Template
LDA
April 6, 2016
df <- read.xlsx(file="top.species.xlsx",1)
colnames(df)[which(colnames(df)=="Scientific.name")] <- "name"
df$logSPPR <- log10(df$SPPR)p <- ggplot(data=df, aes(x=TL, y=log10(SPPR), colour=name))+
geom_point(size=1)+
scale_x_continuous("Trophic level")+
scale_y_continuous("SPPR (kg-NPP/kg-fish)")+
theme(text = element_text(size=8), legend.position="none")+
geom_smooth(method=lm, se=FALSE, colour="black", size=1)+
ggtitle("Figure 1. Correlation between SPPR and trophic level")+
facet_wrap(~name, scales="fixed")
p
# Create a model to test if coefficients are statistically significantly different from 0
model <- glm(logSPPR ~ name+name*TL, data=df, family=gaussian)
summary(model)##
## Call:
## glm(formula = logSPPR ~ name + name * TL, family = gaussian,
## data = df)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -1.15447 -0.27205 -0.01345 0.26837 1.18990
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 1.75931 1.46384 1.202 0.2301
## nameBrosme brosme -2.04232 1.87504 -1.089 0.2767
## nameClupea harengus -3.41031 1.86162 -1.832 0.0677 .
## nameGadus morhua -3.41698 1.68097 -2.033 0.0427 *
## nameHippoglossoides platessoides 0.20098 1.89525 0.106 0.9156
## nameIllex illecebrosus -1.46438 1.94391 -0.753 0.4517
## nameLophius americanus 0.12725 1.92378 0.066 0.9473
## nameMallotus villosus -3.91042 3.32114 -1.177 0.2397
## nameMelanogrammus aeglefinus -0.48406 2.10149 -0.230 0.8179
## nameMerluccius bilinearis -2.34033 1.80458 -1.297 0.1954
## namePandalus borealis -3.61988 2.01253 -1.799 0.0728 .
## namePollachius virens -1.43212 1.76130 -0.813 0.4166
## namePomatomus saltatrix -3.29376 3.48109 -0.946 0.3446
## nameReinhardtius hippoglossoides -0.61716 1.93103 -0.320 0.7494
## nameSarda sarda -1.56346 2.32311 -0.673 0.5013
## nameScomber japonicus -0.36443 1.74562 -0.209 0.8347
## nameScomber scombrus -1.25672 1.66955 -0.753 0.4520
## nameSqualus acanthias 1.85876 1.95436 0.951 0.3421
## nameThunnus thynnus -3.27724 2.35819 -1.390 0.1653
## nameUrophycis chuss -0.93915 2.21927 -0.423 0.6724
## nameUrophycis tenuis -1.75210 1.77718 -0.986 0.3247
## nameXiphias gladius -3.73230 3.13482 -1.191 0.2345
## TL 0.32034 0.41867 0.765 0.4446
## nameBrosme brosme:TL 0.59212 0.50946 1.162 0.2458
## nameClupea harengus:TL 0.81475 0.54285 1.501 0.1341
## nameGadus morhua:TL 0.84349 0.47049 1.793 0.0737 .
## nameHippoglossoides platessoides:TL -0.09639 0.54344 -0.177 0.8593
## nameIllex illecebrosus:TL 0.28554 0.54109 0.528 0.5980
## nameLophius americanus:TL 0.04862 0.51751 0.094 0.9252
## nameMallotus villosus:TL 0.91647 1.01423 0.904 0.3667
## nameMelanogrammus aeglefinus:TL 0.07113 0.61106 0.116 0.9074
## nameMerluccius bilinearis:TL 0.62617 0.49665 1.261 0.2081
## namePandalus borealis:TL 1.08303 0.68455 1.582 0.1144
## namePollachius virens:TL 0.39004 0.48701 0.801 0.4236
## namePomatomus saltatrix:TL 0.85724 0.86769 0.988 0.3237
## nameReinhardtius hippoglossoides:TL 0.15573 0.51681 0.301 0.7633
## nameSarda sarda:TL 0.43139 0.61126 0.706 0.4807
## nameScomber japonicus:TL 0.02199 0.50294 0.044 0.9651
## nameScomber scombrus:TL 0.28203 0.47415 0.595 0.5523
## nameSqualus acanthias:TL -0.38226 0.53240 -0.718 0.4731
## nameThunnus thynnus:TL 0.82880 0.61005 1.359 0.1750
## nameUrophycis chuss:TL 0.22778 0.64087 0.355 0.7224
## nameUrophycis tenuis:TL 0.50169 0.48730 1.030 0.3038
## nameXiphias gladius:TL 0.96880 0.77892 1.244 0.2143
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for gaussian family taken to be 0.1848093)
##
## Null deviance: 207.639 on 472 degrees of freedom
## Residual deviance: 79.283 on 429 degrees of freedom
## AIC: 587.51
##
## Number of Fisher Scoring iterations: 2Check by another model.
model <- lmList(logSPPR~TL | name, data=df,
na.action=na.exclude)
summary(model)## Call:
## Model: logSPPR ~ TL | name
## Data: df
##
## Coefficients:
## (Intercept)
## Estimate Std. Error t value Pr(>|t|)
## Anarhichas lupus 1.2584181 1.4989485 0.8395340 0.4018167068
## Brosme brosme -0.1692006 1.0900315 -0.1552254 0.8767446520
## Clupea harengus -4.8179778 1.3591872 -3.5447493 0.0004535685
## Gadus morhua -1.9532317 0.7883059 -2.4777585 0.0137535486
## Hippoglossoides platessoides 1.9797885 1.1143379 1.7766500 0.0766064624
## Illex illecebrosus -0.7211318 1.2089844 -0.5964773 0.5512917074
## Lophius americanus 1.8568521 1.4078252 1.3189508 0.1881590377
## Mallotus villosus -2.1257643 2.5811207 -0.8235819 0.4108103192
## Melanogrammus aeglefinus 0.4933043 1.3743031 0.3589487 0.7198777960
## Merluccius bilinearis -0.9079437 1.0208939 -0.8893615 0.3744984327
## Pandalus borealis -1.6915621 1.2152882 -1.3919020 0.1649498829
## Pollachius virens -0.1628028 0.8680935 -0.1875407 0.8513594371
## Pomatomus saltatrix 12.4474755 4.7795939 2.6042956 0.0096497671
## Reinhardtius hippoglossoides -0.2893402 1.3351474 -0.2167103 0.8285766876
## Sarda sarda -0.4384124 1.6301267 -0.2689437 0.7881518735
## Scomber japonicus -0.5159272 1.5131110 -0.3409711 0.7333562774
## Scomber scombrus -1.3592430 1.0798960 -1.2586796 0.2090931587
## Squalus acanthias 2.8943954 1.1445195 2.5289175 0.0119372680
## Thunnus thynnus -2.6745255 1.7112498 -1.5629077 0.1190945330
## Urophycis chuss 1.1894276 1.4298000 0.8318839 0.4061148056
## Urophycis tenuis -0.5786607 1.0212794 -0.5666037 0.5713934588
## Xiphias gladius -4.6993212 2.7036315 -1.7381515 0.0831770701
## TL
## Estimate Std. Error t value Pr(>|t|)
## Anarhichas lupus 0.3942158 0.4322773 0.9119513 3.625030e-01
## Brosme brosme 0.8850474 0.2750589 3.2176650 1.429097e-03
## Clupea harengus 2.1036897 0.4136727 5.0853967 6.362212e-07
## Gadus morhua 1.2266691 0.2036493 6.0234394 4.831289e-09
## Hippoglossoides platessoides 0.2044638 0.3207330 0.6374892 5.242768e-01
## Illex illecebrosus 0.8684425 0.3233993 2.6853565 7.635296e-03
## Lophius americanus 0.3589878 0.3435035 1.0450775 2.968014e-01
## Mallotus villosus 1.2185994 0.7996993 1.5238221 1.285726e-01
## Melanogrammus aeglefinus 0.6035896 0.4049160 1.4906539 1.370692e-01
## Merluccius bilinearis 1.0369250 0.2564211 4.0438364 6.641525e-05
## Pandalus borealis 1.3446764 0.4733385 2.8408346 4.797410e-03
## Pollachius virens 0.8454936 0.2206632 3.8316025 1.541268e-04
## Pomatomus saltatrix -2.0526227 1.1304674 -1.8157292 7.037792e-02
## Reinhardtius hippoglossoides 0.7974903 0.3190438 2.4996263 1.294913e-02
## Sarda sarda 0.9910877 0.4032874 2.4575224 1.453713e-02
## Scomber japonicus 0.9473341 0.4691361 2.0193162 4.431468e-02
## Scomber scombrus 1.1586474 0.3112481 3.7225854 2.341464e-04
## Squalus acanthias 0.1119836 0.2924895 0.3828637 7.020832e-01
## Thunnus thynnus 1.4506124 0.4136860 3.5065539 5.210008e-04
## Urophycis chuss 0.4043846 0.4178451 0.9677860 3.339057e-01
## Urophycis tenuis 0.9502061 0.2541034 3.7394465 2.196216e-04
## Xiphias gladius 1.9673561 0.6443372 3.0533020 2.459534e-03
##
## Residual standard error: 0.3661009 on 310 degrees of freedomp1 <- ggplot(data=df, aes(x=NPP, y=SPPR, colour=name))+
geom_point(size=1)+
scale_x_continuous("Total NPP", trans="log10")+
scale_y_continuous("SPPR (kg-NPP/kg-fish)", trans="log10")+
theme(text = element_text(size=8), legend.position="none")+
geom_smooth(method=lm, se=FALSE, colour="black")+
ggtitle("Figure 2. Correlation between SPPR and Total NPP")+
facet_wrap(~name, scales="fixed")
p1## Warning: Removed 4 rows containing non-finite values (stat_smooth).
# Create a model to test if coefficients are statistically significantly different from 0
model <- glm(logSPPR ~ name+name*NPP, data=df, family=gaussian)
