Fin Whale CEE analysis
Elliott L. Hazen
4/17/2018
PCA summaries for Dive, Angle, and TrackPlot
PCA summaries
Dive data evaluation
## Importance of components:
## Comp.1 Comp.2 Comp.3
## Standard deviation 1.5916751 0.5668540 0.38111260
## Proportion of Variance 0.8444766 0.1071078 0.04841561
## Cumulative Proportion 0.8444766 0.9515844 1.00000000
##
## Loadings:
## Comp.1 Comp.2 Comp.3
## DT -0.570 -0.674 0.470
## MXD -0.598 -0.800
## L -0.564 0.737 0.373
##
## Comp.1 Comp.2 Comp.3
## SS loadings 1.000 1.000 1.000
## Proportion Var 0.333 0.333 0.333
## Cumulative Var 0.333 0.667 1.000
Angular data evaluation
## Importance of components:
## Comp.1 Comp.2 Comp.3 Comp.4 Comp.5
## Standard deviation 1.5667103 0.9869789 0.9006729 0.62681873 0.6059521
## Proportion of Variance 0.4909163 0.1948255 0.1622423 0.07858034 0.0734356
## Cumulative Proportion 0.4909163 0.6857417 0.8479841 0.92656440 1.0000000
##
## Loadings:
## Comp.1 Comp.2 Comp.3 Comp.4 Comp.5
## Dpit 0.491 0.131 -0.491 0.701
## SumRoll -0.537 0.206 0.609 0.543
## MXPitch -0.542 -0.160 0.237 -0.786
## Apit -0.391 -0.831 -0.287 0.258
## StartHead -0.155 0.973 0.134 -0.105
##
## Comp.1 Comp.2 Comp.3 Comp.4 Comp.5
## SS loadings 1.0 1.0 1.0 1.0 1.0
## Proportion Var 0.2 0.2 0.2 0.2 0.2
## Cumulative Var 0.2 0.4 0.6 0.8 1.0TP data evaluation
## Importance of components:
## Comp.1 Comp.2 Comp.3
## Standard deviation 1.4094946 0.9999567 0.115807658
## Proportion of Variance 0.6622251 0.3333045 0.004470471
## Cumulative Proportion 0.6622251 0.9955295 1.000000000
##
## Loadings:
## Comp.1 Comp.2 Comp.3
## TPDiveV -0.707 0.707
## TPsurfaceV -0.707 -0.707
## TPturn 1.000
##
## Comp.1 Comp.2 Comp.3
## SS loadings 1.000 1.000 1.000
## Proportion Var 0.333 0.333 0.333
## Cumulative Var 0.333 0.667 1.000GAMM summaries for Dive, Angle, and TrackPlot
GAMM summaries
Dive data evaluation
##
## Family: gaussian
## Link function: identity
##
## Formula:
## Ax1 ~ TreatmentST + TreatmentType + TreatmentST:TreatmentType +
## s(MaxRL, bs = "ts", k = 5) + s(AvgRL, k = 5, bs = "ts") +
## s(SELcum, k = 5, bs = "ts") + BstatePB
##
## Parametric coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) -1.1766 1.8100 -0.650 0.517
## TreatmentST 1.1862 1.6262 0.729 0.467
## TreatmentType -1.0557 1.1341 -0.931 0.354
## BstatePB -0.5519 0.4010 -1.376 0.171
## TreatmentST:TreatmentType 0.9199 0.9721 0.946 0.346
##
## Approximate significance of smooth terms:
## edf Ref.df F p-value
## s(MaxRL) 2.1888 4 11.755 5.77e-11 ***
## s(AvgRL) 0.9871 4 1.624 0.00871 **
## s(SELcum) 0.3195 4 0.123 0.22328
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## R-sq.(adj) = 0.485
## Scale est. = 1.2302 n = 131## [1] 461.3926
Dive data evaluation - during
##
## Family: gaussian
## Link function: identity
##
## Formula:
## KAx1dur$Ax1 ~ TreatmentType + BstatePB:TreatmentType + s(MaxRL,
## bs = "ts", k = 5) + s(SELcum, bs = "ts", k = 5) + s(AvgRL,
## k = 5, bs = "ts") + BstatePB
##
## Parametric coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 1.5348 1.7042 0.901 0.370
## TreatmentType -1.4418 1.3500 -1.068 0.288
## BstatePB -1.5808 1.1288 -1.400 0.164
## TreatmentType:BstatePB 0.8437 0.8091 1.043 0.299
##
## Approximate significance of smooth terms:
## edf Ref.df F p-value
## s(MaxRL) 2.249e+00 4 10.733 1.14e-10 ***
## s(SELcum) 1.114e-07 4 0.000 0.5129
## s(AvgRL) 7.865e-01 4 0.713 0.0565 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## R-sq.(adj) = 0.466
## Scale est. = 1.1914 n = 124## [1] 430.2873
GAMM summaries
