secr

Package: secr
Type: Package
Title: Spatially Explicit Capture-Recapture
Version: 2.10.3
Depends: R (>= 3.2.0), methods
Imports: abind, graphics, grDevices, MASS, utils, parallel, nlme, sp,
mgcv, raster, stats
Suggests: maptools, spsurvey, rgdal, knitr, gdistance, rgeos
VignetteBuilder: knitr
Date: 2016-05-13
Author: Murray Efford
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Description: Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.
License: GPL (>= 2)
LazyData: yes
LazyDataCompression: xz
URL: http://www.otago.ac.nz/density
NeedsCompilation: yes
Packaged: 2016-05-13 05:02:51 UTC; Murray
Repository: CRAN
Date/Publication: 2016-05-13 22:58:29

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'secr' ...
** package 'secr' successfully unpacked and MD5 sums checked
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c detectfn.c -o detectfn.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c polygon.c -o polygon.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c secr.c -o secr.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c sighting.c -o sighting.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c simsecr.c -o simsecr.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c trapping.c -o trapping.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c unmarked.c -o unmarked.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c utils.c -o utils.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o secr.so detectfn.o polygon.o secr.o sighting.o simsecr.o trapping.o unmarked.o utils.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/secr/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'secr'
    finding HTML links ... done
    AIC.secr                                html  
    CV                                      html  
    D.designdata                            html  
    DA                                      html  
    DENSITY                                 html  
    Dsurface                                html  
    FAQ                                     html  
    LLsurface                               html  
    LRtest                                  html  
    OVpossum                                html  
    PG                                      html  
    finding level-2 HTML links ... done

    Parallel                                html  
    RMarkInput                              html  
    Rsurface                                html  
    SPACECAP                                html  
    addCovariates                           html  
    addSightings                            html  
    addTelemetry                            html  
    autoini                                 html  
    capthist                                html  
    capthistfn                              html  
    circular                                html  
    clone                                   html  
    closedN                                 html  
    closure                                 html  
    cluster                                 html  
    coef.secr                               html  
    confint.secr                            html  
    contour                                 html  
    coulombe                                html  
    covariates                              html  
    deermouse                               html  
    deletemaskpoints                        html  
    derivedMS                               html  
    details                                 html  
    detectfn                                html  
    detector                                html  
    deviance.secr                           html  
    discretize                              html  
    distancetotrap                          html  
    ellipse.secr                            html  
    empirical                               html  
    esaplot                                 html  
    esaplotsecr                             html  
    expected.n                              html  
    fx.total                                html  
    fxi                                     html  
    hcov                                    html  
    head                                    html  
    homerange                               html  
    hornedlizard                            html  
    ip.secr                                 html  
    join                                    html  
    logit                                   html  
    logmultinom                             html  
    make.capthist                           html  
    make.mask                               html  
    make.systematic                         html  
    make.traps                              html  
    make.tri                                html  
    mask                                    html  
    mask.check                              html  
    model.average                           html  
    ms                                      html  
    ovenbird                                html  
    ovensong                                html  
    par.secr.fit                            html  
    pdot                                    html  
    plot.capthist                           html  
    plot.mask                               html  
    plot.popn                               html  
    plot.secr                               html  
    plot.traps                              html  
    plotmaskedge                            html  
    pmixProfileLL                           html  
    pointsInPolygon                         html  
    polyarea                                html  
    popn                                    html  
    possum                                  html  
    predict.secr                            html  
    predictDsurface                         html  
    print.capthist                          html  
    print.secr                              html  
    print.traps                             html  
    randomHabitat                           html  
    raster2                                 html  
    rbind.capthist                          html  
    rbind.popn                              html  
    rbind.traps                             html  
    read.mask                               html  
    read.telemetry                          html  
    read.traps                              html  
    rectangularMask                         html  
    reduce                                  html  
    reduce.capthist                         html  
    region.N                                html  
    score.test                              html  
    secr-package                            html  
    secr.design.MS                          html  
    secr.fit                                html  
    secr.make.newdata                       html  
    secr.model.density                      html  
    secr.model.detection                    html  
    secr.models                             html  
    secr.test                               html  
    secrdemo                                html  
    secrtest                                html  
    session                                 html  
    sighting                                html  
    signal                                  html  
    signalmatrix                            html  
    sim.capthist                            html  
    sim.popn                                html  
    sim.secr                                html  
    simpopndetails                          html  
    skink                                   html  
    smooths                                 html  
    snip                                    html  
    sort                                    html  
    spacing                                 html  
    speed                                   html  
    stoatDNA                                html  
    strip.legend                            html  
    subset.capthist                         html  
    subset.mask                             html  
    subset.popn                             html  
    subset.traps                            html  
    suggest.buffer                          html  
    summary.capthist                        html  
    summary.mask                            html  
    summary.traps                           html  
    timevaryingcov                          html  
    transformations                         html  
    trap.builder                            html  
    traps                                   html  
    trapsfn                                 html  
    trim                                    html  
    troubleshooting                         html  
    usage                                   html  
    usagePlot                               html  
    userdist                                html  
    utility                                 html  
    vcov.secr                               html  
    verify                                  html  
    write                                   html  
    writeGPS                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (secr)
Making 'packages.html' ... done