summary(model)##
## Call:
## glm(formula = logSPPR ~ name + name * NPP, family = gaussian,
## data = df)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -1.03596 -0.26866 -0.02809 0.26427 1.19301
##
## Coefficients:
## Estimate Std. Error t value
## (Intercept) 3.142e+00 1.733e-01 18.133
## nameBrosme brosme 4.053e-01 2.481e-01 1.634
## nameClupea harengus -1.055e+00 2.484e-01 -4.246
## nameGadus morhua -1.349e-02 2.142e-01 -0.063
## nameHippoglossoides platessoides -4.310e-01 2.351e-01 -1.833
## nameIllex illecebrosus -9.071e-01 3.152e-01 -2.878
## nameLophius americanus 3.368e-01 2.470e-01 1.364
## nameMallotus villosus -1.272e+00 2.442e-01 -5.208
## nameMelanogrammus aeglefinus -2.078e-01 2.378e-01 -0.874
## nameMerluccius bilinearis 1.866e-01 2.349e-01 0.794
## namePandalus borealis -1.392e+00 2.478e-01 -5.618
## namePollachius virens -1.407e-01 2.352e-01 -0.598
## namePomatomus saltatrix 4.435e-01 2.138e-01 2.075
## nameReinhardtius hippoglossoides -2.670e-01 2.355e-01 -1.134
## nameSarda sarda 2.861e-01 2.130e-01 1.344
## nameScomber japonicus -5.067e-01 2.074e-01 -2.443
## nameScomber scombrus -4.153e-01 1.935e-01 -2.147
## nameSqualus acanthias 2.002e-01 2.714e-01 0.738
## nameThunnus thynnus -2.869e-01 2.542e-01 -1.129
## nameUrophycis chuss -2.275e-01 2.666e-01 -0.853
## nameUrophycis tenuis 5.078e-01 2.393e-01 2.122
## nameXiphias gladius -2.602e-01 3.051e-01 -0.853
## NPP -6.364e-05 3.352e-05 -1.899
## nameBrosme brosme:NPP 2.207e-05 5.082e-05 0.434
## nameClupea harengus:NPP 7.056e-05 5.100e-05 1.383
## nameGadus morhua:NPP -2.478e-05 4.386e-05 -0.565
## nameHippoglossoides platessoides:NPP 7.051e-05 4.864e-05 1.450
## nameIllex illecebrosus:NPP 1.693e-04 8.694e-05 1.948
## nameLophius americanus:NPP 4.157e-05 5.185e-05 0.802
## nameMallotus villosus:NPP 5.429e-05 5.056e-05 1.074
## nameMelanogrammus aeglefinus:NPP -1.422e-05 4.589e-05 -0.310
## nameMerluccius bilinearis:NPP 1.824e-05 4.665e-05 0.391
## namePandalus borealis:NPP 5.320e-05 5.018e-05 1.060
## namePollachius virens:NPP 9.379e-05 4.912e-05 1.909
## namePomatomus saltatrix:NPP 5.097e-05 3.367e-05 1.514
## nameReinhardtius hippoglossoides:NPP 1.444e-04 5.635e-05 2.563
## nameSarda sarda:NPP 5.245e-05 3.367e-05 1.558
## nameScomber japonicus:NPP 5.875e-05 3.367e-05 1.745
## nameScomber scombrus:NPP 5.774e-05 3.366e-05 1.716
## nameSqualus acanthias:NPP 7.305e-05 6.344e-05 1.151
## nameThunnus thynnus:NPP 1.664e-04 5.082e-05 3.275
## nameUrophycis chuss:NPP 1.833e-05 4.901e-05 0.374
## nameUrophycis tenuis:NPP -1.661e-05 4.689e-05 -0.354
## nameXiphias gladius:NPP 2.067e-04 6.471e-05 3.194
## Pr(>|t|)
## (Intercept) < 2e-16 ***
## nameBrosme brosme 0.10305
## nameClupea harengus 2.67e-05 ***
## nameGadus morhua 0.94982
## nameHippoglossoides platessoides 0.06747 .
## nameIllex illecebrosus 0.00420 **
## nameLophius americanus 0.17339
## nameMallotus villosus 2.97e-07 ***
## nameMelanogrammus aeglefinus 0.38262
## nameMerluccius bilinearis 0.42745
## namePandalus borealis 3.47e-08 ***
## namePollachius virens 0.55005
## namePomatomus saltatrix 0.03861 *
## nameReinhardtius hippoglossoides 0.25749
## nameSarda sarda 0.17980
## nameScomber japonicus 0.01497 *
## nameScomber scombrus 0.03239 *
## nameSqualus acanthias 0.46099
## nameThunnus thynnus 0.25974
## nameUrophycis chuss 0.39403
## nameUrophycis tenuis 0.03443 *
## nameXiphias gladius 0.39424
## NPP 0.05828 .
## nameBrosme brosme:NPP 0.66429
## nameClupea harengus:NPP 0.16724
## nameGadus morhua:NPP 0.57245
## nameHippoglossoides platessoides:NPP 0.14784
## nameIllex illecebrosus:NPP 0.05209 .
## nameLophius americanus:NPP 0.42315
## nameMallotus villosus:NPP 0.28352
## nameMelanogrammus aeglefinus:NPP 0.75683
## nameMerluccius bilinearis:NPP 0.69591
## namePandalus borealis:NPP 0.28966
## namePollachius virens:NPP 0.05687 .
## namePomatomus saltatrix:NPP 0.13077
## nameReinhardtius hippoglossoides:NPP 0.01072 *
## nameSarda sarda:NPP 0.12000
## nameScomber japonicus:NPP 0.08171 .
## nameScomber scombrus:NPP 0.08696 .
## nameSqualus acanthias:NPP 0.25018
## nameThunnus thynnus:NPP 0.00114 **
## nameUrophycis chuss:NPP 0.70859
## nameUrophycis tenuis:NPP 0.72333
## nameXiphias gladius:NPP 0.00151 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for gaussian family taken to be 0.198843)
##
## Null deviance: 207.639 on 472 degrees of freedom
## Residual deviance: 85.304 on 429 degrees of freedom
## AIC: 622.12
##
## Number of Fisher Scoring iterations: 2Check by another model.
model <- lmList(logSPPR~NPP | name, data=df,
