(test)]
leaf.dat <- test
##Check the contents of the fit.spline object for PS
carts <- levels(leaf.dat$Snapshot.ID.Tag)
fit <- fitSpline(subset(leaf.dat, Snapshot.ID.Tag == carts),
response = "Length.2", response.smoothed = "sLength.2",
x="xDays",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
na.x.action = "exclude", na.y.action = "allx",
deriv=1, suffices.deriv="AGRdv",
extra.rate = c(RGRdv = "RGR"))
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 splitSplines with small example\n")
test_that("exampleData_spltSplines", {
skip_if_not_installed("growthPheno")
skip_on_cran()
library(growthPheno)
data(exampleData)
t <- splitSplines(longi.dat, response="PSA", x="xDAP",
smoothing.segments = list(c(28,34), c(35,42)), df = 5)
testthat::expect_equal(nrow(t), 280)
testthat::expect_equal(ncol(t), 38)
testthat::expect_true(all(unique(t$xDAP) == c(28, 30:42)))
testthat::expect_false(all(abs(t$PSA.smooth-longi.dat$sPSA) < 1e-04))
testthat::expect_warning(
plotLongitudinal(t, x = "xDAP", response = "PSA.smooth",
facet.y = "Treatment.1", alpha = 0.75,
ggplotFuncs = list(geom_vline(xintercept=35, linetype="longdash",
alpha = 0.5, size=0.75, colour = "blue"))))
})
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#### This set of tests, including those involving fitSpline, can be removed when splitSplines is deprecated.
## splitSplines is the only function that calls fitSpline.
## All of these tests have been converted to use smoothSpline and byIndv4Times_SplinesGRs.
cat("#### Test fitSpline using NCSS with leaf data when there are missing values\n")
test_that("leaf_growthPheno", {
skip_if_not_installed("growthPheno")
skip_on_cran()
library(dae)
library(ggplot2)
library(growthPheno)
# A small subset of Exp 270 leaf tracking data
data(testSpline)
responses <- names(test)[5:ncol(test)]
##Test the fail options for NCSS
testthat::expect_error(splitSplines(test, response = "Area", x="xDays",
individuals = "Snapshot.ID.Tag",
df = 4, na.x.action = "fail"))
testthat::expect_error(splitSplines(test, response = "Length.1", x="xDays",
individuals = "Snapshot.ID.Tag",
df = 4, na.y.action = "fail"))
##Fit some splines - exclude y
leaf.dat <- test
testthat::expect_warning(
for (resp in responses)
leaf.dat <- splitSplines(leaf.dat, response = resp, x="xDays", df = 4),
regexp = "Need at least 4 distinct x values to fit a spline - all fitted values set to NA")
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1.smooth)), 82)
testthat::expect_equal(sum(is.na(leaf.dat$Area.smooth)), 3)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.3.smooth[13:24])), 4)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.3.smooth[49:60])), 0)
##trim
leaf.dat <- test
for (resp in responses)
leaf.dat <- splitSplines(leaf.dat, response = resp, x="xDays",
df = 4, na.y.action = "trim")
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1.smooth)), 86)
testthat::expect_lt(abs(leaf.dat$Length.1.smooth[57] - 11.067455), 1e-05)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.3.smooth[13:24])), 4)
##Test ltrimx
leaf.dat <- test
for (resp in responses)
leaf.dat <- splitSplines(leaf.dat, response = resp, x="xDays",
df = 4, na.y.action = "ltrim",
deriv=1, suffices.deriv="AGRdv",
extra.rate = c(RGRdv = "RGR"))
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$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1.smooth)), 87)
testthat::expect_lt(abs(leaf.dat$Length.1.smooth[57] - 11.067455), 1e-05)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.3.smooth[13:24])), 7)
leaf.dat.noC <- leaf.dat
##Test ltrimx with correctBoundaries
leaf.dat <- test
for (resp in responses)
leaf.dat <- splitSplines(leaf.dat, response = resp, x="xDays",
df = 4, 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$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1.smooth)), 87)
testthat::expect_lt(abs(leaf.dat$Length.1.smooth[57] - 11.05895), 1e-05)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.3.smooth[13:24])), 7)
leaf.dat$Length.1.smooth.noC <- leaf.dat.noC$Length.1.smooth
leaf.dat$Length.2.smooth.noC <- leaf.dat.noC$Length.2.smooth
leaf.dat$Length.3.smooth.noC <- leaf.dat.noC$Length.3.smooth
ggplot(leaf.dat, aes(x = xDays, y = Length.1)) +
geom_line() + geom_line(aes(x = xDays, Length.1.smooth), colour = "blue") +
