Bat survey in Plumas National Forest through the use of acoustic bat detectors

author: Derek Corcoran

Last update: 2015-06-02

Introduction

To study bat occupancy in the Plumas National Forest by surveying acustically different areas of the forest, the three objective species for this survey are the Pallid Bat, the Townsend’s Long-eared Bat, and the California Bat. Nevertheless, there is at least 14 species that form the bat ensemble in the National Forest, the list of species is the following

Objective of the study

To determine the factors that influence bat occupancy in heterogeneous environments of Plumas National Forest, including areas corresponding to the Moonlight Fire and the Storrie Fire. Comparing and complementing biotic and abiotic variables.

Specific research questions and the factors that might influence them

1. Which factors affect bat occupancy in burned forest?

Does bat occupancy differ with the duration of time since the fire?

  • Explanatory variable = burn age at sampling sites (mean number of years between fires for a given point and the time till the last fire for a given point).

Does bat occupancy differ with burn intensity

  • Explanatory variable = burn intensity (in the following figure we see the layers that will allow us to work with burn intensity, this layers are burn intensity of the soil, burn intensity of the canopy, and Burn intensity of the basal area)

Does bat occupancy differ with forest type

  • Explanatory variable = Stand type
  • Explanatory variable = Forest type (type of forest typified in Vegetation existing
  • Abiotic variables (Altitud)
  • Explanatory variable = Historic burn age

Does bat occupancy differ with roost site availability?

  • Explanatory variable = Associated forest metrics (Lidar???, distance to water)

Concidering that we will work using lidar images, the layers to use will be acquired later, since most of this variables are only presented for del black polygon in the next figure.

## Warning in polypath(x = mcrds[, 1], y = mcrds[, 2], border = border, col =
## col, : "legend" is not a graphical parameter

Which factors affect bat occupancy in unburned forest?

  • explanatory vstance to road, distance to water)

Is occupancy affected by presence of heterospecifics?

is bat occupancy affected by presence of other bats? (competition)

  • Explanatory variable, occupancy of other bats (based on this study)

is bat occupancy affected by the presence of preys?

  • Explanatory variable, athropod emergence (Loren’s Study), athropod abundace (Our study)

Sampling desing and sampling unit

In order for us to study bat occupancy and to spatially predict it using the factors described in the previous section, most of the diversity of the forest has to be included in the model. To include that variability, I classified the environments using the following layers (Topography, Intervals between fires, Forest Type, Distance to roads, Nesting Habitat quality for Spotted owl, foraging Habitat quality for Spotted owl, Habitat Quality for Marten) [to be included tomorrow, distance to rivers, and distance to roads/path]

Check for correlation between rasters

First will scale every layer so that it goes from 0 to 1, in order for no layer to have more weight in the classification. And then we check the correlation between rasters. in the next graph/table, we see the relationship between our predictive variables. Here we see that we might want to take one of the two habitat quality layers for the Spotted Owl (R=0.74), and since we are using the spoted owl as a potential predator, we will keep the foraging habitat quality.

## Loading required package: sp
           slope

Min. 0.000000 1st Qu. 2.873498 Median 5.359555 3rd Qu. 8.648955 Max. 28.828351 NA’s 35684.000000

Clasification

Now we will use kmeans to sort the area into 5 types of habitat using the abovementioned rasterstack, and it will be ploted with different colors for every type of environment.

More info on how to do this clasification in https://geoscripting-wur.github.io/AdvancedRasterAnalysis/

separate layers acording to places with or without fire

Now we will separate the whole area in two subtypes burned areas and non-buned areas, based on the burn severity layers

Extract Random points from each habitat type with equal number in fire and non fire

During the first year of sampling 120 samples will be colected, 60 in burned areas, and 60 in non-burned areas, within each, 12 random points will be sampled in each habtitat type defined by the K-means classification.

