tangled: tangled: a package for analysis and plotting of effects of...

In robschick/tangled: Creates data objects and plots for Knowlton, Schick et al. manuscript on entanglement

tangled: a package for analysis and plotting of effects of entanglement on right whales

Description

The tangled package takes output from the model described in Schick et al. 2013, PLoS-ONE. In the package we analyse the data, prepare it for plotting and make plot objects to be used in the entanglement paper. This paper (Knowlton, Schick, et al. in prep) describes the effect of entanglements on the health and survival of right whales. There are 5 main components to the package: 1) extraction summary; 2) changes in health over time; 3) health during entanglements; 4) sub-lethal impacts of impaired health; and 5) effects on survival. I'll document those briefly in the sections below, but they are spelled out in greater detail in each of the vignettes that accompany this package.

Extraction summary

The goal of this section is to show for the readers how we extract health information with respect to the start/end times and duration of the entanglements. The important function is winDiagram

Changes in Health

This part of the package describes how we plot changes in health over time as a function of entanglement severity. There are 4 prep functions: prepSlopeHealthData, prepSlopeHealthDataBarplot, prepSlopeHealthDataMedian, and prepSlopeHealthDataAnnotation; there is 1 plot function: plotSlopeHealth.

Health during entanglements

While the Changes in Health section describes the change across the entanglement period - the goal of this analysis is to examine health during the period. There are 2 main functions: prepBoxplotHealthData and plotBoxplotHealth.

Sub-lethal impacts of entanglement

This section documents the amount of time animals are spending in impaired health status during their entanglements. The idea is to see if animals are spending more time in worse health - as defined by the reproductive threshold enumerated in Rolland et al. (2016) Marine Ecology Progress Series 542:265-82. We compare health below this threshold status as a function of increasing entanglement severity and complexity. There are 4 main functions: prepThreshDataUnImp, prepThreshDataRepro, prepHealthThresholdPlotData, and plotHealthThreshold.

Effects of survival

This section examines survival of entangled right whales as a function of injury category. As with the other sections, it combines data prep \& analysis with data plotting. Unlike the others, we also add a section comparing the statistics of the different curves and models. There are 6 main functions: calcpresdSurvdat, calckdpaSurvdat both of which prepare the survival data for each of the three types: known dead, presumed dead, and presumed alive. The next 2 functions: calcKMCurves and calcKMCurvesSevGen prepare Kaplan-Meier survivorship data. Finally, plotSurv and potSurvGenderSeverity make the plots of this survivorship data.

robschick/tangled documentation built on May 9, 2022, 4:07 p.m.