skink: Skink Pitfall Data

Description Usage Details Source References See Also Examples

Description

Data from a study of skinks (Oligosoma infrapunctatum and O. lineoocellatum) in New Zealand.

Usage

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Details

Lizards were studied over several years on a steep bracken-covered hillside on Lake Station in the Upper Buller Valley, South Island, New Zealand. Pitfall traps (sunken cans baited with a morsel of fruit in sugar syrup) were set in two large grids, each 11 x 21 traps nominally 5 meters apart, surveyed by tape and compass (locations determined later with precision surveying equipment - see Examples). Three diurnal lizard species were trapped: Oligosoma infrapunctatum, O. lineoocellatum and O. polychroma (Scincidae). The smallest species O. polychroma was seldom caught and these data are not included. The two other species are almost equal in average size (about 160 mm total length); they are long-lived and probably mature in their second or third year. The study aimed to examine their habitat use and competitive interactions.

Traps were set for 12 3-day sessions over 1995–1996, but some sessions yielded very few captures because skinks were inactive, and some sessions were incomplete for logistical reasons. The data are from sessions 6 and 7 in late spring (17–20 October 1995 and 14–17 November 1995). Traps were cleared daily; the few skinks present when traps were closed on the morning of the fourth day are treated as Day 3 captures. Individuals were marked uniquely by clipping one toe on each foot. Natural toe loss caused some problems with long-term identification; captures were dropped from the dataset when identity was uncertain. Released animals were occasionally recaptured in a different trap on the same day; these records were also discarded.

The data are provided as two two-session capthist objects ‘infraCH’ and ‘lineoCH’. Also included is ‘LStraps’, the traps object with the coordinates and covariates of the trap sites (these data are also embedded in each of the capthist objects). Pitfall traps are multi-catch traps so detector(LStraps) = ‘multi’.

Habitat data for each trap site are included as a dataframe of trap covariates in LStraps. Ground cover and vegetation were recorded for a 1-m radius plot at each trap site. The dataframe also gives the total number of captures of each species by site on 31 days between April 1995 and March 1996, and the maximum potential annual solar radiation calculated from slope and aspect (Frank and Lee 1966). Each site was assigned to a habitat class by fuzzy clustering (Kaufman and Rousseauw 1990; package cluster) of a distance matrix using the ground cover, vegetation and solar radiation variables. Sites in class 1 were open with bare ground or low-canopy vegetation including the heath-like Leucopogon fraseri and grasses; sites in class 2 had more-closed vegetation, lacking Leucopogon fraseri and with a higher canopy that often included Coriaria arborea. Site variables are listed with definitions in the attribute habitat.variables of LStraps (see Examples).

Object Description
infraCH multi-session capthist object O. infrapunctatum
lineoCH multi-session capthist object O. lineoocellatum
LStraps traps object -- Lake Station grids

Source

M. G. Efford, B. W. Thomas and N. J. Spencer unpublished data.

References

Efford, M. G., Spencer, N. J., Thomas, B. W., Mason, R. F. and Williams, P. In prep. Distribution of sympatric skink species in relation to habitat.

Frank, E. C. and Lee , R. (1966) Potential solar beam irradiation on slopes. United States Forest Service Research Paper RM-118.

Kaufman, L. and Rousseauw, P. J. (1990) Finding groups in data: an introduction to cluster analysis. John Wiley & Sons, New York.

Spencer, N. J., Thomas, B. W., Mason, R. F. and Dugdale, J. S. (1998) Diet and life history variation in the sympatric lizards Oligosoma nigriplantare polychroma and Oligosoma lineoocellatum. New Zealand Journal of Zoology 25: 457–463.

