Nothing
## ---- setup, include=FALSE, cache=FALSE--------------
library(knitr)
# Are the packages used in examples installed?
eval_chunks <- requireNamespace("ggspectra", quietly = TRUE) &&
requireNamespace("photobiologyWavebands", quietly = TRUE)
# eval_colorSpec <- requireNamespace("colorSpec", quietly = TRUE) && eval_chunks
eval_colorSpec <- eval_chunks
eval_pavo <- requireNamespace("pavo", quietly = TRUE) && eval_chunks
eval_hyperSpec <- requireNamespace("hyperSpec", quietly = TRUE) && eval_chunks
opts_chunk$set(fig.align='center', fig.show='hold',
fig.width=7, fig.height=6, size="footnotesize",
eval=eval_chunks)
options(replace.assign = TRUE, width = 55,
warnPartialMatchAttr = FALSE,
warnPartialMatchDollar = FALSE,
warnPartialMatchArgs = FALSE)
# setting TZ may be needed in some geographic locations as some Windows TZ
# strings are not recognized by all versions of R
Sys.setenv(TZ = 'UTC')
## ---- message=FALSE----------------------------------
library(photobiology)
library(photobiologyWavebands)
library(photobiologyInOut)
library(lubridate)
library(ggspectra)
library(readr)
library(colorSpec)
if (eval_pavo) {library(pavo)}
if (eval_hyperSpec) {library(hyperSpec)}
## ----------------------------------------------------
# plot defaults
theme_set(theme_bw()) # ggplot2
set_annotations_default(annotations = c("+", "title:what:when"))
# decrease lines printed
options(tibble.print_max = 5,
tibble.print_min = 3,
photobiology.strict.range = NA_integer_)
## ----------------------------------------------------
jaz.raw.file <-
system.file("extdata", "spectrum.jaz",
package = "photobiologyInOut", mustWork = TRUE)
jazraw.spct <- read_oo_jazdata(file = jaz.raw.file)
jazraw.spct <- trim_wl(jazraw.spct, range = c(250, 900))
## ----------------------------------------------------
autoplot(jazraw.spct)
## ----------------------------------------------------
getWhenMeasured(jazraw.spct)
## ----------------------------------------------------
getInstrDesc(jazraw.spct)
## ----------------------------------------------------
getInstrSettings(jazraw.spct)
## ----------------------------------------------------
jaz.s.irrad.file <-
system.file("extdata", "spectrum.JazIrrad",
package = "photobiologyInOut", mustWork = TRUE)
jaz.spct <- read_oo_jazirrad(file = jaz.s.irrad.file)
jaz0.spct <- jaz.spct
jaz.spct <- trim_wl(jaz.spct, range = c(290, 800))
## ----------------------------------------------------
autoplot(jaz.spct)
## ----------------------------------------------------
jaz.spct <- fshift(jaz0.spct, range = c(255, 290), f = "mean")
jaz.spct <- trim_wl(jaz.spct, range = c(290, 800))
autoplot(jaz.spct)
## ----------------------------------------------------
jaz.spct <- smooth_spct(jaz.spct)
autoplot(jaz.spct)
## ----------------------------------------------------
e_irrad(jaz.spct, PAR()) # W m-2
## ----------------------------------------------------
autoplot(read_oo_jazirrad(file = jaz.s.irrad.file))
## ----------------------------------------------------
autoplot(read_oo_jazirrad(file = jaz.s.irrad.file),
range = c(250,850))
## ----------------------------------------------------
autoplot(smooth_spct(read_oo_jazirrad(file = jaz.s.irrad.file)),
range = c(250,850))
## ----------------------------------------------------
q.raw.file <-
system.file("extdata", "spectrum.SSIrrad",
package = "photobiologyInOut", mustWork = TRUE)
autoplot(read_oo_ssirrad(file = q.raw.file))
## ----------------------------------------------------
file.name <-
system.file("extdata", "enlighten-wasatch-scope.csv",
package = "photobiologyInOut", mustWork = TRUE)
wasatch.raw.spct <-
read_wasatch_csv(file = file.name, extra.cols = "drop")
## ----------------------------------------------------
summary(wasatch.raw.spct)
## ----------------------------------------------------
autoplot(wasatch.raw.spct)
## ----------------------------------------------------
ava.raw.file <-
system.file("extdata", "spectrum-avaspec.csv",
package = "photobiologyInOut", mustWork = TRUE)
autoplot(read_avaspec_csv(file = ava.raw.file),
range = c(280, 900), unit.out = "photon")
