Christopher M. Wojan
Department of Biology
New Mexico State University
Las Cruces, NM, USA
E-mail: [email protected]

Shannon M. Knapp
Economics, Applied Statistics, and International Business Department
New Mexico State University
Las Cruces, NM, USA
E-mail: [email protected]

Karen E. Mabry
Department of Biology
New Mexico State University
Las Cruces, NM, USA
E-mail: [email protected]

SECR_Wojan_MultiSession_v7_1.R (MD5: de06a7bd07f3d7feb96d1e9c69cb05b8)   R code for SECR analysis

MultiSession20131112captures.txt (MD5: 7dab2facef2bb179cacc4dcbdd8abcc2)   mark-recapture data for population density estimates

MultiSession20131112sessions.txt (MD5: d3f25b235e111124755bfd4fa6b3b1c0)   data identifying trap sessions

MultiSession20131112traps.txt (MD5: f2df71eaf8eb8e29a3bdd3aba49c4560)   data identifying X,Y UTM coordinates of trap locations

NatalSettleLocations20131118.csv (MD5: d1dd10122476ff05f1092369ca619483)   X,Y UTM coordinates of pre- and post-dispersal locations of radio-tracked animals

NatalSettleLocations20131118long.csv (MD5: 94e43854158cfb8ba61d7ab3752f2d7d)   X,Y UTM coordinates of pre- and post-dispersal locations of radio-tracked animals in long format

NatalSettleLocationsSet2_20140103.csv (MD5: )   X,Y UTM coordinates of pre- and post-dispersal locations of trapped animals

NatalSettleLocationsSet2_20140103long.csv (MD5: )    X,Y UTM coordinates of pre- and post-dispersal locations of trapped animals in long format

SECR_Wojan_MultiSession_v7_1_20140707_out.txt (MD5: 98d356356211c7b780bff18a985dd604)   R code to create an output file holding the results of the SECR analysis

SECR_Wojan_MultiSession_v7_1.R

This is the R script used to run the spatially-explicit capture-recapture (SECR) analysis. Except for changing directory references, this file (along with the accompanying 3 data files) could be used to recreate the analysis used in this manuscript.

MultiSession20131112captures.txt

This file contains the mark-recapture information for the individual mice used in the population density estimates (focal dispersers are not included in this file).

The variables are:

• trap – this is the unique number for each trap. These numbers correspond to the variable "trapID" in the file MultiSession20131112traps.txt, which gives the (X,Y) coordinates for each trap number. Coordinates are in UTM Zone 10.
• id – this is a unique identifier to each individual mouse used in the population density estimates.  These do not include or correspond to any of the dispersing mice used in the analysis.
• session – this is a uniquely coded time period corresponding to a multi-day trapping session. See the variable "sessionID" in the file MultiSession20131112sessions.txt for the information for each session including the number of trap nights and date.

MultiSession20131112sessions.txt

This file contains data identifying each session (the variable "session" in the file MultiSession20131112captures.txt).

The variables are:

• sessionID – these are unique identifiers for each multi-day trapping session and correspond to the variable "session" in the file MultiSession20131112captures.txt
• nights – this is the number of trapping nights for each trapping session (either 2 or 3)
• year – this is the year during which that trapping session was conducted.
• month – this is the month during which the first night of the trapping session was conducted, 1=January, 2=February, 3=March, etc.
• firstday – this is the date of the month for the first night of the multiple nights of trapping for that trapping session

For example, sessionID=1 was for 3 nights beginning on 23 June 2004.

MultiSession20131112traps.txt

This file contains the trap location data (this becomes the R data frame "trapcoords")
The variables are:

• trapID – these are simply unique identifiers (1 to 43) for each trap and correspond to the variable "trap" in the file MultiSession20131112captures.txt
• UTMx – this is the x-axis UTM coordinate for each trap (UTM Zone 10)
• UTMy – this is the y-axis UTM coordinate for each trap (UTM Zone 10)

NatalSettleLocations20131118.csv

This file contains the UTM coordinates (Zone 10) for each disperser from the radio-tracked data set ("Set 1").

The variables are:

• ID - this is a unique identifier for a dispersing individual
• natalX – this is the x-axis UTM coordinate of the disperser at its natal site
• natalY – this is the y-axis UTM coordinate of the disperser at its natal site
• natalsession - this identifies the trapping session for the natal period and corresponds to the variable "session" in the file MultiSession20131112captures.txt and the variable "sessionID" in the file MultiSession20131112sessions.txt
• settleX - this is the x-axis UTM coordinate of the disperser at its settlement site
• settleY - this is the y-axis UTM coordinate of the disperser at its settlement site
• settlesession - this identifies the trapping session for the settlement period and corresponds to the variable "session" in the file MultiSession20131112captures.txt and the variable "sessionID" in the file MultiSession20131112sessions.txt
• set - this identifies that these dispersers belong to "Set 1" (the radio-tracked set of dispersers)

NatalSettleLocations20131118long.csv

This file contains the UTM coordinates (Zone 10) for each disperser from the radio-tracked data set ("Set 1").

The variables are:

• Period – this identifies if the location is the dispersers "natal" or "settle" location
• ID – this is a unique identifier for a dispersing individual
• UTMx – this is the x-axis UTM coordinate for the location (natal/settle)
• UTMy – this is the y-axis UTM coordinate for the location (natal/settle)
• session – this identifies the trapping session and corresponds to the variable "session" in the file MultiSession20131112captures.txt and the variable "sessionID" in the file MultiSession20131112sessions.txt
• set – this identifies that these dispersers belong to "Set 1" (the  radio-tracked set of dispersers)

 NatalSettleLocationsSet2_20140103.csv

This file contains the UTM coordinates (Zone 10) for each disperser from the live-trapped data set ("Set 2").

The variables are:

• ID - this is a unique identifier for a dispersing individual
• natalX – this is the x-axis UTM coordinate of the disperser at its natal site
• natalY – this is the y-axis UTM coordinate of the disperser at its natal site
• natalsession - this identifies the trapping session for the natal period and corresponds to the variable "session" in the file MultiSession20131112captures.txt and the variable "sessionID" in the file MultiSession20131112sessions.txt
• settleX - this is the x-axis UTM coordinate of the disperser at its settlement site
• settleY - this is the y-axis UTM coordinate of the disperser at its settlement site
• settlesession - - this identifies the trapping session for the settlement period and corresponds to the variable "session" in the file MultiSession20131112captures.txt and the variable "sessionID" in the file MultiSession20131112sessions.txt
• set - this identifies that these dispersers belong to "Set 2" (the  live-trapped set of dispersers)

NatalSettleLocationsSet2_20140103long.csv

This file contains the UTM coordinates (Zone 10) for each disperser from the live-trapped data set ("Set 2").

The variables are:

• Period – this identifies if the location is the dispersers "natal" or "settle" location
• ID – this is a unique identifier for a dispersing individual
• UTMx – this is the x-axis UTM coordinate for the location (natal/settle)
• UTMy – this is the y-axis UTM coordinate for the location (natal/settle)
• session – this identifies the trapping session and corresponds to the variable "session" in the file MultiSession20131112captures.txt and the variable "sessionID" in the file MultiSession20131112sessions.txt
• set – this identifies that these dispersers belong to "Set 2" (the live-trapped set of dispersers)

SECR_Wojan_MultiSession_v7_1_20140707_out.txt

The R-script (SECR_Wojan_MultiSession_v7_1.R) is set up to create an output text file holding the key results (e.g., posterior distribution summary statistics) of the analysis. This is the output file used in the paper. Details are contained in the R-script (SECR_Wojan_MultiSession_v7_1.R)