geom_line(aes(x = xDays, Length.1.smooth.noC), colour = "red") +
facet_wrap(~ Snapshot.ID.Tag)
##Test utrimx
leaf.dat <- test
for (resp in responses)
leaf.dat <- splitSplines(leaf.dat, response = resp, x="xDays",
df = 4, 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$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1.smooth)), 92)
testthat::expect_lt(abs(leaf.dat$Length.1.smooth[57] - 11.067455), 1e-05)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.3.smooth[13:24])), 9)
##Test utrimx
leaf.dat <- test
for (resp in responses)
leaf.dat <- splitSplines(leaf.dat, response = resp, x="xDays",
df = 4, 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$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1.smooth)), 93)
testthat::expect_lt(abs(leaf.dat$Length.1.smooth[57] - 11.067455), 1e-05)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.3.smooth[13:24])), 12)
testthat::expect_equal(sum(is.na(leaf.dat$Length.3.smooth[94:96])), 3)
##Test omit in fitSpline - Length 3
leaf.dat <- test
carts <- levels(leaf.dat$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]] <- fitSpline(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",
deriv=1, suffices.deriv="AGRdv",
extra.rate = c(RGRdv = "RGR"))
testthat::expect_equal(nrows[[cart]], nrow(fit[[cart]]$predictions))
}
##Test omit in fitSpline - Length 2 with a 0 length data.frame
fit <- vector(mode = "list", length = 0)
nrows <- list(11,12,12,12,9,12,0,9)
names(nrows) <- carts
for (cart in carts)
{
fit[[cart]] <- fitSpline(subset(leaf.dat, Snapshot.ID.Tag == cart),
response = "Length.2", response.smoothed = "sLength.2",
x="xDays",
df = 4, na.x.action = "omi", na.y.action = "omit",
deriv=1, suffices.deriv="AGRdv",
extra.rate = c(RGRdv = "RGR"))
testthat::expect_equal(nrows[[cart]], nrow(fit[[cart]]$predictions))
}
testthat::expect_equal(ncol(fit[[cart]]$predictions), 4)
##Test omit in splitSplines - get full data.frame because of merge in splitSplines
leaf.dat <- test
for (resp in responses)
leaf.dat <- splitSplines(leaf.dat, response = resp, x="xDays",
df = 4,
na.x.action = "omi", na.y.action = "omit")
testthat::expect_equal(nrow(leaf.dat), 96)
testthat::expect_equal(ncol(leaf.dat), 12)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1.smooth)), 82)
leaf.dat <- test
for (resp in responses)
leaf.dat <- splitSplines(leaf.dat, response = resp, x="xDays",
df = 4, na.y.action = "omit")
##Test omit in fitSpline - Length 2 with a 0 length data.frame
leaf.dat <- test
carts <- levels(leaf.dat$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]] <- fitSpline(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]] <- fitSpline(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 fitSpline 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)
##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 <- splitSplines(leaf.dat, response="Area", x="xDays",
df = 4, smoothing.method = "log",
deriv=1, suffices.deriv="RGRdv",
extra.rate = c(AGRdv = "AGR"))
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(2.993617, 3.682534, 4.568932)) > 1e-03,
na.rm = TRUE))
testthat::expect_false(any(abs(leaf.dat$Area.smooth.RGRdv.log[1:3] -
c(0.1878992, 0.1913271, 0.1955440)) > 1e-03,
na.rm = TRUE))
#Manual calculation of log smooth
leaf.dat <- splitSplines(leaf.dat, response = "Area.log", x="xDays",
df = 4)
leaf.dat$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 <- splitSplines(leaf.dat, response="Area", x="xDays",
df = 4, deriv=1, suffices.deriv="AGRdv",
extra.rate = c(RGRdv = "RGR"))
testthat::expect_false(any(abs(leaf.dat$Area.smooth[1:3] -
c(14.48536, 18.89667, 23.69953)) > 1e-03,
na.rm = TRUE))
testthat::expect_false(any(abs(leaf.dat$Area.smooth.AGRdv[1:3] -
c(4.341943, 4.550298, 5.099377)) > 1e-03,
na.rm = TRUE))
testthat::expect_false(any(abs(leaf.dat$Area.smooth.RGRdv[1:3] -
c(0.2997469, 0.2407990, 0.2151678)) > 1e-03,
na.rm = TRUE))
})
cat("#### Test correctBoundaries for NCSS in fitSpline using a single plant from Rice germplasm\n")
test_that("area_correctBoundaries", {
skip_if_not_installed("growthPheno")
skip_on_cran()
library(dae)
library(ggplot2)
library(growthPheno)
data(area.dat)
