DOI: 10.6084/m9.figshare.3562398
title: Supplement 1. Details of the spatially-explicit capture–recapture model, including R code and all data files.

description: File List SECR_Wojan_MultiSession_v7_1.R (MD5: de06a7bd07f3d7feb96d1e9c69cb05b8) <i>R code for SECR analysis</i> MultiSession20131112captures.txt (MD5: 7dab2facef2bb179cacc4dcbdd8abcc2) <i>mark-recapture data for population density estimates</i> MultiSession20131112sessions.txt (MD5: d3f25b235e111124755bfd4fa6b3b1c0) <i>data identifying trap sessions</i> MultiSession20131112traps.txt (MD5: f2df71eaf8eb8e29a3bdd3aba49c4560) <i>data identifying X,Y UTM coordinates of trap locations</i> NatalSettleLocations20131118.csv (MD5: d1dd10122476ff05f1092369ca619483) <i>X,Y UTM coordinates of pre- and post-dispersal locations of radio-tracked animals</i> NatalSettleLocations20131118long.csv (MD5: 94e43854158cfb8ba61d7ab3752f2d7d)<i> X,Y UTM coordinates of pre- and post-dispersal locations of radio-tracked animals in long format</i> NatalSettleLocationsSet2_20140103.csv (MD5: ) <i>X,Y UTM coordinates of pre- and post-dispersal locations of trapped animals</i> NatalSettleLocationsSet2_20140103long.csv (MD5: )<i> X,Y UTM coordinates of pre- and post-dispersal locations of trapped animals in long format</i> SECR_Wojan_MultiSession_v7_1_20140707_out.txt (MD5: 98d356356211c7b780bff18a985dd604) <i>R code to create an output file holding the results of the SECR analysis</i> Description <b>SECR_Wojan_MultiSession_v7_1.R</b> 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. <b>MultiSession20131112captures.txt</b> 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. <b>MultiSession20131112sessions.txt</b> 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. <b>MultiSession20131112traps.txt</b> This file contains the trap location data (this becomes the R data frame "trapcoords")<br> 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) <b>NatalSettleLocations20131118.csv</b> 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) <b>NatalSettleLocations20131118long.csv</b> 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) <b> </b><b>NatalSettleLocationsSet2_20140103.csv</b> 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 ...