Nothing
## ----include=FALSE------------------------------------------------------------
library("incR")
data("incR_rawdata") # loading the data
head(incR_rawdata)
## ----eval = TRUE--------------------------------------------------------------
incR_rawdata_prep <- incRprep(data = incR_rawdata,
date.name = "DATE",
date.format= "%d/%m/%Y %H:%M",
timezone="GMT",
temperature.name="temperature")
head(incR_rawdata_prep, 3)
## ----eval = TRUE--------------------------------------------------------------
data(incR_envdata) # environmental data
head (incR_envdata)
# then use incRenv to merge environmental data
incR_data <- incRenv (data.nest = incR_rawdata_prep, # data set prepared by incRprep
data.env = incR_envdata,
env.temperature.name = "env_temperature",
env.date.name = "DATE",
env.date.format = "%d/%m/%Y %H:%M",
env.timezone = "GMT")
head (incR_data, 3)
## -----------------------------------------------------------------------------
incubation.analysis <- incRscan (data=incR_data,
temp.name="temperature",
lower.time=22,
upper.time=3,
sensitivity=0.15,
temp.diff.threshold =5,
maxNightVariation=2,
env.temp="env_temp")
## -----------------------------------------------------------------------------
names(incubation.analysis)
# incRscan output
head(incubation.analysis$incRscan_data)
head(incubation.analysis$incRscan_threshold)
## -----------------------------------------------------------------------------
my_plot <- incRplot(data = incubation.analysis$incRscan_data,
time.var = "dec_time",
day.var = "date",
inc.temperature.var = "temperature",
env.temperature.var = "env_temp",
vector.incubation = "incR_score")
# a ggplot plot is created that can be modified by the user
my_plot + ggplot2::labs(x = "Time", y = "Temperature")
## -----------------------------------------------------------------------------
incRatt(data = incubation.analysis[[1]], vector.incubation = "incR_score")
## -----------------------------------------------------------------------------
incRact(data = incubation.analysis[[1]],
time_column = "time",
vector.incubation = "incR_score")
## ----eval = TRUE--------------------------------------------------------------
incRt(data = incubation.analysis[[1]],
temp.name = "temperature",
limits = c(5,21), # time window
coor = NULL,
activity.times = FALSE,
civil.twilight = FALSE,
time.zone = NULL)
## ----eval = TRUE--------------------------------------------------------------
incRt(data = incubation.analysis[[1]],
temp.name = "temperature",
limits = NULL,
coor = NULL,
activity.times = TRUE, # incRact is called to define time window
civil.twilight = FALSE,
time.zone = "GMT",
time_column= "time",
vector.incubation="incR_score")
## ----eval = TRUE--------------------------------------------------------------
incRt(data = incubation.analysis[[1]],
temp.name = "temperature",
limits = NULL,
coor = c(39.5, 40.5), # choose your coordinates
activity.times = FALSE,
civil.twilight = TRUE,
time.zone = "GMT")
## ----eval = TRUE--------------------------------------------------------------
bouts <- incRbouts(data = incubation.analysis[[1]],
vector.incubation = "incR_score",
sampling.rate = incubation.analysis[[1]]$dec_time[56] - incubation.analysis[[1]]$dec_time[55], # sampling interval
dec_time = "dec_time",
temp = "temperature")
# the results are in two tables
names(bouts)
# bouts per day
head(bouts$day_bouts)
# bout specific data
head(bouts$total_bouts)
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