#Load in libraries
library(readr)
library(lme4)
## Loading required package: Matrix
## Warning: package 'Matrix' was built under R version 3.5.3
library(car)
## Warning: package 'car' was built under R version 3.5.3
## Loading required package: carData
## Warning: package 'carData' was built under R version 3.5.2
library(emmeans)
## Warning: package 'emmeans' was built under R version 3.5.3
#Spring2018 data
setwd("c:/users/Paul/Documents/Rwork")
firstspringdata<- read.csv(file="firstspringdata.csv")
str(firstspringdata)
## 'data.frame': 20 obs. of 8 variables:
## $ Season : int 64 64 64 64 64 64 64 64 64 64 ...
## $ Time : Factor w/ 1 level "S1": 1 1 1 1 1 1 1 1 1 1 ...
## $ Site : Factor w/ 5 levels "Bachelor","College",..: 3 4 1 5 2 3 4 1 5 2 ...
## $ Deer : Factor w/ 2 levels "Con","Excl": 1 1 1 1 1 2 2 2 2 2 ...
## $ Honeysuckle: Factor w/ 2 levels "H ","NH": 1 1 1 1 1 1 1 1 1 1 ...
## $ Treatment : Factor w/ 4 levels "ConH","ConNH",..: 1 1 1 1 1 3 3 3 3 3 ...
## $ min_OM : num 29.9 22.9 36.6 27.7 66.1 ...
## $ NetNitr_OM : num 32 23.6 38.4 29.2 47.4 ...
model1 <- lm(NetNitr_OM ~ Treatment,data = firstspringdata)
summary(model1)
##
## Call:
## lm(formula = NetNitr_OM ~ Treatment, data = firstspringdata)
##
## Residuals:
## Min 1Q Median 3Q Max
## -10.518 -4.061 -0.484 4.096 13.272
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 34.118 3.157 10.808 9.22e-09 ***
## TreatmentConNH -5.732 4.464 -1.284 0.217
## TreatmentExcH -7.704 4.464 -1.726 0.104
## TreatmentExcNH -10.416 4.464 -2.333 0.033 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 7.059 on 16 degrees of freedom
## Multiple R-squared: 0.2683, Adjusted R-squared: 0.1311
## F-statistic: 1.956 on 3 and 16 DF, p-value: 0.1614
anova(model1)
## Analysis of Variance Table
##
## Response: NetNitr_OM
## Df Sum Sq Mean Sq F value Pr(>F)
## Treatment 3 292.36 97.452 1.9558 0.1614
## Residuals 16 797.24 49.827
model1aov<-aov(NetNitr_OM ~ Treatment,data = firstspringdata)
posthoc1 <- TukeyHSD(x=model1aov, 'Treatment', conf.level=0.95)
posthoc1
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = NetNitr_OM ~ Treatment, data = firstspringdata)
##
## $Treatment
## diff lwr upr p adj
## ConNH-ConH -5.732 -18.50477 7.04077 0.5855554
## ExcH-ConH -7.704 -20.47677 5.06877 0.3433513
## ExcNH-ConH -10.416 -23.18877 2.35677 0.1318043
## ExcH-ConNH -1.972 -14.74477 10.80077 0.9702765
## ExcNH-ConNH -4.684 -17.45677 8.08877 0.7238964
## ExcNH-ExcH -2.712 -15.48477 10.06077 0.9282176
plot(posthoc1)
############# Whole season data #####
seasonal_data<- read.csv(file="seasonal_data.csv")
str(seasonal_data)