See Also

capthist, covariates

Examples

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summary (infraCH)
summary (lineoCH)

## check mean distance to nearest trap etc.
summary(LStraps)

## LStraps has several site covariates; terse descriptions are in
##  an extra attribute that may be displayed thus
attr(LStraps, "habitat.variables")

## For density modelling we need covariate values at each point in the
## habitat mask. This requires both on-grid interpolation and
## extrapolation beyond the grids. One (crude) possibility is to
## extrapolate a mask covariate from a covariate of the nearest trap:

LSmask <- make.mask(LStraps, buffer = 30, type = "trapbuffer")
temp <- nearesttrap(LSmask, LStraps)
habclass <- covariates(LStraps)$class[temp]
habclass <- factor (habclass, levels = c(1,2))
covariates(LSmask) <- data.frame(habclass)

## plot mask with colour-coded covariate
par(fg = "white")  ## white pixel borders
plot (LSmask, covariate = "habclass", dots = FALSE, axes = FALSE,
    col = c("yellow", "green"), border = 0)
plot(LStraps, add = TRUE, detpar = list(pch = 16))
par(fg = "black")    ## default

Example output

This is secr 3.2.0. For overview type ?secr
$`6`
Object class       capthist 
Detector type      multi 
Detector number    462 
Average spacing    4.036128 m 
x-range            2487398 2487521 m 
y-range            5939014 5939104 m 

Counts by occasion 
                    1   2   3 Total
n                  90  54  71   215
u                  90  40  33   163
f                 120  34   9   163
M(t+1)             90 130 163   163
losses              0   0   0     0
detections         90  54  71   215
detectors visited  71  45  57   173
detectors used    462 462 462  1386

$`7`
Object class       capthist 
Detector type      multi 
Detector number    462 
Average spacing    4.036128 m 
x-range            2487398 2487521 m 
y-range            5939014 5939104 m 

Counts by occasion 
                    1   2   3 Total
n                 155 142 137   434
u                 155  85  38   278
f                 163  74  41   278
M(t+1)            155 240 278   278
losses              0   0   0     0
detections        155 142 137   434
detectors visited 112 107 100   319
detectors used    462 462 462  1386

$`6`
Object class       capthist 
Detector type      multi 
Detector number    462 
Average spacing    4.036128 m 
x-range            2487398 2487521 m 
y-range            5939014 5939104 m 

Counts by occasion 
                    1   2   3 Total
n                  30  17  28    75
u                  30  15  19    64
f                  53  11   0    64
M(t+1)             30  45  64    64
losses              0   0   0     0
detections         30  17  28    75
detectors visited  27  16  23    66
detectors used    462 462 462  1386

$`7`
Object class       capthist 
Detector type      multi 
Detector number    462 
Average spacing    4.036128 m 
x-range            2487398 2487521 m 
y-range            5939014 5939104 m 

Counts by occasion 
                    1   2   3 Total
n                  48  39  38   125
u                  48  29  19    96
f                  70  23   3    96
M(t+1)             48  77  96    96
losses              0   0   0     0
detections         48  39  38   125
detectors visited  45  38  35   118
detectors used    462 462 462  1386

Object class       traps 
Detector type      multi 
Detector number    462 
Average spacing    4.036128 m 
x-range            2487398 2487521 m 
y-range            5939014 5939104 m 
         Variable                                            Description
1            Grid                                 Code for area (1 or 2)
2           INFRA            Total captures O.infrapunctatum Apr95-Mar96
3           LINEO            Total captures O.lineoocellatum Apr95-Mar96
4            POLY                Total captures O.polychroma Apr95-Mar96
5         BarePct                              Bare ground percent cover
6       StonesPct                             Loose stones percent cover
7        PilesPct                               Rock piles percent cover
8      GrassesPct                                 Graminae percent cover
9        ForbsPct                                    Forbs percent cover
10    CanBrackPct                   Bracken percent of vegetation canopy
11        HtBrack                                   Height of bracken cm
12         Tutu01                Coriaria arborea (0) absent (1) present
13    Cyathodes01 Leucopogon (=Cyathodes) fraseri (0) absent (1) present
14 SedgesRushes01                Sedges or rushes (0) absent (1) present
15        Black01                Rubus fruticosus (0) absent (1) present
16       SOLARRAD               Maximum potential annual solar radiation
17          class         Habitat class based on fuzzy clustering 1 or 2
18    membership2                 Probability belongs in habitat class 2

secr documentation built on Oct. 18, 2021, 9:06 a.m.