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
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.
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
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]
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
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/
Now we will separate the whole area in two subtypes burned areas and non-buned areas, based on the burn severity layers
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.
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## Path to PROJ.4 shared files: C:/Users/usuario/Documents/R/win-library/3.2/rgdal/proj
## Loading required package: lattice
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## Attaching package: 'dplyr'
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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 |
## 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
Abundance estimation | Estimation High | Estimation Low |
---|---|---|
19720.2 | 24518.73 | 14501.36 |
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 |
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 |