## ----------------------------------------------------
macam.raw.file <-
system.file("extdata", "spectrum.DTA",
package = "photobiologyInOut", mustWork = TRUE)
autoplot(read_macam_dta(file = macam.raw.file))
## ----------------------------------------------------
licor_espd.file <-
system.file("extdata", "LI-180-irradiance.txt",
package = "photobiologyInOut", mustWork = TRUE)
li180.spct <- read_li180_txt(file = licor_espd.file)
## ----------------------------------------------------
li180.spct
cat(comment(li180.spct))
getInstrDesc(li180.spct)
getInstrSettings(li180.spct)
autoplot(li180.spct, unit.out = "photon")
## ----------------------------------------------------
licor.file <-
system.file("extdata", "spectrum.PRN",
package = "photobiologyInOut", mustWork = TRUE)
licor.spct <- read_licor_prn(file = licor.file, tz = "EET")
## ----------------------------------------------------
licor.spct
cat(comment(licor.spct))
autoplot(licor.spct, unit.out = "photon")
## ----------------------------------------------------
licor.file <-
system.file("extdata", "reflectance.PRN",
package = "photobiologyInOut", mustWork = TRUE)
licor.spct <- read_licor_prn(file = licor.file, s.qty = "Rfr")
## ----------------------------------------------------
licor.spct
cat(comment(licor.spct))
autoplot(licor.spct)
## ----------------------------------------------------
file.name <-
system.file("extdata", "spectrum-psi-spectrapen-SP.csv",
package = "photobiologyInOut", mustWork = TRUE)
psi.mspct <- read_spectrapen_csv(file = file.name,
tz = "UTC")
summary(psi.mspct)
autoplot(psi.mspct, annotations = "")
## ----------------------------------------------------
summary(psi.mspct[["spct.14"]])
autoplot(psi.mspct[["spct.14"]])
## ----------------------------------------------------
file.name <-
system.file("extdata", "cid-spectravue-Rpc-Measurements.csv",
package = "photobiologyInOut", mustWork = TRUE)
cid_Rpc.spct <- read_cid_spectravue_csv(file = file.name)
summary(cid_Rpc.spct)
autoplot(smooth_spct(cid_Rpc.spct, method = "supsmu"),
range = c(400, 1000), annotations = "") %+%
ylim(0, 0.55)
## ----------------------------------------------------
cs.day.file <-
system.file("extdata", "cr6-day.dat",
package = "photobiologyInOut", mustWork = TRUE)
## ---- eval=FALSE-------------------------------------
# # not run
# read_lines(yoctopuce_hour.file, n_max = 10)
## ----------------------------------------------------
day.dat <- read_csi_dat(file = cs.day.file)
day.dat
## ----------------------------------------------------
cs_hour.file <-
system.file("extdata", "cr6-hour.dat",
package = "photobiologyInOut", mustWork = TRUE)
hour.dat <- read_csi_dat(file = cs_hour.file)
ggplot(hour.dat, aes(TIMESTAMP, PAR_Den_Avg)) + geom_line()
## ----------------------------------------------------
yoctopuce_hour.file <-
system.file("extdata", "yoctopuce-data.csv",
package = "photobiologyInOut", mustWork = TRUE)
## ---- eval=FALSE-------------------------------------
# # not run
# read_lines(yoctopuce_hour.file, n_max = 10)
## ----------------------------------------------------
hour.dat <- read_yoctopuce_csv(file = yoctopuce_hour.file)
ggplot(hour.dat, aes(ISO.time, temperature.avg)) + geom_line()
## ----------------------------------------------------
tuv.file <-
system.file("extdata", "usrout.txt",
package = "photobiologyInOut", mustWork = TRUE)
tuv.spct <- read_tuv_usrout(file = tuv.file,
date = ymd("2014-03-21"))
summary(subset(tuv.spct, spct.idx == "A"))
tuv.spct
## ---- fig.height=10----------------------------------
autoplot(tuv.spct, annotations = c("colour.guide")) +
facet_wrap(~as.character(date), ncol = 2)
## ----------------------------------------------------
tuv.mspct <- subset2mspct(tuv.spct)
summary(tuv.mspct)
autoplot(tuv.mspct)
## ----------------------------------------------------
tuv_nd.spct <- read_tuv_usrout(file = tuv.file)
when_measured(tuv_nd.spct)
## ----------------------------------------------------
qtuv.file <-
system.file("extdata", "qtuv.txt",
package = "photobiologyInOut", mustWork = TRUE)