## rgdal: version: 0.9-2, (SVN revision 526)
## Geospatial Data Abstraction Library extensions to R successfully loaded
## Loaded GDAL runtime: GDAL 1.11.2, released 2015/02/10
## Path to GDAL shared files: C:/Users/usuario/Documents/R/win-library/3.2/rgdal/gdal
## GDAL does not use iconv for recoding strings.
## Loaded PROJ.4 runtime: Rel. 4.9.1, 04 March 2015, [PJ_VERSION: 491]
## Path to PROJ.4 shared files: C:/Users/usuario/Documents/R/win-library/3.2/rgdal/proj
## Loading required package: lattice
## Loading required package: latticeExtra
## Loading required package: RColorBrewer

Values

## 
## Attaching package: 'dplyr'
## 
## The following objects are masked from 'package:raster':
## 
##     intersect, select, union
## 
## The following object is masked from 'package:stats':
## 
##     filter
## 
## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union
Mean value for every variable for each ID which combines prior classification (1 to 5) and fire or no fire (f or nf)
ID Height Fire Interval Distance to Road Sage Stage Distance to Water
1nf 1143.428 18.92636 70.70175 14.687060 0.00000
1f 1066.892 16.14099 381.48419 14.475234 0.00000
2nf 1798.345 14.70257 135.51784 4.956801 0.00000
2f 1733.110 16.35523 234.08921 5.477256 0.00000
3nf 1741.085 15.92650 277.42844 6.558292 342.73342
3f 1665.289 15.78163 305.06839 4.767730 341.64344
4nf 1777.849 24.37396 304.86406 16.390226 62.43815
4f 1673.955 13.77037 567.23379 14.868093 27.02978
5nf 1092.211 14.48702 189.65352 5.285532 0.00000
5f 1169.350 13.36700 315.70665 5.507521 0.00000

Simulated sampling Dynamic modeling

First we simulate our detection history for our 120 sites with four primary sampling periods, and three secondary sampling periods each.

##        nPars    AIC delta   AICwt cumltvWt
## Model1     2 481.49  0.00 0.99931     1.00
## Model3     7 496.92 15.43 0.00045     1.00
## Model2     8 498.12 16.62 0.00025     1.00

Estimation of abundance for the Whole National Forest for Bat Species X with 95% confidence interval estimation
Abundance estimation Estimation High Estimation Low
19720.2 24518.73 14501.36