fity <- smooth.spline(area.dat$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 <- fitSpline(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 <- fitSpline(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 <- fitSpline(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$RGRC, na.rm = TRUE) - 0.000893429) < 1e-04)
})
cat("#### Test fitSpline using PS with leaf data when there are missing values\n")
test_that("leaf_growthPheno", {
skip_if_not_installed("growthPheno")
skip_on_cran()
library(dae)
library(ggplot2)
library(growthPheno)
# A small subset of Exp 270 leaf tracking data
data(testSpline)
responses <- names(test)[5:ncol(test)]
##Test the fail options for PS
testthat::expect_error(splitSplines(test, response = "Area", x="xDays",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
na.x.action = "fail"))
testthat::expect_error(splitSplines(test, response = "Length.1", x="xDays",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
na.y.action = "fail"))
##Fit some splines - exclude y
leaf.dat <- test
resp <- responses[2]
testthat::expect_warning(
for (resp in responses)
leaf.dat <- splitSplines(leaf.dat, response = resp, x="xDays",
spline.type = "PS", lambda = 0.1, npspline.segments = 4),
regexp = "Need at least 4 distinct x values to fit a spline - all fitted values set to NA")
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1.smooth)), 82)
testthat::expect_equal(sum(is.na(leaf.dat$Area.smooth)), 3)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.3.smooth[13:24])), 4)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.3.smooth[49:60])), 0)
##trim
leaf.dat <- test
testthat::expect_warning(
for (resp in responses)
leaf.dat <- splitSplines(leaf.dat, response = resp, x="xDays",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
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$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1.smooth)), 86)
testthat::expect_lt(abs(leaf.dat$Length.1.smooth[57] - 11.07072), 1e-05)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.3.smooth[13:24])), 4)
##Test ltrimx
leaf.dat <- test
for (resp in responses)
leaf.dat <- splitSplines(leaf.dat, response = resp, x="xDays",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
na.y.action = "ltrim",
deriv=1, suffices.deriv="AGRdv",
extra.rate = c(RGRdv = "RGR"))
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$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1.smooth)), 87)
testthat::expect_lt(abs(leaf.dat$Length.1.smooth[57] - 11.07072), 1e-05)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.3.smooth[13:24])), 7)
leaf.dat.noC <- leaf.dat
##Test ltrimx with correctBoundaries (which is ignored)
leaf.dat <- test
for (resp in responses)
leaf.dat <- splitSplines(leaf.dat, response = resp, x="xDays",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
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$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1.smooth)), 87)
testthat::expect_lt(abs(leaf.dat$Length.1.smooth[57] - 11.07072), 1e-05)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.3.smooth[13:24])), 7)
##Test utrimx
leaf.dat <- test
for (resp in responses)
leaf.dat <- splitSplines(leaf.dat, response = resp, x="xDays",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
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$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1.smooth)), 92)
testthat::expect_lt(abs(leaf.dat$Length.1.smooth[57] - 11.02593), 1e-05)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.3.smooth[13:24])), 9)
##Test utrimx
leaf.dat <- test
for (resp in responses)
leaf.dat <- splitSplines(leaf.dat, response = resp, x="xDays",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
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$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1.smooth)), 93)
testthat::expect_lt(abs(leaf.dat$Length.1.smooth[57] - 11.02593), 1e-05)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.3.smooth[13:24])), 12)
testthat::expect_equal(sum(is.na(leaf.dat$Length.3.smooth[94:96])), 3)
##Test omit in fitSpline - Length 3
leaf.dat <- test
carts <- levels(leaf.dat$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]] <- fitSpline(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]]$predictions))
}
##Test omit in fitSpline - Length 2 with a 0 length data.frame
