Regression equation produces model outside of all data

Question

I'm fairly confused to why I produce a regression equation that is so outside of the range of all data in dataset. I have a feeling the equation is very sensitive to data with a big spread but Im still confused. Any assistance would be greatly appreciated, stats certainly isn't my first language!

For reference this is a geochemical thermodynamics problem: Im trying to fit the Maier-Kelley equation to some experimental data. The Maier-Kelley equation describes how the equilibrium constant (K), in this case dolomite dissolving in water, changes with temperature (T in this case in Kelvin).

log K = A + B.T + C/T + D.logT + E/T^2

To cut a long story short (see Hyeong and Capuano., 2001 if interested) the equilibrium constant (K) is the same as Log_Ca_Mg (ratio of calcium to magnesium ion acitivities).

The experimental data uses groundwater data from different locations and different depths (so identified by FIELD and DepthID - which are my random variables).

I have included 3 datasets

(Problem)Dataset 1:https://pastebin.com/fe2r2ebA

(Working)Dataset 2:https://pastebin.com/gFgaJ2c8

(Working)Dataset 3:https://pastebin.com/X5USaaNA

Using the following code, for dataset 1

> dat1 <- read.csv("PATH_TO_DATASET_1.txt", header = TRUE,sep="	")
> fm1 <- lmer(Log_Ca_Mg ~ 1 + kelvin + I(kelvin^-1) + I(log10(kelvin)) + I(kelvin^-2) + (1|FIELD) +(1|DepthID),data=dat1)

Warning messages:
1: Some predictor variables are on very different scales: consider rescaling 
2: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.0196619 (tol = 0.002, component 1)
3: Some predictor variables are on very different

> summary(fm1)
Linear mixed model fit by REML. t-tests use Satterthwaite's method ['lmerModLmerTest']
Formula: Log_Ca_Mg ~ 1 + kelvin + I(kelvin^-1) + I(log10(kelvin)) + I(kelvin^-2) +      (1 | FIELD) + (1 | DepthID)
   Data: dat1

REML criterion at convergence: -774.7

Scaled residuals: 
    Min      1Q  Median      3Q     Max 
-3.5464 -0.4538 -0.0671  0.3736  6.4217 

Random effects:
 Groups   Name        Variance Std.Dev.
 DepthID  (Intercept) 0.01035  0.1017  
 FIELD    (Intercept) 0.01081  0.1040  
 Residual             0.01905  0.1380  
Number of obs: 1175, groups:  DepthID, 675; FIELD, 410

Fixed effects:
                   Estimate Std. Error         df t value Pr(>|t|)
(Intercept)       3.368e+03  1.706e+03  4.582e-02   1.974    0.876
kelvin            4.615e-01  2.375e-01  4.600e-02   1.943    0.876
I(kelvin^-1)     -1.975e+05  9.788e+04  4.591e-02  -2.018    0.875
I(log10(kelvin)) -1.205e+03  6.122e+02  4.582e-02  -1.968    0.876
I(kelvin^-2)      1.230e+07  5.933e+06  4.624e-02   2.073    0.873

Correlation of Fixed Effects:
            (Intr) kelvin I(^-1) I(10()
kelvin       0.999                     
I(kelvn^-1) -1.000 -0.997              
I(lg10(kl)) -1.000 -0.999  0.999       
I(kelvn^-2)  0.998  0.994 -0.999 -0.997
fit warnings:
Some predictor variables are on very different scales: consider rescaling
convergence code: 0
Model failed to converge with max|grad| = 0.0196619 (tol = 0.002, component 1)

For Dataset 2

> summary(fm2)
Linear mixed model fit by REML. t-tests use Satterthwaite's method ['lmerModLmerTest']
Formula: Log_Ca_Mg ~ 1 + kelvin + I(kelvin^-1) + I(log10(kelvin)) + I(kelvin^-2) +      (1 | FIELD) + (1 | DepthID)
   Data: dat2

REML criterion at convergence: -1073.8

Scaled residuals: 
    Min      1Q  Median      3Q     Max 
-3.0816 -0.4772 -0.0581  0.3650  5.6209 

Random effects:
 Groups   Name        Variance Std.Dev.
 DepthID  (Intercept) 0.007368 0.08584 
 FIELD    (Intercept) 0.014266 0.11944 
 Residual             0.023048 0.15182 
Number of obs: 1906, groups:  DepthID, 966; FIELD, 537