APENDIX

Apendix 1

Values recorded for each selected sampling point toghether with it’s ID
Long Lat Height Fire Interval Distance to Road Vegetation Type Distance to Water ID
120.91 39.98 1145.27 15.81 424.21 12.41 0.00 1nf
121.09 40.02 983.53 11.68 0.00 10.22 0.00 1nf
120.87 39.96 1237.23 25.68 0.00 12.37 0.00 1nf
121.00 39.94 1279.09 21.48 0.00 11.73 0.00 1nf
120.80 39.87 1424.25 15.16 424.21 15.47 0.00 1nf
121.38 39.75 797.21 21.40 0.00 18.00 0.00 1nf
120.82 40.08 1241.51 19.82 0.00 14.47 0.00 1nf
120.98 40.04 1010.16 26.50 0.00 18.00 0.00 1nf
121.40 39.67 757.34 17.29 0.00 10.82 0.00 1nf
120.64 40.10 1411.36 16.00 0.00 18.00 0.00 1nf
120.55 39.73 1428.79 12.89 0.00 16.76 0.00 1nf
120.99 40.04 1005.39 23.42 0.00 18.00 0.00 1nf
120.80 40.18 1280.15 16.42 0.00 17.61 0.00 1f
121.25 39.72 731.23 16.00 0.00 12.28 0.00 1f
121.25 39.66 946.98 14.42 848.42 13.27 0.00 1f
121.21 40.07 1098.96 19.60 1428.69 14.79 0.00 1f
121.22 40.11 1302.51 16.00 324.43 18.00 0.00 1f
120.84 40.19 1410.15 17.48 908.19 10.71 0.00 1f
121.22 40.11 1243.52 15.68 0.00 17.04 0.00 1f
121.42 39.83 584.98 16.00 0.00 10.43 0.00 1f
120.79 40.20 1393.51 16.00 533.80 18.00 0.00 1f
120.76 40.21 1335.86 14.71 0.00 14.14 0.00 1f
121.11 40.04 1039.99 20.12 534.28 18.00 0.00 1f
121.47 39.73 434.85 11.25 0.00 9.42 0.00 1f
120.71 39.93 2069.65 7.16 0.00 6.93 0.00 2nf
120.60 39.85 2004.34 16.00 0.00 4.29 0.00 2nf
121.13 39.87 1790.30 16.00 325.57 7.00 0.00 2nf
121.02 39.67 1580.89 16.00 0.00 6.93 0.00 2nf
120.39 40.05 1911.05 16.00 324.74 3.00 0.00 2nf
121.04 39.75 1771.12 16.00 0.00 6.54 0.00 2nf
121.03 40.14 1678.18 15.74 0.00 3.00 0.00 2nf
120.62 39.94 1859.34 14.79 325.26 3.00 0.00 2nf
120.60 40.23 1734.92 16.00 0.00 3.00 0.00 2nf
121.01 40.08 1725.45 15.74 0.00 5.79 0.00 2nf
120.68 39.77 1548.83 11.00 0.00 3.00 0.00 2nf
121.20 39.93 1906.07 16.00 650.64 7.00 0.00 2nf
121.14 40.15 1530.05 12.56 324.27 7.68 0.00 2f
120.72 40.23 1635.56 12.30 0.00 3.00 0.00 2f
120.64 40.16 1739.43 16.00 533.90 3.53 0.00 2f
120.26 40.10 1908.27 14.97 424.21 5.67 0.00 2f
120.84 40.21 1643.31 11.93 0.00 5.80 0.00 2f
120.79 39.85 1594.26 14.38 0.00 2.77 0.00 2f
120.26 39.85 1773.72 23.05 0.00 9.02 0.00 2f
121.22 39.92 1863.16 16.00 776.73 7.00 0.00 2f
120.29 40.12 1903.38 26.00 424.21 2.00 0.00 2f
121.11 39.83 1725.65 24.36 325.75 5.66 0.00 2f
120.61 40.09 1870.59 12.13 0.00 6.38 0.00 2f
121.29 39.86 1609.96 12.58 0.00 7.21 0.00 2f
120.63 40.07 1605.53 18.51 324.63 12.26 324.63 3nf