## 'data.frame': 80 obs. of 8 variables:
## $ Season : int 64 64 64 64 64 183 183 183 183 183 ...
## $ Time : Factor w/ 4 levels "S1","S2","S3",..: 1 1 1 1 1 2 2 2 2 2 ...
## $ Site : Factor w/ 5 levels "Bachelor","College",..: 3 4 1 5 2 3 4 1 5 2 ...
## $ Deer : Factor w/ 2 levels "Con","Excl": 1 1 1 1 1 1 1 1 1 1 ...
## $ Honeysuckle: Factor w/ 2 levels "H ","NH": 1 1 1 1 1 1 1 1 1 1 ...
## $ Treatment : Factor w/ 4 levels "ConH","ConNH",..: 1 1 1 1 1 1 1 1 1 1 ...
## $ min_OM : num 29.9 22.9 36.6 27.7 66.1 ...
## $ NetNitr_OM : num 32 23.6 38.4 29.2 47.4 ...
model2 <- lm(NetNitr_OM ~ Treatment*Time,data = seasonal_data)
summary(model2)
##
## Call:
## lm(formula = NetNitr_OM ~ Treatment * Time, data = seasonal_data)
##
## Residuals:
## Min 1Q Median 3Q Max
## -10.518 -2.957 -0.076 2.544 13.272
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 34.118 2.151 15.859 < 2e-16 ***
## TreatmentConNH -5.732 3.042 -1.884 0.06418 .
## TreatmentExcH -7.704 3.042 -2.532 0.01384 *
## TreatmentExcNH -10.416 3.042 -3.424 0.00109 **
## TimeS2 -22.698 3.042 -7.460 3.14e-10 ***
## TimeS3 -27.470 3.042 -9.029 5.77e-13 ***
## TimeS4 -20.078 3.042 -6.599 9.93e-09 ***
## TreatmentConNH:TimeS2 6.708 4.303 1.559 0.12400
## TreatmentExcH:TimeS2 7.288 4.303 1.694 0.09524 .
## TreatmentExcNH:TimeS2 9.454 4.303 2.197 0.03169 *
## TreatmentConNH:TimeS3 5.874 4.303 1.365 0.17705
## TreatmentExcH:TimeS3 12.346 4.303 2.869 0.00559 **
## TreatmentExcNH:TimeS3 10.064 4.303 2.339 0.02252 *
## TreatmentConNH:TimeS4 3.437 4.435 0.775 0.44127
## TreatmentExcH:TimeS4 1.054 4.303 0.245 0.80728
## TreatmentExcNH:TimeS4 1.480 4.303 0.344 0.73201
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 4.811 on 63 degrees of freedom
## (1 observation deleted due to missingness)
## Multiple R-squared: 0.8031, Adjusted R-squared: 0.7563
## F-statistic: 17.13 on 15 and 63 DF, p-value: < 2.2e-16
anova(model2)
## Analysis of Variance Table
##
## Response: NetNitr_OM
## Df Sum Sq Mean Sq F value Pr(>F)
## Treatment 3 281.4 93.81 4.0538 0.01066 *
## Time 3 5312.7 1770.89 76.5251 < 2e-16 ***
## Treatment:Time 9 353.2 39.25 1.6960 0.10870
## Residuals 63 1457.9 23.14
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
model2aov<-aov(NetNitr_OM ~ Treatment*Time,data = seasonal_data)
posthoc2 <- TukeyHSD(x=model2aov,conf.level=0.95)
posthoc2
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = NetNitr_OM ~ Treatment * Time, data = seasonal_data)