Angular data evaluation
##
## Family: gaussian
## Link function: identity
##
## Formula:
## KAngle$Ax1 ~ TreatmentST + TreatmentType + TreatmentST:TreatmentType +
## s(MaxRL, bs = "ts", k = 5) + s(AvgRL, k = 5, bs = "ts") +
## s(SELcum, k = 5, bs = "ts") + BstatePB
##
## Parametric coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) -1.9548 1.7460 -1.120 0.265
## TreatmentST 1.6317 1.6967 0.962 0.338
## TreatmentType -0.4682 1.0726 -0.436 0.663
## BstatePB -0.1814 0.3080 -0.589 0.557
## TreatmentST:TreatmentType 0.4771 1.0191 0.468 0.640
##
## Approximate significance of smooth terms:
## edf Ref.df F p-value
## s(MaxRL) 2.123e+00 4 16.782 1.33e-14 ***
## s(AvgRL) 1.165e+00 4 3.912 0.00012 ***
## s(SELcum) 2.072e-07 4 0.000 0.45822
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## R-sq.(adj) = 0.491
## Scale est. = 1.3912 n = 131## [1] 467.1679
##
## Family: gaussian
## Link function: identity
##
## Formula:
## KAngledur$Ax1 ~ TreatmentType + BstatePB:TreatmentType + s(MaxRL,
## bs = "ts", k = 5) + s(AvgRL, k = 5, bs = "ts") + s(SELcum,
## k = 5, bs = "ts") + BstatePB
##
## Parametric coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 0.9135 1.1221 0.814 0.418
## TreatmentType -0.7931 0.9699 -0.818 0.416
## BstatePB -1.0423 0.6958 -1.498 0.139
## TreatmentType:BstatePB 0.7226 0.5382 1.343 0.184
##
## Approximate significance of smooth terms:
## edf Ref.df F p-value
## s(MaxRL) 1.528e+00 4 6.264 1.94e-06 ***
## s(AvgRL) 1.019e+00 4 1.411 0.0168 *
## s(SELcum) 5.023e-09 4 0.000 0.2883
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## R-sq.(adj) = 0.372
## Scale est. = 1.3311 n = 75## [1] 260.627
Trackplot data evaluation
##
## Family: gaussian
## Link function: identity
##
## Formula:
## KTP$Ax1 ~ TreatmentType + s(MaxRL, k = 5, bs = "ts") + BstatePB
##
## Parametric coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) -1.0200 1.4930 -0.683 0.496
## TreatmentType 1.1297 1.0673 1.058 0.292
## BstatePB -0.5685 0.5896 -0.964 0.337
##
## Approximate significance of smooth terms:
## edf Ref.df F p-value
## s(MaxRL) 4.493e-08 4 0 0.79
##
## R-sq.(adj) = 0.16
## Scale est. = 0.05548 n = 104## [1] 94.02113
##
## Family: gaussian
## Link function: identity
##
## Formula:
## KTPdur$Ax1 ~ TreatmentType + s(MaxRL, bs = "ts", k = 5) + s(AvgRL,
## bs = "ts", k = 5) + BstatePB
##
## Parametric coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) -3.589 3.624 -0.990 0.333
## TreatmentType 4.067 2.560 1.589 0.126
## BstatePB -2.017 1.568 -1.286 0.212
##
## Approximate significance of smooth terms:
## edf Ref.df F p-value
## s(MaxRL) 7.410e-01 4 0.659 0.107
## s(AvgRL) 5.021e-09 4 0.000 0.510
##
## R-sq.(adj) = 0.521
## Scale est. = 0.025968 n = 26## [1] 28.79216
Boxplot summaries
Dive data bar plots
MFA dive data bar plots
PRN dive data bar plots