121.00 40.09 1706.44 11.00 1068.23 3.00 324.52 3nf
120.42 39.87 1798.85 12.92 325.59 9.18 325.59 3nf
120.61 40.00 2196.98 25.10 0.00 9.45 324.97 3nf
121.01 39.86 1747.54 16.00 0.00 7.00 325.64 3nf
121.13 40.00 1625.41 16.00 424.21 6.68 324.96 3nf
121.25 39.88 1504.05 14.05 325.52 3.00 325.52 3nf
120.64 39.92 2027.00 16.00 0.00 3.06 534.61 3nf
120.81 39.98 2005.92 13.70 534.43 5.16 325.05 3nf
121.04 40.00 1386.61 15.96 0.00 7.14 324.96 3nf
120.93 39.67 1575.38 15.33 326.53 6.04 326.53 3nf
121.14 39.82 1713.31 16.55 0.00 6.73 325.83 3nf
121.10 40.11 1269.03 19.21 0.00 10.98 324.45 3f
121.05 40.13 1858.57 11.24 0.00 3.00 324.32 3f
121.22 39.98 1938.91 18.01 1068.89 5.99 325.07 3f
121.39 39.82 1249.11 11.00 0.00 3.08 325.81 3f
121.21 39.98 1919.29 21.99 1292.65 4.01 325.07 3f
120.70 39.98 1915.46 15.85 325.07 3.03 424.21 3f
121.34 39.93 1385.62 11.00 325.28 8.35 325.28 3f
121.47 39.88 1256.71 11.00 0.00 4.00 325.55 3f
121.31 39.89 1479.87 13.17 0.00 4.51 325.46 3f
120.31 40.10 1986.92 26.10 648.93 2.13 324.47 3f
120.63 39.82 1790.49 16.00 0.00 5.12 325.83 3f
120.76 40.15 1933.48 14.80 0.00 3.00 424.21 3f
120.49 40.10 1773.75 35.00 324.50 14.00 0.00 4nf
120.64 40.09 1469.14 16.00 324.52 18.00 0.00 4nf
120.70 40.02 1577.16 15.49 0.00 15.41 0.00 4nf
120.42 39.96 1690.96 35.00 325.14 14.00 0.00 4nf
120.75 39.98 2092.74 40.00 325.05 20.00 325.05 4nf
120.69 39.88 1510.62 13.94 424.21 10.52 0.00 4nf
120.47 40.02 1737.61 12.87 324.85 15.84 0.00 4nf
120.68 40.04 1611.01 16.00 424.21 18.00 0.00 4nf
120.64 40.03 1529.61 16.00 534.28 18.00 0.00 4nf
120.63 39.99 2359.56 40.00 0.00 20.00 0.00 4nf
120.53 39.82 1661.37 12.19 651.61 12.91 0.00 4nf
120.64 39.99 2320.65 40.00 0.00 20.00 424.21 4nf
120.84 40.20 1472.90 16.00 533.80 12.97 0.00 4f
121.27 40.04 1500.33 11.00 2598.20 12.00 0.00 4f
120.36 40.13 1839.87 11.00 0.00 16.00 324.36 4f
120.32 39.92 1902.04 20.98 325.36 15.17 0.00 4f
120.80 40.21 1692.60 16.00 533.77 18.00 0.00 4f
120.61 40.17 1566.06 12.06 324.14 13.24 0.00 4f
121.19 40.09 1501.27 16.00 775.39 18.00 0.00 4f
120.50 40.17 1797.37 11.00 324.16 16.00 0.00 4f
120.81 40.23 1688.66 11.18 0.00 12.09 0.00 4f
120.53 40.15 1786.37 11.00 533.95 16.00 0.00 4f
120.83 40.21 1596.95 15.20 323.96 15.59 0.00 4f
120.57 40.10 1743.04 13.82 534.09 13.37 0.00 4f
121.30 39.69 1080.55 11.00 0.00 4.03 0.00 5nf
120.93 39.71 1498.99 18.44 0.00 10.10 0.00 5nf
121.10 39.56 1112.92 11.00 0.00 3.00 0.00 5nf
121.33 39.69 1048.93 12.70 0.00 6.91 0.00 5nf
121.09 39.58 1184.67 11.00 0.00 3.00 0.00 5nf