na.action=na.exclude)
summary(model)## Call:
## Model: logSPPR ~ NPP | name
## Data: df
##
## Coefficients:
## (Intercept)
## Estimate Std. Error t value Pr(>|t|)
## Anarhichas lupus 2.785237 0.2729883 10.202770 0.000000e+00
## Brosme brosme 3.457855 0.1989972 17.376402 0.000000e+00
## Clupea harengus 2.011896 0.1907130 10.549341 0.000000e+00
## Gadus morhua 3.122721 0.1400277 22.300727 0.000000e+00
## Hippoglossoides platessoides 2.640162 0.1668067 15.827669 0.000000e+00
## Illex illecebrosus 2.153018 0.2683553 8.023012 2.131628e-14
## Lophius americanus 3.354158 0.1929894 17.380013 0.000000e+00
## Mallotus villosus 1.825052 0.1946772 9.374763 0.000000e+00
## Melanogrammus aeglefinus 2.869743 0.1746661 16.429881 0.000000e+00
## Merluccius bilinearis 3.464389 0.1729471 20.031496 0.000000e+00
## Pandalus borealis 1.831971 0.1854752 9.877175 0.000000e+00
## Pollachius virens 3.049317 0.1651895 18.459511 0.000000e+00
## Pomatomus saltatrix 5.115783 0.5837840 8.763144 0.000000e+00
## Reinhardtius hippoglossoides 2.726441 0.1707774 15.964881 0.000000e+00
## Sarda sarda 3.033852 0.4121478 7.361076 1.652234e-12
## Scomber japonicus 2.644065 0.3236158 8.170382 7.993606e-15
## Scomber scombrus 2.832721 0.1877295 15.089381 0.000000e+00
## Squalus acanthias 3.226796 0.2195242 14.699045 0.000000e+00
## Thunnus thynnus 2.858781 0.2005316 14.256014 0.000000e+00
## Urophycis chuss 2.668432 0.2419349 11.029545 0.000000e+00
## Urophycis tenuis 3.538447 0.1834178 19.291731 0.000000e+00
## Xiphias gladius 2.910885 0.2942926 9.891126 0.000000e+00
## NPP
## Estimate Std. Error t value
## Anarhichas lupus -2.763140e-05 3.900118e-05 -0.7084760
## Brosme brosme -3.110010e-05 3.858281e-05 -0.8060610
## Clupea harengus 1.618146e-05 3.829695e-05 0.4225261
## Gadus morhua -8.643421e-05 2.811427e-05 -3.0743893
## Hippoglossoides platessoides 1.252325e-05 3.458867e-05 0.3620622
## Illex illecebrosus 1.186751e-04 7.836367e-05 1.5144154
## Lophius americanus -7.088978e-06 3.970808e-05 -0.1785273
## Mallotus villosus -5.284396e-06 3.774679e-05 -0.1399959
## Melanogrammus aeglefinus -7.143809e-05 3.138057e-05 -2.2765070
## Merluccius bilinearis -5.840093e-05 3.257943e-05 -1.7925707
## Pandalus borealis -1.936831e-05 3.692363e-05 -0.5245504
## Pollachius virens 2.585027e-05 3.539429e-05 0.7303513
## Pomatomus saltatrix -1.864350e-04 7.848884e-05 -2.3753064
## Reinhardtius hippoglossoides 9.961077e-05 4.451701e-05 2.2375888
## Sarda sarda 9.162083e-05 6.771877e-05 1.3529608
## Scomber japonicus -1.919375e-05 5.231503e-05 -0.3668880
## Scomber scombrus -4.184333e-05 3.624793e-05 -1.1543647
## Squalus acanthias 2.890241e-05 5.338700e-05 0.5413754
## Thunnus thynnus 1.074043e-04 3.909138e-05 2.7475175
## Urophycis chuss -1.812055e-05 3.794463e-05 -0.4775525
## Urophycis tenuis -6.781879e-05 3.320690e-05 -2.0423100
## Xiphias gladius 1.451377e-04 6.146095e-05 2.3614614
## Pr(>|t|)
## Anarhichas lupus 0.479182109
## Brosme brosme 0.420825571
## Clupea harengus 0.672933996
## Gadus morhua 0.002296958
## Hippoglossoides platessoides 0.717552204
## Illex illecebrosus 0.130939423
## Lophius americanus 0.858425466
## Mallotus villosus 0.888754119
## Melanogrammus aeglefinus 0.023497177
## Merluccius bilinearis 0.074016515
## Pandalus borealis 0.600270685
## Pollachius virens 0.465727076
## Pomatomus saltatrix 0.018142322
## Reinhardtius hippoglossoides 0.025958102
## Sarda sarda 0.177054038
## Scomber japonicus 0.713952878
## Scomber scombrus 0.249239791
## Squalus acanthias 0.588637692
## Thunnus thynnus 0.006356310
## Urophycis chuss 0.633305268
## Urophycis tenuis 0.041966638
## Xiphias gladius 0.018821307
##
## Residual standard error: 0.4314629 on 310 degrees of freedomp2 <- ggplot(data=df, aes(x=PB, y=SPPR, colour=name))+
geom_point(size=1)+
scale_x_continuous("Specific production rate", trans="log10")+
scale_y_continuous("SPPR (kg-NPP/kg-fish)", trans="log10")+
theme(text = element_text(size=8), legend.position="none")+
geom_smooth(method=lm, se=FALSE, colour="black")+
ggtitle("Figure 3.Correlation between SPPR and Specific production rate (P/B)")+
facet_wrap(~name, scales="fixed")
p2## Warning: Removed 9 rows containing non-finite values (stat_smooth).## Warning: Removed 9 rows containing missing values (geom_point).