Incorporate prey
Set-up prey-dive relationships
Explore prey-dive relationships
##
## Call:
## lm(formula = maxlunges ~ krilldens)
##
## Residuals:
## Min 1Q Median 3Q Max
## -4.0391 -1.4852 -0.4074 1.5097 4.1252
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 5.416314 1.472584 3.678 0.0104 *
## krilldens -0.006806 0.005247 -1.297 0.2422
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 2.795 on 6 degrees of freedom
## Multiple R-squared: 0.219, Adjusted R-squared: 0.08884
## F-statistic: 1.682 on 1 and 6 DF, p-value: 0.2422
##
## Call:
## lm(formula = maxlunges ~ krilldens)
##
## Residuals:
## Min 1Q Median 3Q Max
## -4.0391 -1.4852 -0.4074 1.5097 4.1252
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 5.416314 1.472584 3.678 0.0104 *
## krilldens -0.006806 0.005247 -1.297 0.2422
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 2.795 on 6 degrees of freedom
## Multiple R-squared: 0.219, Adjusted R-squared: 0.08884
## F-statistic: 1.682 on 1 and 6 DF, p-value: 0.2422
##
## Call:
## lm(formula = maxlunges ~ krilldens)
##
## Residuals:
## Min 1Q Median 3Q Max
## -4.0391 -1.4852 -0.4074 1.5097 4.1252
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 5.416314 1.472584 3.678 0.0104 *
## krilldens -0.006806 0.005247 -1.297 0.2422
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 2.795 on 6 degrees of freedom
## Multiple R-squared: 0.219, Adjusted R-squared: 0.08884
## F-statistic: 1.682 on 1 and 6 DF, p-value: 0.2422
##
## Call:
## lm(formula = maxlunges ~ numpatches)
##
## Residuals:
## Min 1Q Median 3Q Max
## -4.3189 -2.0316 0.3898 2.2519 3.1141
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 4.8859 1.3399 3.646 0.0108 *
## numpatches -0.2835 0.2742 -1.034 0.3411
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 2.913 on 6 degrees of freedom
## Multiple R-squared: 0.1512, Adjusted R-squared: 0.009733
## F-statistic: 1.069 on 1 and 6 DF, p-value: 0.3411##
## Call:
## lm(formula = maxlunges ~ numpatches + krilldens)
##
## Residuals:
## 1 2 3 4 5 6 7 8
## 1.59110 -2.49356 0.33599 -3.53422 -0.93378 1.83497 0.06156 3.13793
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 6.543371 1.660365 3.941 0.0109 *
## numpatches -0.319545 0.251782 -1.269 0.2603
## krilldens -0.007424 0.005023 -1.478 0.1994
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 2.662 on 5 degrees of freedom
## Multiple R-squared: 0.4093, Adjusted R-squared: 0.173
## F-statistic: 1.732 on 2 and 5 DF, p-value: 0.2682
##
## Call:
## lm(formula = maxlunges ~ meandep)
##
## Residuals:
## Min 1Q Median 3Q Max
## -3.1090 -1.0298 0.4531 1.1157 1.7676
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 1.49153 0.94678 1.575 0.1662
## meandep 0.04707 0.01321 3.564 0.0119 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 1.791 on 6 degrees of freedom
## Multiple R-squared: 0.6792, Adjusted R-squared: 0.6257
## F-statistic: 12.7 on 1 and 6 DF, p-value: 0.01187##
## Call:
## lm(formula = maxlunges ~ numpatches + krilldens + meandep)
##
## Residuals:
## 1 2 3 4 5 6 7 8
## -1.3366 0.4653 0.4178 -1.9860 -0.3413 0.7614 0.9972 1.0222
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 2.853076 1.412615 2.020 0.1135