##
## $Treatment
## diff lwr upr p adj
## ConNH-ConH -1.5649211 -5.631847 2.5020050 0.7410381
## ExcH-ConH -2.5320000 -6.546447 1.4824474 0.3509170
## ExcNH-ConH -5.1665000 -9.180947 -1.1520526 0.0063656
## ExcH-ConNH -0.9670789 -5.034005 3.0998471 0.9228360
## ExcNH-ConNH -3.6015789 -7.668505 0.4653471 0.1005322
## ExcNH-ExcH -2.6345000 -6.648947 1.3799474 0.3160925
##
## $Time
## diff lwr upr p adj
## S2-S1 -16.835500 -20.849947 -12.8210526 0.0000000
## S3-S1 -20.399000 -24.413447 -16.3845526 0.0000000
## S4-S1 -18.660214 -22.727140 -14.5932879 0.0000000
## S3-S2 -3.563500 -7.577947 0.4509474 0.0993276
## S4-S2 -1.824714 -5.891640 2.2422121 0.6390992
## S4-S3 1.738786 -2.328140 5.8057121 0.6735947
##
## $`Treatment:Time`
## diff lwr upr p adj
## ConNH:S1-ConH:S1 -5.732 -16.586760 5.1227603 0.8732267
## ExcH:S1-ConH:S1 -7.704 -18.558760 3.1507603 0.4625779
## ExcNH:S1-ConH:S1 -10.416 -21.270760 0.4387603 0.0732771
## ConH:S2-ConH:S1 -22.698 -33.552760 -11.8432397 0.0000000
## ConNH:S2-ConH:S1 -21.722 -32.576760 -10.8672397 0.0000001
## ExcH:S2-ConH:S1 -23.114 -33.968760 -12.2592397 0.0000000
## ExcNH:S2-ConH:S1 -23.660 -34.514760 -12.8052397 0.0000000
## ConH:S3-ConH:S1 -27.470 -38.324760 -16.6152397 0.0000000
## ConNH:S3-ConH:S1 -27.328 -38.182760 -16.4732397 0.0000000
## ExcH:S3-ConH:S1 -22.828 -33.682760 -11.9732397 0.0000000
## ExcNH:S3-ConH:S1 -27.822 -38.676760 -16.9672397 0.0000000
## ConH:S4-ConH:S1 -20.078 -30.932760 -9.2232397 0.0000011
## ConNH:S4-ConH:S1 -22.373 -33.886212 -10.8597880 0.0000003
## ExcH:S4-ConH:S1 -26.728 -37.582760 -15.8732397 0.0000000
## ExcNH:S4-ConH:S1 -29.014 -39.868760 -18.1592397 0.0000000
## ExcH:S1-ConNH:S1 -1.972 -12.826760 8.8827603 0.9999989
## ExcNH:S1-ConNH:S1 -4.684 -15.538760 6.1707603 0.9729617
## ConH:S2-ConNH:S1 -16.966 -27.820760 -6.1112397 0.0000600
## ConNH:S2-ConNH:S1 -15.990 -26.844760 -5.1352397 0.0001981
## ExcH:S2-ConNH:S1 -17.382 -28.236760 -6.5272397 0.0000357
## ExcNH:S2-ConNH:S1 -17.928 -28.782760 -7.0732397 0.0000180
## ConH:S3-ConNH:S1 -21.738 -32.592760 -10.8832397 0.0000001
## ConNH:S3-ConNH:S1 -21.596 -32.450760 -10.7412397 0.0000002
## ExcH:S3-ConNH:S1 -17.096 -27.950760 -6.2412397 0.0000510
## ExcNH:S3-ConNH:S1 -22.090 -32.944760 -11.2352397 0.0000001
## ConH:S4-ConNH:S1 -14.346 -25.200760 -3.4912397 0.0013699
## ConNH:S4-ConNH:S1 -16.641 -28.154212 -5.1277880 0.0002845
## ExcH:S4-ConNH:S1 -20.996 -31.850760 -10.1412397 0.0000003
## ExcNH:S4-ConNH:S1 -23.282 -34.136760 -12.4272397 0.0000000
## ExcNH:S1-ExcH:S1 -2.712 -13.566760 8.1427603 0.9999266
## ConH:S2-ExcH:S1 -14.994 -25.848760 -4.1392397 0.0006480
## ConNH:S2-ExcH:S1 -14.018 -24.872760 -3.1632397 0.0019855
## ExcH:S2-ExcH:S1 -15.410 -26.264760 -4.5552397 0.0003969
## ExcNH:S2-ExcH:S1 -15.956 -26.810760 -5.1012397 0.0002064
## ConH:S3-ExcH:S1 -19.766 -30.620760 -8.9112397 0.0000017
## ConNH:S3-ExcH:S1 -19.624 -30.478760 -8.7692397 0.0000021
## ExcH:S3-ExcH:S1 -15.124 -25.978760 -4.2692397 0.0005564
## ExcNH:S3-ExcH:S1 -20.118 -30.972760 -9.2632397 0.0000011
## ConH:S4-ExcH:S1 -12.374 -23.228760 -1.5192397 0.0116246
## ConNH:S4-ExcH:S1 -14.669 -26.182212 -3.1557880 0.0024499
## ExcH:S4-ExcH:S1 -19.024 -29.878760 -8.1692397 0.0000044
## ExcNH:S4-ExcH:S1 -21.310 -32.164760 -10.4552397 0.0000002
## ConH:S2-ExcNH:S1 -12.282 -23.136760 -1.4272397 0.0127658
## ConNH:S2-ExcNH:S1 -11.306 -22.160760 -0.4512397 0.0330957
## ExcH:S2-ExcNH:S1 -12.698 -23.552760 -1.8432397 0.0083188
## ExcNH:S2-ExcNH:S1 -13.244 -24.098760 -2.3892397 0.0046585
## ConH:S3-ExcNH:S1 -17.054 -27.908760 -6.1992397 0.0000538
## ConNH:S3-ExcNH:S1 -16.912 -27.766760 -6.0572397 0.0000641
## ExcH:S3-ExcNH:S1 -12.412 -23.266760 -1.5572397 0.0111816
## ExcNH:S3-ExcNH:S1 -17.406 -28.260760 -6.5512397 0.0000347
## ConH:S4-ExcNH:S1 -9.662 -20.516760 1.1927603 0.1346397
## ConNH:S4-ExcNH:S1 -11.957 -23.470212 -0.4437880 0.0341260
## ExcH:S4-ExcNH:S1 -16.312 -27.166760 -5.4572397 0.0001340
## ExcNH:S4-ExcNH:S1 -18.598 -29.452760 -7.7432397 0.0000077
## ConNH:S2-ConH:S2 0.976 -9.878760 11.8307603 1.0000000
## ExcH:S2-ConH:S2 -0.416 -11.270760 10.4387603 1.0000000
## ExcNH:S2-ConH:S2 -0.962 -11.816760 9.8927603 1.0000000
## ConH:S3-ConH:S2 -4.772 -15.626760 6.0827603 0.9682743
## ConNH:S3-ConH:S2 -4.630 -15.484760 6.2247603 0.9755660
## ExcH:S3-ConH:S2 -0.130 -10.984760 10.7247603 1.0000000
## ExcNH:S3-ConH:S2 -5.124 -15.978760 5.7307603 0.9433573
## ConH:S4-ConH:S2 2.620 -8.234760 13.4747603 0.9999525
## ConNH:S4-ConH:S2 0.325 -11.188212 11.8382120 1.0000000
## ExcH:S4-ConH:S2 -4.030 -14.884760 6.8247603 0.9933859
## ExcNH:S4-ConH:S2 -6.316 -17.170760 4.5387603 0.7725645
## ExcH:S2-ConNH:S2 -1.392 -12.246760 9.4627603 1.0000000
## ExcNH:S2-ConNH:S2 -1.938 -12.792760 8.9167603 0.9999991
## ConH:S3-ConNH:S2 -5.748 -16.602760 5.1067603 0.8708883
## ConNH:S3-ConNH:S2 -5.606 -16.460760 5.2487603 0.8907582
## ExcH:S3-ConNH:S2 -1.106 -11.960760 9.7487603 1.0000000
## ExcNH:S3-ConNH:S2 -6.100 -16.954760 4.7547603 0.8132854
## ConH:S4-ConNH:S2 1.644 -9.210760 12.4987603 0.9999999
## ConNH:S4-ConNH:S2 -0.651 -12.164212 10.8622120 1.0000000
## ExcH:S4-ConNH:S2 -5.006 -15.860760 5.8487603 0.9528823
## ExcNH:S4-ConNH:S2 -7.292 -18.146760 3.5627603 0.5569308
## ExcNH:S2-ExcH:S2 -0.546 -11.400760 10.3087603 