# Create a model to test if coefficients are statistically significantly different from 0
model <- glm(logSPPR ~ name+name*PB, data=df, family=gaussian)
summary(model)##
## Call:
## glm(formula = logSPPR ~ name + name * PB, family = gaussian,
## data = df)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -1.41054 -0.26651 0.00176 0.26018 1.43345
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 3.692407 0.295427 12.499 < 2e-16
## nameBrosme brosme 0.360723 0.387162 0.932 0.352022
## nameClupea harengus -1.106903 0.359978 -3.075 0.002243
## nameGadus morhua -0.398379 0.336374 -1.184 0.236950
## nameHippoglossoides platessoides -0.925854 0.368371 -2.513 0.012332
## nameIllex illecebrosus -1.126454 0.350152 -3.217 0.001395
## nameLophius americanus 0.086107 0.365108 0.236 0.813671
## nameMallotus villosus -1.495252 0.409768 -3.649 0.000296
## nameMelanogrammus aeglefinus -0.829293 0.363373 -2.282 0.022976
## nameMerluccius bilinearis -0.162973 0.346085 -0.471 0.637953
## namePandalus borealis -2.232226 0.544642 -4.099 4.99e-05
## namePollachius virens -0.024063 0.356565 -0.067 0.946227
## namePomatomus saltatrix 0.248183 0.396471 0.626 0.531667
## nameReinhardtius hippoglossoides -0.026528 0.340781 -0.078 0.937988
## nameSarda sarda -0.002147 0.390247 -0.006 0.995612
## nameScomber japonicus -0.761501 0.386058 -1.973 0.049208
## nameScomber scombrus -0.993359 0.323887 -3.067 0.002302
## nameSqualus acanthias 0.205239 0.385276 0.533 0.594518
## nameThunnus thynnus -1.164804 0.482811 -2.413 0.016269
## nameUrophycis chuss -0.716415 0.391204 -1.831 0.067763
## nameUrophycis tenuis 0.268412 0.360223 0.745 0.456611
## nameXiphias gladius -0.727076 0.369813 -1.966 0.049950
## PB -1.899101 0.647347 -2.934 0.003533
## nameBrosme brosme:PB 0.158774 0.884651 0.179 0.857650
## nameClupea harengus:PB 1.171571 0.706024 1.659 0.097783
## nameGadus morhua:PB 1.201253 0.679672 1.767 0.077887
## nameHippoglossoides platessoides:PB 1.838040 0.761388 2.414 0.016202
## nameIllex illecebrosus:PB 1.878490 0.668233 2.811 0.005168
## nameLophius americanus:PB 0.890389 0.824559 1.080 0.280835
## nameMallotus villosus:PB 1.550296 0.696050 2.227 0.026458
## nameMelanogrammus aeglefinus:PB 1.366100 0.754536 1.811 0.070930
## nameMerluccius bilinearis:PB 1.164122 0.714374 1.630 0.103942
## namePandalus borealis:PB 2.057331 0.706828 2.911 0.003799
## namePollachius virens:PB 0.634291 0.768138 0.826 0.409414
## namePomatomus saltatrix:PB 1.297943 0.699262 1.856 0.064131
## nameReinhardtius hippoglossoides:PB 0.756548 0.717386 1.055 0.292219
## nameSarda sarda:PB 1.454566 0.690572 2.106 0.035769
## nameScomber japonicus:PB 1.486953 0.691445 2.151 0.032086
## nameScomber scombrus:PB 1.839715 0.674539 2.727 0.006652
## nameSqualus acanthias:PB 0.229125 0.975213 0.235 0.814363
## nameThunnus thynnus:PB 3.733385 1.126599 3.314 0.001000
## nameUrophycis chuss:PB 1.213484 0.867792 1.398 0.162744
## nameUrophycis tenuis:PB 0.268386 0.798902 0.336 0.737081
## nameXiphias gladius:PB 2.738097 0.721855 3.793 0.000171
##
## (Intercept) ***
## nameBrosme brosme
## nameClupea harengus **
## nameGadus morhua
## nameHippoglossoides platessoides *
## nameIllex illecebrosus **
## nameLophius americanus
## nameMallotus villosus ***
## nameMelanogrammus aeglefinus *
## nameMerluccius bilinearis
## namePandalus borealis ***
## namePollachius virens
## namePomatomus saltatrix
## nameReinhardtius hippoglossoides
## nameSarda sarda
## nameScomber japonicus *
## nameScomber scombrus **
## nameSqualus acanthias
## nameThunnus thynnus *
## nameUrophycis chuss .
## nameUrophycis tenuis
## nameXiphias gladius *
## PB **
## nameBrosme brosme:PB
## nameClupea harengus:PB .
## nameGadus morhua:PB .
## nameHippoglossoides platessoides:PB *
## nameIllex illecebrosus:PB **
## nameLophius americanus:PB
## nameMallotus villosus:PB *
## nameMelanogrammus aeglefinus:PB .
## nameMerluccius bilinearis:PB
## namePandalus borealis:PB **
## namePollachius virens:PB
## namePomatomus saltatrix:PB .
## nameReinhardtius hippoglossoides:PB
## nameSarda sarda:PB *
## nameScomber japonicus:PB *
## nameScomber scombrus:PB **
## nameSqualus acanthias:PB
## nameThunnus thynnus:PB ***
## nameUrophycis chuss:PB
## nameUrophycis tenuis:PB
## nameXiphias gladius:PB ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for gaussian family taken to be 0.1897084)
##
## Null deviance: 206.486 on 463 degrees of freedom
## Residual deviance: 79.678 on 420 degrees of freedom
## (9 observations deleted due to missingness)
## AIC: 589.25
##
## Number of Fisher Scoring iterations: 2Check by another model.
model <- lmList(logSPPR~PB | name, data=df,
na.action=na.exclude)
summary(model)## Call:
## Model: logSPPR ~ PB | name
## Data: df
##
## Coefficients:
## (Intercept)
## Estimate Std. Error t value Pr(>|t|)
## Anarhichas lupus 3.602937 0.5980997 6.023974 4.817017e-09
## Brosme brosme 3.958837 0.2432424 16.275278 0.000000e+00
## Clupea harengus 2.577960 0.2101128 12.269408 0.000000e+00
## Gadus morhua 3.245514 0.1574353 20.614900 0.000000e+00
## Hippoglossoides platessoides 2.722946 0.2261258 12.041731 0.000000e+00
## Illex illecebrosus 2.516253 0.1898686 13.252604 0.000000e+00
## Lophius americanus 3.711902 0.2146667 17.291463 0.000000e+00
## Mallotus villosus 2.200156 0.3047821 7.218782 4.069856e-12
## Melanogrammus aeglefinus 2.731831 0.2108068 12.958931 0.000000e+00
## Merluccius bilinearis 3.877482 0.2137897 18.136900 0.000000e+00
## Pandalus borealis 1.478523 0.4231699 3.493923 5.452927e-04
## Pollachius virens 3.747949 0.1915581 19.565603 0.000000e+00
## Pomatomus saltatrix 2.880269 0.6243703 4.613078 5.812767e-06
## Reinhardtius hippoglossoides 3.570912 0.1755526 20.340987 0.000000e+00
## Sarda sarda 3.576229 0.3598244 9.938819 0.000000e+00
## Scomber japonicus 3.651848 0.3150483 11.591391 0.000000e+00
## Scomber scombrus 2.782539 0.2063734 13.483033 