plotseq: Plot Sequence of Observations

In mbtyers/riverdist: River Network Distance Computation and Applications

Plot Sequence of Observations

Description

Plots the sequence of observations or movements of each individual (given as segment and vertex). This function is primarily intended for use with mouthdistbysurvey, but will also work with riverdistanceseq and upstreamseq.

Usage

plotseq(
  seqbysurvey,
  type = "boxplot",
  xlab = "",
  ylab = "",
  main = "",
  cex.axisX = 0.8,
  lowerbound = NULL,
  upperbound = NULL,
  boundtype = "negative",
  surveysareDates = F,
  ...
)

Arguments

seqbysurvey	A matrix returned from mouthdistbysurvey, riverdistanceseq, or upstreamseq.
type	The type of plot to generate. Options are "boxplot","dotplot","boxline",or "dotline". Defaults to "boxplot".
xlab	X-axis label
ylab	Y-axis label
main	Plot title
cex.axisX	Character expansion factor for X-axis labels
lowerbound	An optional vector of lower survey bounds
upperbound	An optional vector of upper survey bounds
boundtype	Method of plotting survey bounds. Options are "positive", "negative" (default), and "lines".
surveysareDates	If surveys are in Date format (see as.Date), a value of TRUE allows the x-coordinates points to be spaced apart according to date, not equidistantly. Defaults to FALSE. Any formatting of the survey variable must be done within the original call to mouthdistbysurvey, riverdistanceseq, or upstreamseq. Dates must already be formatted as dates, or in the form "YYYY-MM-DD" or "YYYY/MM/DD".
...	Additional plotting parameters

Note

Plots are intended as descriptive only. Any ANOVA-like inference that is suggested from these plots is strongly discouraged. The user is instead advised to use a mixed-effects model or some other inferential tool that accounts for repeated-measures and/or temporal autocorrelation.

Author(s)

Matt Tyers

Examples

data(Gulk, fakefish)

x <- mouthdistbysurvey(unique=fakefish$fish.id, survey=fakefish$flight.date, 
    seg=fakefish$seg, vert=fakefish$vert, rivers=Gulk)
    
plotseq(seqbysurvey=x)
plotseq(seqbysurvey=x, type="boxline")
plotseq(seqbysurvey=x, type="dotplot")
plotseq(seqbysurvey=x, type="dotline")

plotseq(seqbysurvey=x, type="dotline", surveysareDates=TRUE)

from_upstreamseq <- upstreamseq(unique=fakefish$fish.id, 
   survey=fakefish$flight, seg=fakefish$seg, vert=fakefish$vert, 
   rivers=Gulk)
plotseq(seqbysurvey=from_upstreamseq)

mbtyers/riverdist documentation built on Jan. 16, 2024, 12:34 a.m.