fit <- list()
nrows <- list(11,12,12,12,9,12,0,9)
names(nrows) <- carts
for (cart in carts)
{
fit[[cart]] <- fitSpline(subset(leaf.dat, Snapshot.ID.Tag == cart),
response = "Length.2", response.smoothed = "sLength.2",
x="xDays",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
na.x.action = "omi", na.y.action = "omit",
deriv=1, suffices.deriv="AGRdv",
extra.rate = c(RGRdv = "RGR"))
testthat::expect_equal(nrows[[cart]], nrow(fit[[cart]]$predictions))
}
testthat::expect_equal(ncol(fit[[cart]]$predictions), 4)
##Test omit in splitSplines - get full data.frame because of merge in splitSplines
leaf.dat <- test
for (resp in responses)
leaf.dat <- splitSplines(leaf.dat, response = resp, x="xDays",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
na.x.action = "omi", na.y.action = "omit")
testthat::expect_equal(nrow(leaf.dat), 96)
testthat::expect_equal(ncol(leaf.dat), 12)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1)), 85)
testthat::expect_equal(sum(!is.na(leaf.dat$Length.1.smooth)), 82)
leaf.dat <- test
for (resp in responses)
leaf.dat <- splitSplines(leaf.dat, response = resp, x="xDays",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
na.y.action = "omit")
##Test omit in fitSpline - Length 2 with a 0 length data.frame
leaf.dat <- test
carts <- levels(leaf.dat$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]] <- fitSpline(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]] <- fitSpline(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 splitSplines 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)
##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 <- splitSplines(leaf.dat, response="Area", x="xDays",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
smoothing.method = "log",
deriv=1, suffices.deriv="RGRdv",
extra.rate = c(AGRdv = "AGR"))
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$Area.smooth.RGRdv.log[1:3] -
c(0.1893088, 0.1924901, 0.1950459)) > 1e-03,
na.rm = TRUE))
#Manual calculation of log smooth
leaf.dat <- splitSplines(leaf.dat, response = "Area.log", x="xDays",
spline.type = "PS", lambda = 0.1, npspline.segments = 4)
leaf.dat$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 <- splitSplines(leaf.dat, response="Area", x="xDays",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
deriv=1, suffices.deriv="AGRdv",
extra.rate = c(RGRdv = "RGR"))
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$Area.smooth.RGRdv[1:3] -
c(0.2625059, 0.2263110, 0.2098839)) > 1e-03,
na.rm = TRUE))
#identity smoothing scale calculation of AGR and RGR - default calculation of npspline.segments
leaf.dat <- splitSplines(leaf.dat, response="Area", x="xDays",
spline.type = "PS", lambda = 0.1,
deriv=1, suffices.deriv="AGRdv",
extra.rate = c(RGRdv = "RGR"))
testthat::expect_false(any(abs(leaf.dat$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 fitSpline 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)
responses <- names(test)[5:ncol(test)]
leaf.dat <- test
##Check the contents of the fit.spline object for PS
carts <- levels(leaf.dat$Snapshot.ID.Tag)
fit <- fitSpline(subset(leaf.dat, Snapshot.ID.Tag == carts),
response = "Length.2", response.smoothed = "sLength.2",
x="xDays",
spline.type = "PS", lambda = 0.1, npspline.segments = 4,
na.x.action = "exclude", na.y.action = "allx",
deriv=1, suffices.deriv="AGRdv",
extra.rate = c(RGRdv = "RGR"))
testthat::expect_true(all(c(fit$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$xgrid) , 1)
})
cat("#### Test splitSplines with small example\n")
test_that("exampleData_spltSplines", {
skip_if_not_installed("growthPheno")
skip_on_cran()
library(growthPheno)
data(exampleData)
t <- splitSplines(longi.dat, response="PSA", x="xDAP",
smoothing.segments = list(c(28,34), c(35,42)), df = 5)
testthat::expect_equal(nrow(t), 280)
testthat::expect_equal(ncol(t), 38)
testthat::expect_true(all(unique(t$xDAP) == c(28, 30:42)))
testthat::expect_false(all(abs(t$PSA.smooth-longi.dat$sPSA) < 1e-04))
testthat::expect_warning(
plotLongitudinal(t, x = "xDAP", response = "PSA.smooth",
facet.y = "Treatment.1", alpha = 0.75,
ggplotFuncs = list(geom_vline(xintercept=35, linetype="longdash",
alpha = 0.5, size=0.75, colour = "blue"))))
})
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