0.000000e+00
## Squalus acanthias 3.583709 0.2420234 14.807284 0.000000e+00
## Thunnus thynnus 2.583814 0.3507086 7.367412 1.586731e-12
## Urophycis chuss 2.723715 0.2663125 10.227514 0.000000e+00
## Urophycis tenuis 3.886584 0.2078737 18.696855 0.000000e+00
## Xiphias gladius 3.104245 0.2111263 14.703260 0.000000e+00
## PB
## Estimate Std. Error t value
## Anarhichas lupus -1.76673932 1.0490041 -1.68420624
## Brosme brosme -1.62041561 0.5632417 -2.87694542
## Clupea harengus -0.72057340 0.2694590 -2.67414876
## Gadus morhua -0.71957375 0.2106564 -3.41586501
## Hippoglossoides platessoides -0.06737824 0.3968532 -0.16978127
## Illex illecebrosus -0.00334410 0.1548715 -0.02159274
## Lophius americanus -0.97130323 0.4812758 -2.01818414
## Mallotus villosus -0.35766362 0.2548193 -1.40359689
## Melanogrammus aeglefinus -0.37563748 0.3706517 -1.01345132
## Merluccius bilinearis -1.57988401 0.4578340 -3.45077910
## Pandalus borealis 0.17418887 0.2627308 0.66299374
## Pollachius virens -1.32981943 0.3840391 -3.46271871
## Pomatomus saltatrix 1.17554744 0.8043210 1.46154012
## Reinhardtius hippoglossoides -1.09180790 0.3119202 -3.50027954
## Sarda sarda -0.02369637 0.3999142 -0.05925363
## Scomber japonicus -1.44982411 0.3841791 -3.77382325
## Scomber scombrus -0.30732858 0.4243290 -0.72426951
## Squalus acanthias -0.81223125 0.7137235 -1.13801947
## Thunnus thynnus 1.84765444 0.8448982 2.18683664
## Urophycis chuss -0.35670906 0.5549485 -0.64277871
## Urophycis tenuis -1.57806006 0.4433013 -3.55979105
## Xiphias gladius 0.72494067 0.2961337 2.44801777
## Pr(>|t|)
## Anarhichas lupus 0.0931483473
## Brosme brosme 0.0042939876
## Clupea harengus 0.0078891520
## Gadus morhua 0.0007205403
## Hippoglossoides platessoides 0.8652928972
## Illex illecebrosus 0.9827867128
## Lophius americanus 0.0444331072
## Mallotus villosus 0.1614398323
## Melanogrammus aeglefinus 0.3116349693
## Merluccius bilinearis 0.0006364958
## Pandalus borealis 0.5078272282
## Pollachius virens 0.0006099232
## Pomatomus saltatrix 0.1448801705
## Reinhardtius hippoglossoides 0.0005329379
## Sarda sarda 0.9527882722
## Scomber japonicus 0.0001926005
## Scomber scombrus 0.4694465327
## Squalus acanthias 0.2559911081
## Thunnus thynnus 0.0295015670
## Urophycis chuss 0.5208428227
## Urophycis tenuis 0.0004293320
## Xiphias gladius 0.0149186351
##
## Residual standard error: 0.3991039 on 310 degrees of freedomp3 <- ggplot(data=df, aes(x=PQ, y=SPPR, colour=name))+
geom_point(size=1)+
scale_x_continuous("P/Q", trans="log10")+
scale_y_continuous("SPPR (kg-NPP/kg-fish)", trans="log10")+
theme(text = element_text(size=8), legend.position="none")+
geom_smooth(method=lm, se=FALSE, colour="black")+
ggtitle("Figure 4. Correlation between SPPR and growth efficiency (P/Q)")+
facet_wrap(~name, scales="fixed")
p3
# Create a model to test if coefficients are statistically significantly different from 0
model <- glm(logSPPR ~ name+name*PQ, data=df, family=gaussian)
summary(model)##
## Call:
## glm(formula = logSPPR ~ name + name * PQ, family = gaussian,
## data = df)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -1.50455 -0.27784 0.00667 0.28571 1.15594
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 3.17472 0.49420 6.424 3.53e-10
## nameBrosme brosme 0.93219 0.58885 1.583 0.114146
## nameClupea harengus -0.83771 0.59236 -1.414 0.158026
## nameGadus morhua -0.62099 0.53624 -1.158 0.247488
## nameHippoglossoides platessoides -0.52325 0.56849 -0.920 0.357870
## nameIllex illecebrosus -0.72949 0.55066 -1.325 0.185964
## nameLophius americanus 0.40653 0.52813 0.770 0.441862
## nameMallotus villosus -0.98964 0.59451 -1.665 0.096714
## nameMelanogrammus aeglefinus -0.28034 0.59588 -0.470 0.638265
## nameMerluccius bilinearis -0.08726 0.52683 -0.166 0.868522
## namePandalus borealis -2.05428 0.55894 -3.675 0.000268
## namePollachius virens -0.02916 0.52506 -0.056 0.955736
## namePomatomus saltatrix 0.39266 0.52228 0.752 0.452575
## nameReinhardtius hippoglossoides 0.16166 0.52718 0.307 0.759258
## nameSarda sarda 0.21650 0.52426 0.413 0.679843
## nameScomber japonicus -0.53799 0.51820 -1.038 0.299773
## nameScomber scombrus -0.13264 0.53891 -0.246 0.805702
## nameSqualus acanthias 0.32354 0.51949 0.623 0.533740
## nameThunnus thynnus 0.14243 0.52754 0.270 0.787304
## nameUrophycis chuss -0.86953 1.23307 -0.705 0.481082
## nameUrophycis tenuis 0.24353 0.52652 0.463 0.643935
## nameXiphias gladius 0.32309 0.53017 0.609 0.542580
## PQ -1.91365 3.09734 -0.618 0.537011
## nameBrosme brosme:PQ -3.59867 3.86822 -0.930 0.352730
## nameClupea harengus:PQ 0.58243 3.61021 0.161 0.871911
## nameGadus morhua:PQ 3.02091 3.21124 0.941 0.347374
## nameHippoglossoides platessoides:PQ 2.33566 3.36190 0.695 0.487592
## nameIllex illecebrosus:PQ 2.32574 3.21159 0.724 0.469356
## nameLophius americanus:PQ 0.93872 3.20588 0.293 0.769806
## nameMallotus villosus:PQ 0.41790 3.37277 0.124 0.901448
## nameMelanogrammus aeglefinus:PQ 0.01576 3.71350 0.004 0.996615
## nameMerluccius bilinearis:PQ 2.23456 3.21564 0.695 0.487493
## namePandalus borealis:PQ 4.80844 3.31233 1.452 0.147321
## namePollachius virens:PQ 1.73958 3.20974 0.542 0.588121
## namePomatomus saltatrix:PQ 0.78617 3.16403 0.248 0.803888
## nameReinhardtius hippoglossoides:PQ 0.84307 3.19451 0.264 0.791974
## nameSarda sarda:PQ 1.13047 3.16449 0.357 0.721090
## nameScomber japonicus:PQ 1.54739 3.13962 0.493 0.622365
## nameScomber scombrus:PQ -0.76327 3.40059 -0.224 0.822512
## nameSqualus acanthias:PQ 1.13392 3.19277 0.355 0.722650
## nameThunnus thynnus:PQ 1.58481 3.21828 0.492 0.622660
## nameUrophycis chuss:PQ 4.70298 8.51026 0.553 0.580808
## nameUrophycis tenuis:PQ 1.35193 3.20958 0.421 0.673807
## nameXiphias gladius:PQ 1.71419 3.21985 0.532 0.594737
##
## (Intercept) ***
## nameBrosme brosme
## nameClupea harengus
## nameGadus morhua
## nameHippoglossoides platessoides
## nameIllex illecebrosus
## nameLophius americanus
## nameMallotus villosus .