qtuv.spct <- read_qtuv_txt(file = qtuv.file)
summary(qtuv.spct)
qtuv.spct
## ----------------------------------------------------
uvspec.2col.file <-
system.file("extdata", "uvspec-plain-2col.dat",
package = "photobiologyInOut", mustWork = TRUE)
lrt.df <- read.table(file = uvspec.2col.file,
col.names = c("w.length", "s.e.irrad"))
uvspec.01.spct <- source_spct(w.length = lrt.df$w.length,
s.e.irrad = lrt.df$s.e.irrad * 1e-3)
summary(uvspec.01.spct)
cat(comment(uvspec.01.spct))
autoplot(uvspec.01.spct, range = c(250, 2500), unit.out = "photon")
## ----------------------------------------------------
uvspec.disort.file <-
system.file("extdata", "uvspec-disort.dat",
package = "photobiologyInOut", mustWork = TRUE)
uvspec.02.spct <- read_uvspec_disort(uvspec.disort.file)
summary(uvspec.02.spct)
cat(comment(uvspec.02.spct))
autoplot(uvspec.02.spct, unit.out = "photon")
## ----------------------------------------------------
ggplot(uvspec.02.spct) +
geom_line() +
geom_line(aes(y = s.e.irrad.diff), linetype = "dashed")
## ----------------------------------------------------
uvspec.disort.inp.file <-
system.file("extdata", "uvspec-disort.inp",
package = "photobiologyInOut", mustWork = TRUE)
comment(uvspec.02.spct) <- paste(comment(uvspec.02.spct),
read_file(uvspec.disort.inp.file),
sep = "\n\n")
cat(comment(uvspec.02.spct))
## ----------------------------------------------------
uvspec.multi.file <-
system.file("extdata", "uvspec-multi.dat",
package = "photobiologyInOut", mustWork = TRUE)
lbr.multi.spct <- read_uvspec_disort_vesa(uvspec.multi.file)
print(lbr.multi.spct, n = 5)
## ----------------------------------------------------
fmi.file <-
system.file("extdata", "2014-08-21_cum.hel",
package = "photobiologyInOut", mustWork = TRUE)
z.spct <- read_fmi_cum(fmi.file)
class_spct(z.spct)
getWhenMeasured(z.spct)
z.spct
## ----------------------------------------------------
fmi.files <-
system.file("extdata", c("2014-08-21_cum.hel", "2014-08-21_cum.hel"),
package = "photobiologyInOut", mustWork = TRUE)
z.mspct <- read_m_fmi_cum(fmi.files)
class(z.mspct)
getWhenMeasured(z.mspct)
z.mspct
## ---- eval=FALSE-------------------------------------
# fmi.files <- list.files(".", "*cum.hel")
# fmi.files <- paste(".", fmi.files, sep = "")
# z1.mspct <- read_m_fmi_cum(fmi.files)
# class(z1.mspct)
# getWhenMeasured(z1.mspct)
# z1.mspct
## ---- message=FALSE----------------------------------
# because of Google's query limits call will frequently fail without a key
# my.geocode <- ggmap::geocode("Kumpula, Helsinki, Finland", source = "google")
my.geocode <- data.frame(lon = 24.96474, lat = 60.20911)
z2.mspct <-
read_m_fmi_cum(fmi.files,
geocode = my.geocode)
class(z2.mspct)
getWhenMeasured(z2.mspct)
getWhereMeasured(z2.mspct)
z2.mspct
## ----------------------------------------------------
fmi.file <-
system.file("extdata", "2013-05-01.hel",
package = "photobiologyInOut", mustWork = TRUE)
z3.mspct <- read_fmi2mspct(fmi.file)
class(z3.mspct)[1:2]
getWhenMeasured(z3.mspct[[1]])
length(z3.mspct)
names(z3.mspct)
getWhenMeasured(z3.mspct[[1]])
getWhatMeasured(z3.mspct[[1]])
## ----------------------------------------------------
fred.file <-
system.file("extdata", "FReDflowerID_157.csv",
package = "photobiologyInOut", mustWork = TRUE)
fred.spct <- read_FReD_csv(file = fred.file,
label = "Gazania heterochaeta",
geocode = data.frame(lat = -28.8751, lon = 17.2293))
## ----------------------------------------------------
fred.spct
cat(comment(fred.spct))
autoplot(fred.spct)
## ----------------------------------------------------
aster.file <-
system.file("extdata", "drygrass-spectrum.txt",
package = "photobiologyInOut", mustWork = TRUE)
aster.spct <- read_ASTER_txt(file = aster.file)
## ----------------------------------------------------
aster.spct
cat(comment(aster.spct))
autoplot(aster.spct)
## ---- eval=eval_hyperSpec----------------------------
z2.hspct <- mspct2hyperSpec(z2.mspct, "s.e.irrad")
class(z2.hspct)
# plot(z2.hspct)
## ---- eval=eval_hyperSpec----------------------------
data(laser)
class(laser)
laser
plot(laser)