121.12 39.61 1190.37 11.44 326.84 4.33 0.00 5nf
121.04 39.56 978.13 14.24 327.07 4.29 0.00 5nf
120.97 39.62 1471.53 12.09 0.00 3.87 0.00 5nf
121.32 39.69 1074.36 16.00 0.00 8.59 0.00 5nf
121.32 39.73 836.37 16.00 326.22 6.30 0.00 5nf
121.41 39.69 411.05 28.93 1295.72 6.00 0.00 5nf
121.10 39.62 1218.67 11.00 0.00 3.00 0.00 5nf
121.38 39.81 1330.66 13.70 424.21 6.96 0.00 5f
121.20 39.77 1376.71 11.00 326.06 3.00 0.00 5f
121.33 39.64 817.93 11.35 778.97 9.58 0.00 5f
121.16 40.10 1423.66 11.00 324.48 2.96 0.00 5f
121.20 40.12 1378.12 11.61 0.00 5.78 0.00 5f
121.41 39.86 1139.16 11.00 534.77 3.00 0.00 5f
121.33 39.75 985.38 16.00 0.00 8.88 0.00 5f
121.16 40.02 989.16 11.00 424.21 9.00 0.00 5f
121.46 39.78 595.00 29.00 0.00 6.00 0.00 5f
121.16 40.14 1364.65 11.32 324.30 3.96 0.00 5f
121.14 40.13 1477.32 11.00 0.00 3.00 0.00 5f
120.99 39.84 1154.46 12.43 651.47 3.97 0.00 5f
Simulated Sampling values
night1 night2 night3
s1.1nf 1 0 1
s2.1nf 1 1 1
s3.1nf 1 1 1
s4.1nf 1 1 1
s5.1nf 1 1 1
s6.1nf 1 1 0
s7.1nf 1 1 1
s8.1nf 1 1 1
s9.1nf 1 1 0
s10.1nf 1 0 1
s11.1nf 0 1 1
s12.1nf 1 1 1
s1.1f 0 1 1
s2.1f 1 0 0
s3.1f 1 1 1
s4.1f 1 1 1
s5.1f 1 1 1
s6.1f 1 1 1
s7.1f 1 0 1
s8.1f 1 1 1
s9.1f 1 1 0
s10.1f 0 1 1
s11.1f 1 1 0
s12.1f 1 1 1
s1.2nf 0 0 1
s2.2nf 1 0 0
s3.2nf 1 0 1
s4.2nf 1 1 1
s5.2nf 1 1 1
s6.2nf 1 1 1
s7.2nf 1 1 0
s8.2nf 1 1 1
s9.2nf 0 0 1
s10.2nf 0 0 1
s11.2nf 1 1 0
s12.2nf 0 1 1
s1.2f 1 1 0
s2.2f 1 1 1
s3.2f 0 1 1
s4.2f 0 1 0
s5.2f 0 1 1
s6.2f 1 1 1
s7.2f 1 1 0
s8.2f 0 0 0
s9.2f 0 0 1
s10.2f 1 0 0
s11.2f 1 0 1
s12.2f 0 0 0
s1.3nf 1 1 0
s2.3nf 0 1 0
s3.3nf 0 1 0
s4.3nf 0 1 1
s5.3nf 1 0 1
s6.3nf 1 0 1
s7.3nf 1 1 1
s8.3nf 1 0 0
s9.3nf 1 0 1
s10.3nf 0 1 1
s11.3nf 1 1 0
s12.3nf 1 0 1
s1.3f 1 1 0
s2.3f 1 1 0
s3.3f 1 0 0
s4.3f 0 0 0
s5.3f 0 0 0
s6.3f 1 0 1
s7.3f 1 1 0
s8.3f 0 0 1
s9.3f 1 1 0
s10.3f 0 0 0
s11.3f 0 0 1
s12.3f 0 1 1
s1.4nf 1 1 0
s2.4nf 0 0 0
s3.4nf 0 0 0
s4.4nf 0 1 0
s5.4nf 0 0 1
s6.4nf 1 0 1
s7.4nf 0 0 0
s8.4nf 0 0 0
s9.4nf 0 0 1
s10.4nf 1 0 0
s11.4nf 0 0 0
s12.4nf 0 1 1
s1.4f 0 1 0
s2.4f 1 1 0
s3.4f 1 0 0
s4.4f 0 0 0
s5.4f 0 0 0
s6.4f 0 0 0
s7.4f 1 0 0
s8.4f 0 0 0
s9.4f 1 1 0
s10.4f 0 1 0
s11.4f 1 0 1
s12.4f 0 0 0
s1.5nf 1 0 0
s2.5nf 0 0 0
s3.5nf 0 0 0
s4.5nf 0 0 0
s5.5nf 1 0 0
s6.5nf 0 0 0
s7.5nf 0 0 0
s8.5nf 0 0 0
s9.5nf 0 0 0
s10.5nf 0 0 0
s11.5nf 0 0 1
s12.5nf 0 0 0
s1.5f 0 0 0
s2.5f 0 0 0
s3.5f 1 0 0
s4.5f 1 0 0
s5.5f 1 0 0
s6.5f 0 0 0
s7.5f 0 0 1
s8.5f 0 0 0
s9.5f 0 0 0
s10.5f 0 0 0
s11.5f 1 0 1
s12.5f 0 0 0