## nameMelanogrammus aeglefinus
## nameMerluccius bilinearis
## namePandalus borealis ***
## namePollachius virens
## namePomatomus saltatrix
## nameReinhardtius hippoglossoides
## nameSarda sarda
## nameScomber japonicus
## nameScomber scombrus
## nameSqualus acanthias
## nameThunnus thynnus
## nameUrophycis chuss
## nameUrophycis tenuis
## nameXiphias gladius
## PQ
## nameBrosme brosme:PQ
## nameClupea harengus:PQ
## nameGadus morhua:PQ
## nameHippoglossoides platessoides:PQ
## nameIllex illecebrosus:PQ
## nameLophius americanus:PQ
## nameMallotus villosus:PQ
## nameMelanogrammus aeglefinus:PQ
## nameMerluccius bilinearis:PQ
## namePandalus borealis:PQ
## namePollachius virens:PQ
## namePomatomus saltatrix:PQ
## nameReinhardtius hippoglossoides:PQ
## nameSarda sarda:PQ
## nameScomber japonicus:PQ
## nameScomber scombrus:PQ
## nameSqualus acanthias:PQ
## nameThunnus thynnus:PQ
## nameUrophycis chuss:PQ
## nameUrophycis tenuis:PQ
## nameXiphias gladius:PQ
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for gaussian family taken to be 0.2227153)
##
## Null deviance: 207.639 on 472 degrees of freedom
## Residual deviance: 95.545 on 429 degrees of freedom
## AIC: 675.75
##
## Number of Fisher Scoring iterations: 2Check by another model.
model <- lmList(logSPPR~PQ | name, data=df,
na.action=na.exclude)
summary(model)## Call:
## Model: logSPPR ~ PQ | name
## Data: df
##
## Coefficients:
## (Intercept)
## Estimate Std. Error t value Pr(>|t|)
## Anarhichas lupus 2.741628 0.5041130 5.438518 1.091187e-07
## Brosme brosme 3.993590 0.3254329 12.271621 0.000000e+00
## Clupea harengus 2.191985 0.3658652 5.991237 5.771499e-09
## Gadus morhua 2.586800 0.2068416 12.506188 0.000000e+00
## Hippoglossoides platessoides 2.653249 0.2743510 9.671003 0.000000e+00
## Illex illecebrosus 2.336560 0.2654615 8.801881 0.000000e+00
## Lophius americanus 3.466431 0.2048751 16.919727 0.000000e+00
## Mallotus villosus 2.100646 0.3887380 5.403759 1.303252e-07
## Melanogrammus aeglefinus 2.773850 0.3524249 7.870755 5.950795e-14
## Merluccius bilinearis 3.206821 0.1849543 17.338450 0.000000e+00
## Pandalus borealis 1.157955 0.2669043 4.338464 1.943707e-05
## Pollachius virens 3.222974 0.1830314 17.608860 0.000000e+00
## Pomatomus saltatrix 4.721005 0.8367063 5.642369 3.784074e-08
## Reinhardtius hippoglossoides 3.208597 0.1956268 16.401625 0.000000e+00
## Sarda sarda 3.689916 0.5014257 7.358849 1.675993e-12
## Scomber japonicus 2.877578 0.2015324 14.278486 0.000000e+00
## Scomber scombrus 3.044810 0.2276470 13.375139 0.000000e+00
## Squalus acanthias 3.432534 0.1641037 20.916859 0.000000e+00
## Thunnus thynnus 3.989535 0.3485573 11.445854 0.000000e+00
## Urophycis chuss 2.894725 1.1074597 2.613842 9.390020e-03
## Urophycis tenuis 3.251995 0.1961208 16.581586 0.000000e+00
## Xiphias gladius 3.686814 0.3540485 10.413303 0.000000e+00
## PQ
## Estimate Std. Error t value
## Anarhichas lupus -0.74558680 2.9733455 -0.250756867
## Brosme brosme -4.97412046 2.2640406 -2.197010230
## Clupea harengus -0.63176753 1.9587358 -0.322538401
## Gadus morhua 0.84315429 0.8381830 1.005931040
## Hippoglossoides platessoides 0.17413871 1.2684729 0.137282170
## Illex illecebrosus 0.64896530 0.8537006 0.760179064
## Lophius americanus -0.67140439 0.8269531 -0.811901373
## Mallotus villosus -1.17327160 1.4511139 -0.808531693
## Melanogrammus aeglefinus -1.45301915 2.0847770 -0.696966234
## Merluccius bilinearis 0.00143414 0.8285344 0.001730935
## Pandalus borealis 2.78921958 1.1461784 2.433495094
## Pollachius virens -0.37777755 0.8215303 -0.459846141
## Pomatomus saltatrix -7.14349382 6.1968731 -1.152757811
## Reinhardtius hippoglossoides -0.75606858 0.7624376 -0.991646514
## Sarda sarda -0.86496550 3.1025824 -0.278788885
## Scomber japonicus -1.95301903 0.9210043 -2.120531852
## Scomber scombrus -2.78207005 1.4275801 -1.948801339
## Squalus acanthias -0.60776704 0.7402231 -0.821059266
## Thunnus thynnus -4.94925092 2.4204540 -2.044761402
## Urophycis chuss -2.34079122 7.9139110 -0.295781848
## Urophycis tenuis -0.12716053 0.8321649 -0.152806891
## Xiphias gladius -0.96743816 2.3618997 -0.409601715
## Pr(>|t|)
## Anarhichas lupus 0.80216821
## Brosme brosme 0.02875950
## Clupea harengus 0.74726227
## Gadus morhua 0.31523327
## Hippoglossoides platessoides 0.89089688
## Illex illecebrosus 0.44772531
## Lophius americanus 0.41747121
## Mallotus villosus 0.41940462
## Melanogrammus aeglefinus 0.48634624
## Merluccius bilinearis 0.99862003
## Pandalus borealis 0.01551868
## Pollachius virens 0.64594900
## Pomatomus saltatrix 0.24989791
## Reinhardtius hippoglossoides 0.32214337
## Sarda sarda 0.78059273
## Scomber japonicus 0.03475506
## Scomber scombrus 0.05222101
## Squalus acanthias 0.41224346
## Thunnus thynnus 0.04172267
## Urophycis chuss 0.76759472
## Urophycis tenuis 0.87864998
## Xiphias gladius 0.68238102
##
## Residual standard error: 0.4463389 on 310 degrees of freedomp4 <- ggplot(data=df, aes(x=TE, y=SPPR, colour=name))+
geom_point(size=1)+
scale_x_continuous("TE", trans="log10")+
scale_y_continuous("SPPR (kg-NPP/kg-fish)", trans="log10")+
theme(text = element_text(size=8), legend.position="none")+
geom_smooth(method=lm, se=FALSE, colour="black")+
ggtitle("Figure 5. Correlation between SPPR and transfer efficiency")+
facet_wrap(~name, scales="fixed")
p4## Warning: Removed 4 rows containing non-finite values (stat_smooth).
# Create a model to test if coefficients are statistically significantly different from 0
model <- glm(logSPPR ~ name+name*TE, data=df, family=gaussian)
summary(model)##
## Call:
## glm(formula = logSPPR ~ name + name * TE, family = gaussian,
## data = df)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -1.39116 -0.31860 0.02373 0.30934 1.20001
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 3.23768 0.55467 5.837 1.05e-08