## numpatches -0.003094 0.167763 -0.018 0.9862
## krilldens -0.006073 0.002834 -2.143 0.0988 .
## meandep 0.045415 0.013107 3.465 0.0257 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 1.488 on 4 degrees of freedom
## Multiple R-squared: 0.8524, Adjusted R-squared: 0.7417
## F-statistic: 7.699 on 3 and 4 DF, p-value: 0.03879Response Analysis With Prey
Explore data correlations and run PCAs for Dive and Angle
## [1] 0.9861161 0.9153607 0.8744745 0.8439952 0.7700929 0.6203968 0.4439087
## [8] 0.2966010 0.2642416## WilksL F df1 df2 p
## [1,] 5.159505e-05 70.675809 162 4803.928 0.000000e+00
## [2,] 1.871074e-03 43.512802 136 4328.615 0.000000e+00
## [3,] 1.154166e-02 34.109770 112 3843.571 0.000000e+00
## [4,] 4.905199e-02 26.380035 90 3347.037 1.716483e-319
## [5,] 1.705136e-01 18.236228 70 2836.854 5.451851e-178
## [6,] 4.189966e-01 11.188976 52 2310.409 2.758875e-79
## [7,] 6.811759e-01 6.801911 36 1764.631 2.139271e-30
## [8,] 8.483468e-01 4.659432 22 1196.000 9.019572e-12
## [9,] 9.301764e-01 4.496388 10 599.000 3.814082e-06## [,1] [,2] [,3] [,4] [,5]
## [1,] 0.056271565 0.10802089 -0.006493596 -1.12164722 0.85239857
## [2,] 0.026424200 -0.15516177 0.049067529 -0.03462377 0.33575339
## [3,] -0.048471617 0.02614488 -0.005767764 0.06929054 -0.41330437
## [4,] 0.033462155 0.01757563 -0.020450970 0.13012202 -0.08976508
## [5,] NA NA NA NA NA
## [6,] -0.005177475 0.05656431 0.011700591 -0.06562318 0.04290538
## [7,] NA NA NA NA NA
## [8,] -0.028463324 -0.02317721 0.003408252 -0.11604389 0.12313110
## [9,] 0.035282593 -0.09499715 0.010754528 0.02865499 0.04158749
## [10,] -0.032653286 -0.37273360 -0.130921440 -0.05319313 0.60536630
## [11,] 0.710487659 0.38537063 -0.880517850 0.05273242 0.09464848
## [12,] 0.009668180 -0.04255769 -0.101476997 0.09934597 -0.21078867
## [13,] -0.539386351 -1.33644003 -1.138869961 -0.10953275 -0.32172472
## [14,] 0.255856074 1.06954133 1.408875474 -0.38169277 -0.29992055
## [15,] 0.506475781 -0.90243289 0.408650319 -0.16435267 0.05049064
## [16,] -0.044231307 -0.03738445 0.223347013 0.08807413 0.02086804
## [17,] NA NA NA NA NA
## [18,] NA NA NA NA NA
## [,6] [,7] [,8] [,9]
## [1,] -0.86498964 -0.11977361 -0.292884306 0.14120912
## [2,] -0.29548730 -0.06507973 0.475300974 0.55187919
## [3,] 0.14089598 0.09262572 -0.561877281 -0.48312550
## [4,] -0.08111867 -0.25471147 0.068763750 -0.50079804
## [5,] NA NA NA NA
## [6,] -0.08142202 -0.34476097 0.316475219 -0.38793467
## [7,] NA NA NA NA
## [8,] -0.06429772 0.15863442 0.228683370 0.10133435
## [9,] 0.38754086 0.18773876 -0.082595898 -0.39795585
## [10,] 0.54915784 0.27703344 0.408447065 -0.28783660
## [11,] 0.36125521 0.11145368 0.285094565 -0.23653110
## [12,] -0.26424095 0.90457512 0.257768844 -0.08088505
## [13,] 0.27854549 -0.21902887 0.998089411 -0.17345411
## [14,] 0.17463585 0.24790846 -0.900889914 0.82136090
## [15,] -0.10148512 -0.13878482 -0.006446616 0.01352730
## [16,] -0.25595335 -0.04967479 -0.089302990 -0.08979477
## [17,] NA NA NA NA
## [18,] NA NA NA NA## [,1] [,2] [,3] [,4] [,5]
## [1,] 0.089917701 -2.61623156 4.49850948 -2.52115110 -2.31470854
## [2,] 