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Plot activity data

Source: R/fct_plot.R
plot_activity.Rd

Plot activity data

Usage

plot_activity(
  dfrec = NULL,
  time_dfrec = NULL,
  dffit = NULL,
  time_dffit = NULL,
  y_fit = NULL,
  n = ifelse(!is.null(dfrec), nrow(dfrec), NULL),
  plot_hist = ifelse(is.null(dfrec), FALSE, TRUE),
  plot_density = ifelse(is.null(dffit), FALSE, TRUE),
  hist_breaks = ifelse(unit == "clock", 1, (2 * pi)/24),
  x_breaks = ifelse(unit == "clock", 4, ((2 * pi)/24) * 4),
  unit = c("clock", "radians"),
  xlab = ifelse(unit == "clock", "Time (hours)", "Time (radians)"),
  ylab = ifelse(freq, "Count", "Density"),
  freq = TRUE,
  interactive = FALSE
)

Arguments

dfrec

dataframe containing species records

time_dfrec

Name of the column containing times in dfrec. If it is a chron::times object, it will be converted to radians (0 -- 2pi) or clock times (0 -- 24) (depending on unit). Else, it is expected to be in the same unit as unit.

dffit

Dataframe of fitted distribution

time_dffit

Name of the column containing times in dffit. This column must contain numeric values in radians and will be converted if unit is hours.

y_fit

Name of the column containing density in dffit. This column must contain numeric values corresponding to the radians density and will be converted if unit is hours.

n

Count for the observed data. It is required only when you wish to plot the predicted species "density count" (so plot_density is TRUE and freq is FALSE).

plot_hist

Plot the histogram of counts?

plot_density

Plot the activity curve?

hist_breaks

Breaks for the histogram (in hours or radians depending on the value of unit).

x_breaks

Breaks for the x-axis ticks (in hours or radians depending on the value of unit).

unit

Unit for the plot (radians or clock). Will change the density on the y scale and the labels and limits of the x-axis.

xlab

Label for the x-axis

ylab

Label for the y-axis

freq

Display count data (TRUE) or density (FALSE) ?

interactive

Make the plot interactive?

Value

A ggplot representing a histogram of observed activity times from dfrec.

Details

If the column time_dfrec if of type times, automatic conversion to clock times or radians will be performed. Else, the script trusts the user for the provided unit.

  • If plotting a histogram: when freq is TRUE, the height of the bars in each category represents the count that falls in this category. When freq is FALSE, the area of the bar in each category represents the proportion of the data that falls in this category.

  • If plotting a curve: when freq is TRUE: the area under the curve is equal to n when converting the x-scale to hours, even if the x axis is in radians. So the height of the curve does not change between hours and radians. When freq is FALSE, the area under the curve is one and depends on the x unit (so the height of the curve changes between hours and radians). This is to match the original code of plot.actmod.

See also

vignette("activity-patterns", package = "camtrapviz")

Examples

library(activity)
library(chron)
data(recordTableSample, package = "camtrapR")
# Convert hours to times format
recordTableSample$Time <- chron::times(recordTableSample$Time)
# Select the desired species
PBE_records <- recordTableSample[recordTableSample$Species == "PBE", ]

# Plot only data
plot_activity(dfrec = PBE_records,
              time_dfrec = "Time",
              unit = "clock")


# Plot only data (density)
plot_activity(dfrec = PBE_records,
              time_dfrec = "Time",
              unit = "clock",
              freq = FALSE)


# Fit model
# Convert hours to times format
PBE_records$time_radians <- as.numeric(PBE_records$Time)*2*pi
vm <- activity::fitact(PBE_records$time_radians)
pdf_vm <- as.data.frame(vm@pdf)

# Plot data and fitted model in radians
plot_activity(dffit = pdf_vm,
              time_dffit = "x",
              y_fit = "y",
              unit = "radians",
              freq = FALSE,
              n = nrow(PBE_records))


# Plot data and fitted model in hours
plot_activity(dffit = pdf_vm,
              time_dffit = "x",
              y_fit = "y",
              unit = "clock",
              freq = FALSE,
              n = nrow(PBE_records))