## nameBrosme brosme 1.03043 0.81705 1.261 0.2079
## nameClupea harengus -1.40507 0.76456 -1.838 0.0668
## nameGadus morhua 0.20922 0.73153 0.286 0.7750
## nameHippoglossoides platessoides -0.93076 0.76541 -1.216 0.2246
## nameIllex illecebrosus -1.47771 0.94657 -1.561 0.1192
## nameLophius americanus 1.22688 0.80296 1.528 0.1273
## nameMallotus villosus -0.88871 0.81395 -1.092 0.2755
## nameMelanogrammus aeglefinus -0.46314 0.78880 -0.587 0.5574
## nameMerluccius bilinearis 0.83273 0.81111 1.027 0.3052
## namePandalus borealis -1.89080 0.78765 -2.401 0.0168
## namePollachius virens -0.15355 0.75190 -0.204 0.8383
## namePomatomus saltatrix -0.31904 0.60098 -0.531 0.5958
## nameReinhardtius hippoglossoides 0.56738 0.76671 0.740 0.4597
## nameSarda sarda -0.29333 0.60213 -0.487 0.6264
## nameScomber japonicus -0.51237 0.61597 -0.832 0.4060
## nameScomber scombrus -0.44322 0.59907 -0.740 0.4598
## nameSqualus acanthias 0.69339 0.88307 0.785 0.4328
## nameThunnus thynnus -0.91646 0.91600 -1.001 0.3176
## nameUrophycis chuss 0.30619 0.93973 0.326 0.7447
## nameUrophycis tenuis 1.65006 0.81112 2.034 0.0425
## nameXiphias gladius 1.13839 0.86987 1.309 0.1913
## TE -0.02881 0.04343 -0.663 0.5075
## nameBrosme brosme:TE -0.03850 0.06266 -0.614 0.5393
## nameClupea harengus:TE 0.05048 0.05883 0.858 0.3913
## nameGadus morhua:TE -0.02061 0.05663 -0.364 0.7161
## nameHippoglossoides platessoides:TE 0.06300 0.05990 1.052 0.2935
## nameIllex illecebrosus:TE 0.09028 0.07338 1.230 0.2192
## nameLophius americanus:TE -0.05352 0.06189 -0.865 0.3877
## nameMallotus villosus:TE -0.01242 0.06411 -0.194 0.8464
## nameMelanogrammus aeglefinus:TE 0.01547 0.06044 0.256 0.7982
## nameMerluccius bilinearis:TE -0.04205 0.06237 -0.674 0.5006
## namePandalus borealis:TE 0.05675 0.06066 0.936 0.3500
## namePollachius virens:TE 0.03111 0.05805 0.536 0.5922
## namePomatomus saltatrix:TE 0.07455 0.04817 1.547 0.1225
## nameReinhardtius hippoglossoides:TE -0.02537 0.05978 -0.424 0.6715
## nameSarda sarda:TE 0.06010 0.04861 1.236 0.2170
## nameScomber japonicus:TE 0.01464 0.04808 0.305 0.7609
## nameScomber scombrus:TE 0.01726 0.04733 0.365 0.7155
## nameSqualus acanthias:TE -0.01375 0.06775 -0.203 0.8392
## nameThunnus thynnus:TE 0.09776 0.06832 1.431 0.1532
## nameUrophycis chuss:TE -0.03669 0.07262 -0.505 0.6137
## nameUrophycis tenuis:TE -0.09187 0.06242 -1.472 0.1418
## nameXiphias gladius:TE -0.03851 0.06523 -0.590 0.5553
##
## (Intercept) ***
## nameBrosme brosme
## nameClupea harengus .
## nameGadus morhua
## nameHippoglossoides platessoides
## nameIllex illecebrosus
## nameLophius americanus
## nameMallotus villosus
## nameMelanogrammus aeglefinus
## nameMerluccius bilinearis
## namePandalus borealis *
## namePollachius virens
## namePomatomus saltatrix
## nameReinhardtius hippoglossoides
## nameSarda sarda
## nameScomber japonicus
## nameScomber scombrus
## nameSqualus acanthias
## nameThunnus thynnus
## nameUrophycis chuss
## nameUrophycis tenuis *
## nameXiphias gladius
## TE
## nameBrosme brosme:TE
## nameClupea harengus:TE
## nameGadus morhua:TE
## nameHippoglossoides platessoides:TE
## nameIllex illecebrosus:TE
## nameLophius americanus:TE
## nameMallotus villosus:TE
## nameMelanogrammus aeglefinus:TE
## nameMerluccius bilinearis:TE
## namePandalus borealis:TE
## namePollachius virens:TE
## namePomatomus saltatrix:TE
## nameReinhardtius hippoglossoides:TE
## nameSarda sarda:TE
## nameScomber japonicus:TE
## nameScomber scombrus:TE
## nameSqualus acanthias:TE
## nameThunnus thynnus:TE
## nameUrophycis chuss:TE
## nameUrophycis tenuis:TE
## nameXiphias gladius:TE
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for gaussian family taken to be 0.2200918)
##
## Null deviance: 207.639 on 472 degrees of freedom
## Residual deviance: 94.419 on 429 degrees of freedom
## AIC: 670.15
##
## Number of Fisher Scoring iterations: 2Check by another model.
model <- lmList(logSPPR~TE | name, data=df,
na.action=na.exclude)
summary(model)## Call:
## Model: logSPPR ~ TE | name
## Data: df
##
## Coefficients:
## (Intercept)
## Estimate Std. Error t value Pr(>|t|)
## Anarhichas lupus 2.684465 0.7551268 3.554986 4.369397e-04
## Brosme brosme 3.855206 0.6962218 5.537324 6.555126e-08
## Clupea harengus 1.603172 0.5443231 2.945259 3.471122e-03
## Gadus morhua 3.443961 0.5307319 6.489078 3.416885e-10
## Hippoglossoides platessoides 2.387162 0.5503768 4.337323 1.953238e-05
## Illex illecebrosus 1.142633 0.8515787 1.341782 1.806488e-01
## Lophius americanus 4.274722 0.6562375 6.513987 2.953546e-10
## Mallotus villosus 2.241104 0.6467910 3.464959 6.050551e-04
## Melanogrammus aeglefinus 2.838139 0.5878350 4.828122 2.168202e-06
## Merluccius bilinearis 4.577823 0.6744495 6.787495 5.809198e-11
## Pandalus borealis 1.357897 0.5755772 2.359192 1.893472e-02
## Pollachius virens 2.942035 0.5219106 5.637049 3.891594e-08
## Pomatomus saltatrix 4.866336 0.7432756 6.547149 2.431184e-10
## Reinhardtius hippoglossoides 3.254757 0.5993597 5.430391 1.137540e-07
## Sarda sarda 5.153225 0.8239477 6.254310 1.322754e-09
## Scomber japonicus 3.123062 0.6912649 4.517895 8.891859e-06
## Scomber scombrus 2.524178 0.6801890 3.710994 2.446516e-04
## Squalus acanthias 2.278866 0.7654576 2.977129 3.138928e-03
## Thunnus thynnus 1.733610 0.7752030 2.236330 2.604129e-02
## Urophycis chuss 2.583248 0.9600380 2.690777 7.515177e-03
## Urophycis tenuis 4.767005 0.6750347 7.061866 1.084666e-11
## Xiphias gladius 4.135628 0.7003019 5.905494 9.234383e-09
## TE
## Estimate Std. Error t value
## Anarhichas lupus -0.004740285 0.05517320 -0.08591645
## Brosme brosme -0.039182004 0.05074091 -0.77219750
## Clupea harengus 0.036686127 0.04111270 0.89233066
## Gadus morhua -0.051024368 0.04001610 -1.27509597
## Hippoglossoides platessoides 0.024225228 0.04350394 0.55685134
## Illex illecebrosus 0.106097306 0.06517862 1.62779315
## Lophius americanus -0.071183225 0.04852826 -1.46684070
## Mallotus villosus -0.036213794 0.05253350 -0.68934670
## Melanogrammus aeglefinus -0.022801223 0.04405457 -0.51756777
## Merluccius bilinearis -0.102410808 0.04983940 -2.05481611
## Pandalus borealis 0.030100775 0.04322221 0.69641913
## Pollachius virens 0.016108216 0.03968700 0.40588140
## Pomatomus saltatrix -0.084342122 0.05612787 -1.50267819
## Reinhardtius hippoglossoides -0.016861416 0.04678757 -0.36038241
## Sarda sarda -0.127869479 0.06490438 -1.97012095
## Scomber japonicus -0.042833145 0.04944339 -0.86630682
## Scomber scombrus 0.009324305 0.05040365 0.18499267
## Squalus acanthias 0.080624709 0.05805702 1.38871587
## Thunnus thynnus 0.119239986 0.05773803 2.06518983
## Urophycis chuss -0.001021527 0.07009488 -0.01457349
## Urophycis tenuis -0.115123081 0.04984090 -2.30981160
## Xiphias gladius -0.044547461 0.05252271 -0.84815612
## Pr(>|t|)
## Anarhichas lupus 0.93158830
## Brosme brosme 0.44058575
## Clupea harengus 0.37290785
## Gadus morhua 0.20323007
## Hippoglossoides platessoides 0.57803079
## Illex illecebrosus 0.10458464
## Lophius americanus 0.14343311
## Mallotus villosus 0.49112077
## Melanogrammus aeglefinus 0.60512900
## Merluccius bilinearis 0.04073458
## Pandalus borealis 0.48668822
## Pollachius virens 0.68510976
## Pomatomus saltatrix 0.13394002
## Reinhardtius hippoglossoides 0.71880661
## Sarda sarda 0.04971429
## Scomber japonicus 0.38699192
## Scomber scombrus 0.85335576
## Squalus acanthias 0.16591610
## Thunnus thynnus 0.03973610
## Urophycis chuss 0.98838182
## Urophycis tenuis 0.02155533
## Xiphias gladius 0.39700543
##
## Residual standard error: 0.4445776 on 310 degrees of freedomp5 <- ggplot(data=df, aes(x=TL, y=SPPR))+
geom_point(size=1)+
scale_x_continuous("Trophic level")+
scale_y_continuous("SPPR (kg-NPP/kg-fish)", trans="log10")+
theme(text = element_text(size=8), legend.position="none")+
geom_smooth(method=lm, se=FALSE)+
ggtitle("Figure 6. Correlation between SPPR and trophic level")
p5
# Create a model to test if coefficients are statistically significantly different from 0
model <- glm(logSPPR ~ TL, data=df, family=gaussian)
summary(model)##
## Call:
## glm(formula = logSPPR ~ TL, family = gaussian, data = df)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -1.0981 -0.3127 -0.0121 0.3002 1.4166
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) -0.74927 0.16935 -4.424 1.2e-05 ***
## TL 0.97175 0.04497 21.609 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for gaussian family taken to be 0.2213776)
##
## Null deviance: 207.64 on 472 degrees of freedom
## Residual deviance: 104.27 on 471 degrees of freedom
## AIC: 633.08
##
## Number of Fisher Scoring iterations: 2