## ---- eval=eval_hyperSpec----------------------------
wl(laser) <- list (
wl = 1e7 / (1/405e-7 - wl (laser)),
label = expression (lambda / nm)
)
laser
plot(laser)
laser.mspct <-
hyperSpec2mspct(laser, "source_spct", "s.e.irrad", multiplier = 1e-3)
ggplot(laser.mspct[[1]]) +
geom_line() +
stat_peaks(geom = "text", vjust = -1, label.fmt = "%.6g nm", color = "red")
## ---- eval = eval_colorSpec--------------------------
# bug that needs to be fixed
fluorescent.mspct <- colorSpec2mspct(colorSpec::Fs.5nm)
print(fluorescent.mspct, n = 3, n.members = 3)
## ---- eval = eval_colorSpec--------------------------
colorSpec2mspct(colorSpec::Hoya)
## ---- eval = eval_colorSpec--------------------------
fluorescent.spct <- colorSpec2spct(colorSpec::Fs.5nm)
autoplot(fluorescent.spct, annotations = "")
## ---- eval = eval_colorSpec--------------------------
colorSpec2chroma_spct(colorSpec::xyz1931.5nm)
## ---- eval = eval_colorSpec--------------------------
sun.cspec <- spct2colorSpec(sun.spct)
plot(sun.cspec, col = "blue")
## ---- eval = eval_colorSpec--------------------------
spct2colorSpec(yellow_gel.spct)
## ---- eval = eval_colorSpec--------------------------
chroma_spct2colorSpec(beesxyzCMF.spct)
## ----------------------------------------------------
spct_CCT(white_led.source_spct) # correlated color temperature
spct_CRI(white_led.source_spct) # color rendition index
spct_CRI(white_led.source_spct, named = TRUE)
spct_SSI(white_led.source_spct, sun.spct) # spectral similarity index
## ---- eval = eval_pavo-------------------------------
data(sicalis)
class(sicalis)
names(sicalis)
## ---- eval = eval_pavo-------------------------------
sicalis.mspct <- rspec2mspct(sicalis, "reflector_spct", "Rpc")
summary(sicalis.mspct[[1]])
summary(sicalis.mspct[[2]])
summary(sicalis.mspct[[3]])
## ---- eval = eval_pavo-------------------------------
ggplot(rbindspct(sicalis.mspct[1:3])) +
aes(linetype = spct.idx) +
ylim(0,0.3) +
geom_line()
## ---- eval = eval_pavo-------------------------------
print(sicalis.mspct[c(TRUE, FALSE, FALSE)])
ggplot(rbindspct(sicalis.mspct[c(TRUE, FALSE, FALSE)])) +
aes(linetype = spct.idx) +
ylim(0,0.15) +
geom_line() +
ggtitle("'crown' reflectance spectra")
## ---- eval = eval_pavo-------------------------------
refl.by.band <- reflectance(sicalis.mspct, w.band = list(Red(), Green(), Blue(), UVA()))
refl.by.band$body.part <- rep(c("crown", "throat", "breast"), 7)
## ---- eval = eval_pavo-------------------------------
refl.red <- reflectance(sicalis.mspct, w.band = Red())
names(refl.red)[2] <- "red.reflectance"
refl.red$body.part <- rep(c("crown", "throat", "breast"), 7)
ggplot(refl.red, aes(x = body.part, y = red.reflectance)) +
stat_summary(fun.data = "mean_se", color = "red") +
geom_point(alpha = 0.5)
## ----------------------------------------------------
jaz.irrad.comma.file <-
system.file("extdata", "spectrum-comma.JazIrrad",
package = "photobiologyInOut", mustWork = TRUE)
my.locale <- locale(decimal_mark = ",", tz = "EET")
jaz00.spct <- read_oo_jazirrad(file = jaz.irrad.comma.file,
locale = my.locale)
## ----------------------------------------------------
jaz00.spct
## ----------------------------------------------------
jaz.s.irrad.file <-
system.file("extdata", "spectrum.JazIrrad",
package = "photobiologyInOut", mustWork = TRUE)
## ---- warning=FALSE----------------------------------
jaz01.spct <- read_oo_jazirrad(file = jaz.s.irrad.file,
date = NULL)
getWhenMeasured(jaz01.spct)
## ---- warning=FALSE----------------------------------
jaz02.spct <- read_oo_jazirrad(file = jaz.s.irrad.file,
date = ymd_hms("2015-11-15 12:00:00"))
getWhenMeasured(jaz02.spct)
## ---- warning=FALSE----------------------------------
jaz03.spct <- read_oo_jazirrad(file = jaz.s.irrad.file,
date = now())
getWhenMeasured(jaz03.spct)
## ---- message=FALSE,warning=FALSE--------------------
my.geocode <- data.frame(lon = 25.02006, lat = 60.22525)
jaz04.spct <- read_oo_jazirrad(file = jaz.s.irrad.file,
geocode = my.geocode)
jaz04.spct
getWhereMeasured(jaz04.spct)
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