10.015989208 107.90711599 -44.09050000 35.27428511 221.48123788
## [3,] -0.680377504 -0.77162334 -1.66224107 0.61243123 1.19029251
## [4,] 1.231269981 -0.11210257 0.58682770 -0.33172799 -0.42014234
## [5,] 0.577015112 1.63177986 2.89489687 -0.33332773 1.41091553
## [6,] -0.513127869 0.80476261 -2.04378951 0.95904026 1.58567134
## [7,] -10.313557534 -106.16449998 41.15932735 -33.06074290 -219.11549661
## [8,] -0.224557255 0.33311248 0.20661833 -1.25753789 0.04806551
## [9,] -0.002807137 -0.06389689 -0.02485172 -0.01930747 -0.17757773
## [,6] [,7] [,8] [,9]
## [1,] 0.63080129 -4.6299845 3.175887e+00 -6.7113611
## [2,] 33.25688704 201.0201562 -1.153717e+02 24.6634496
## [3,] -0.62802564 -0.9297288 -2.865076e-02 -1.0078587
## [4,] -0.37566663 0.5083763 -3.066329e-01 0.9703369
## [5,] 0.99069348 0.5574275 6.503755e-01 -1.5642222
## [6,] 0.02586457 1.7195962 -2.738701e+00 0.5447087
## [7,] -34.66361229 -197.8894389 1.133666e+02 -18.5986013
## [8,] 0.29021894 -0.2938126 7.104412e-03 -1.7082271
## [9,] -0.32258693 0.7604066 7.365013e-01 -0.6717447
## Importance of components:
## Comp.1 Comp.2 Comp.3
## Standard deviation 1.5965072 0.5525919 0.38184692
## Proportion of Variance 0.8496117 0.1017859 0.04860236
## Cumulative Proportion 0.8496117 0.9513976 1.00000000
##
## Loadings:
## Comp.1 Comp.2 Comp.3
## Dive Time 0.569 -0.691 0.446
## Max Depth 0.596 -0.802
## Lunges 0.566 0.722 0.397
##
## Comp.1 Comp.2 Comp.3
## SS loadings 1.000 1.000 1.000
## Proportion Var 0.333 0.333 0.333
## Cumulative Var 0.333 0.667 1.000
Plot subset of whales that had prey, with prey
3 panel
3-panel scaled to 1 with comparison ratios
3 panel w/ comparison plot on third
Plot summaries by individual
Fit dive and angular GAMMs including prey
##
## Family: gaussian
## Link function: identity
##
## Formula:
## KAx1$Ax1[preposts] ~ TreatmentType + TreatmentST + s(BotDep,
## k = 5, bs = "ts")
##
## Parametric coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) -0.55092 0.97341 -0.566 0.572
## TreatmentType 1.08664 1.11795 0.972 0.331
## TreatmentST 0.08366 0.06524 1.282 0.200
##
## Approximate significance of smooth terms:
## edf Ref.df F p-value
## s(BotDep) 3.682 4 11.33 1.9e-09 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## R-sq.(adj) = 0.268
## Scale est. = 1.2666 n = 618## [1] 1960.995##
## Family: gaussian
## Link function: identity
##
## Formula:
## KAngle.2$Ax1[preposts] ~ TreatmentType + TreatmentST + s(BotDep,
## k = 5, bs = "ts")
##
## Parametric coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) -1.45183 0.66591 -2.180 0.02962 *
## TreatmentType 2.24727 0.73358 3.063 0.00228 **
## TreatmentST 0.11343 0.07025 1.615 0.10691
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Approximate significance of smooth terms:
## edf Ref.df F p-value
## s(BotDep) 1.111 4 6.25 5.14e-07 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## R-sq.(adj) = 0.119
## Scale est. = 1.9689 n = 618## [1] 2212.207## (Intercept) TreatmentType TreatmentST s(BotDep).1 s(BotDep).2
## -0.55092383 1.08664323 0.08365974 -0.85459386 3.69084962
## s(BotDep).3 s(BotDep).4
## 6.43465252 -0.77809110