1.0000000
## ConH:S3-ExcH:S2 -4.356 -15.210760 6.4987603 0.9859510
## ConNH:S3-ExcH:S2 -4.214 -15.068760 6.6407603 0.9897438
## ExcH:S3-ExcH:S2 0.286 -10.568760 11.1407603 1.0000000
## ExcNH:S3-ExcH:S2 -4.708 -15.562760 6.1467603 0.9717389
## ConH:S4-ExcH:S2 3.036 -7.818760 13.8907603 0.9997090
## ConNH:S4-ExcH:S2 0.741 -10.772212 12.2542120 1.0000000
## ExcH:S4-ExcH:S2 -3.614 -14.468760 7.2407603 0.9978774
## ExcNH:S4-ExcH:S2 -5.900 -16.754760 4.9547603 0.8474344
## ConH:S3-ExcNH:S2 -3.810 -14.664760 7.0447603 0.9962760
## ConNH:S3-ExcNH:S2 -3.668 -14.522760 7.1867603 0.9975094
## ExcH:S3-ExcNH:S2 0.832 -10.022760 11.6867603 1.0000000
## ExcNH:S3-ExcNH:S2 -4.162 -15.016760 6.6927603 0.9909065
## ConH:S4-ExcNH:S2 3.582 -7.272760 14.4367603 0.9980730
## ConNH:S4-ExcNH:S2 1.287 -10.226212 12.8002120 1.0000000
## ExcH:S4-ExcNH:S2 -3.068 -13.922760 7.7867603 0.9996703
## ExcNH:S4-ExcNH:S2 -5.354 -16.208760 5.5007603 0.9210853
## ConNH:S3-ConH:S3 0.142 -10.712760 10.9967603 1.0000000
## ExcH:S3-ConH:S3 4.642 -6.212760 15.4967603 0.9750045
## ExcNH:S3-ConH:S3 -0.352 -11.206760 10.5027603 1.0000000
## ConH:S4-ConH:S3 7.392 -3.462760 18.2467603 0.5337630
## ConNH:S4-ConH:S3 5.097 -6.416212 16.6102120 0.9663390
## ExcH:S4-ConH:S3 0.742 -10.112760 11.5967603 1.0000000
## ExcNH:S4-ConH:S3 -1.544 -12.398760 9.3107603 1.0000000
## ExcH:S3-ConNH:S3 4.500 -6.354760 15.3547603 0.9810490
## ExcNH:S3-ConNH:S3 -0.494 -11.348760 10.3607603 1.0000000
## ConH:S4-ConNH:S3 7.250 -3.604760 18.1047603 0.5666782
## ConNH:S4-ConNH:S3 4.955 -6.558212 16.4682120 0.9735766
## ExcH:S4-ConNH:S3 0.600 -10.254760 11.4547603 1.0000000
## ExcNH:S4-ConNH:S3 -1.686 -12.540760 9.1687603 0.9999999
## ExcNH:S3-ExcH:S3 -4.994 -15.848760 5.8607603 0.9537821
## ConH:S4-ExcH:S3 2.750 -8.104760 13.6047603 0.9999128
## ConNH:S4-ExcH:S3 0.455 -11.058212 11.9682120 1.0000000
## ExcH:S4-ExcH:S3 -3.900 -14.754760 6.9547603 0.9952569
## ExcNH:S4-ExcH:S3 -6.186 -17.040760 4.6687603 0.7975230
## ConH:S4-ExcNH:S3 7.744 -3.110760 18.5987603 0.4536467
## ConNH:S4-ExcNH:S3 5.449 -6.064212 16.9622120 0.9421992
## ExcH:S4-ExcNH:S3 1.094 -9.760760 11.9487603 1.0000000
## ExcNH:S4-ExcNH:S3 -1.192 -12.046760 9.6627603 1.0000000
## ConNH:S4-ConH:S4 -2.295 -13.808212 9.2182120 0.9999961
## ExcH:S4-ConH:S4 -6.650 -17.504760 4.2047603 0.7031048
## ExcNH:S4-ConH:S4 -8.936 -19.790760 1.9187603 0.2266113
## ExcH:S4-ConNH:S4 -4.355 -15.868212 7.1582120 0.9920383
## ExcNH:S4-ConNH:S4 -6.641 -18.154212 4.8722120 0.7832461
## ExcNH:S4-ExcH:S4 -2.286 -13.140760 8.5687603 0.9999918
plot(posthoc2)
