1- Are there differences between Open and Closed reaches?

Linear models (example: Temperature’ as function of ‘Canopy’, with ‘Stream (site)’ as random effect) suggest there isn’t.

m2<-lme(Temp.C~Canopy, random=~1|Stream, method="ML", data=Water)
summary(m2)
## Linear mixed-effects model fit by maximum likelihood
##  Data: Water 
##        AIC      BIC    logLik
##   267.9504 276.3278 -129.9752
## 
## Random effects:
##  Formula: ~1 | Stream
##         (Intercept) Residual
## StdDev:   0.6271728 2.042354
## 
## Fixed effects: Temp.C ~ Canopy 
##                 Value Std.Error DF   t-value p-value
## (Intercept)  8.853333 0.4600577 53 19.243965  0.0000
## CanopyOpen  -0.026667 0.5363484 53 -0.049719  0.9605
##  Correlation: 
##            (Intr)
## CanopyOpen -0.583
## 
## Standardized Within-Group Residuals:
##         Min          Q1         Med          Q3         Max 
## -2.10262036 -0.61150371  0.06482749  0.49016623  2.49599611 
## 
## Number of Observations: 60
## Number of Groups: 6
As expected, also no sign. differences in means of the other parameters between reaches
Variable Term Value Std.Error DF t-value p-value
DO CanopyOpen 0.046 0.1730 39 0.266 0.791
DO100 CanopyOpen -0.083 4.598 39 -0.018 0.986
pH CanopyOpen 0.006 0.070 41 0.084 0.934
Conductivity CanopyOpen 4.817 11.324 53 0.425 0.672
Dishcarge CanopyOpen 0.000 126.285 51 0.00 1.0
TIN CanopyOpen 47.5467 69.451 53 0.685 0.497
PO4P CanopyOpen 0.303 4.988 53 0.061 0.952