Software Open Access

SMBC-NZP/MigConnectivity: v0.3.0

Jeffrey A. Hostetler; Mike Hallworth; mhallwor; Clark Rushing

In this release, we added 4 major extensions:

  1. Added a function that allows users to generate probabilistic assignments from intrinstic markers (only stable-hydrogen isotopes are supported for the time being). The isoAssign function provides users with a variety of assignment options. These include using relative abundance as prior information, and using weighted isotope and relative abundance assignments to minimize assignment area and assignment error. This function returns a number of objects that users may be interested in such as a) individual probabilistic assignments, b) likely-vs-unlikely assignment regions, c) population level assignments and d) assignment locations that can be used to estimate migratory connectivity. The estMC function, when called using intrinsic markers uses the targetSites generated within the isoAssign function by default (can be set by user but not recommended at this time). The targetSites are generated from isotope bands equilivant to the standard deviation used to generate the isotope assignments. Preliminary simulations suggest targetSites created in this manner provide the least biased estimate of MC from intrinsic data.
  2. Added a function to allow users to estimate the relative weighting for isotope and relative abundance that minimizes assignment area and assignment error. The resulting weights can be used in the isoAssign function.
  3. Support for estimating migratory connectivity strength from isotope data. This update allows users to take the output from isoAssign and estimate MC from isotope assignments while accounting for assignment uncertainty.
  4. Added functions diffMC and diffMantel, for estimating differences (with uncertainty) between two or more INDEPENDENT estimates of MC or rM, respectively. These functions work well for comparing species.

We also added S3 types and summary/print functions for estMC, estMantel, and isoAssign outputs. The print and summary functions will only work with estimates of migratory connectivity strength from v0.3.0 or later.

Basic plot functions were added for visualizing weightAssign results and isoAssign objects.

Finally, we added reference sections to many of the help files and streamlined vignettes to increase build speed.

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