Fixed effects:
                   Estimate Std. Error         df t value Pr(>|t|)
(Intercept)      -9.366e+01  2.948e+03  1.283e-03  -0.032    0.999
kelvin           -2.798e-02  4.371e-01  1.289e-03  -0.064    0.998
I(kelvin^-1)      2.623e+02  1.627e+05  1.285e-03   0.002    1.000
I(log10(kelvin))  3.965e+01  1.067e+03  1.283e-03   0.037    0.999
I(kelvin^-2)      2.917e+05  9.476e+06  1.294e-03   0.031    0.999

Correlation of Fixed Effects:
            (Intr) kelvin I(^-1) I(10()
kelvin       0.999                     
I(kelvn^-1) -0.999 -0.997              
I(lg10(kl)) -1.000 -0.999  0.999       
I(kelvn^-2)  0.998  0.994 -0.999 -0.997
fit warnings:
Some predictor variables are on very different scales: consider rescaling
convergence code: 0
Model failed to converge with max|grad| = 0.0196967 (tol = 0.002, component 1)

For Dataset 3

> summary(fm2)
Linear mixed model fit by REML. t-tests use Satterthwaite's method ['lmerModLmerTest']
Formula: Log_Ca_Mg ~ 1 + kelvin + I(kelvin^-1) + I(log10(kelvin)) + I(kelvin^-2) +      (1 | FIELD) + (1 | DepthID)
   Data: dat3

REML criterion at convergence: -1590.1

Scaled residuals: 
    Min      1Q  Median      3Q     Max 
-4.2546 -0.4987 -0.0379  0.4313  4.5490 

Random effects:
 Groups   Name        Variance Std.Dev.
 DepthID  (Intercept) 0.01311  0.1145  
 FIELD    (Intercept) 0.01424  0.1193  
 Residual             0.03138  0.1771  
Number of obs: 6674, groups:  DepthID, 3422; FIELD, 1622

Fixed effects:
                   Estimate Std. Error         df t value Pr(>|t|)
(Intercept)       1.260e+03  1.835e+03  9.027e-02   0.687    0.871
kelvin            1.824e-01  2.783e-01  9.059e-02   0.655    0.874
I(kelvin^-1)     -7.289e+04  9.961e+04  9.044e-02  -0.732    0.866
I(log10(kelvin)) -4.529e+02  6.658e+02  9.028e-02  -0.680    0.872
I(kelvin^-2)      4.499e+06  5.690e+06  9.104e-02   0.791    0.860

Correlation of Fixed Effects:
            (Intr) kelvin I(^-1) I(10()
kelvin       0.999                     
I(kelvn^-1) -1.000 -0.997              
I(lg10(kl)) -1.000 -0.999  0.999       
I(kelvn^-2)  0.998  0.994 -0.999 -0.998
fit warnings:
Some predictor variables are on very different scales: consider rescaling
convergence code: 0
unable to evaluate scaled gradient
Model failed to converge: degenerate  Hessian with 1 negative eigenvalues

I've plotted 'all the data' but for the regression analysis there is no data above the red line or bellow the green line. Only points with a log_ca_mg value between the red and green line at any temperature are included in the regression analysis.

So looking at the regressions on a plot dataset 1 is just way off but as there is no data above the red line this just confuses me no end. The regression is sitting in an area where there is no data. For the other two datasets this isn't a problem. Even for datasets with smaller sizes (n=200) its approximately in the same area. The three datasets look relatively similar when plotted individually.

Im kind of lost. Any help in understanding this would be appreciated.

user_5456906 · Answer

What follows is an attempt to diagnose what may be going wrong with your model. It will use Dataset 1 for this discussion:

As described in your question, when one runs the original model with Dataset 1, they recieve warnings:

# original model
fm1 <- lme4::lmer(Log_Ca_Mg ~ 1 + kelvin + I(kelvin^-1) + I(log10(kelvin)) + I(kelvin^-2) + (1|FIELD) +(1|DepthID),data=dat1)

Some predictor variables are on very different scales: consider rescaling convergence code: 0 Model failed to converge with max|grad| = 0.0196619 (tol = 0.002, component 1)

These and other information suggest your model has problems, perhaps related to the predictors being on a different scale.

Since fm1 has several predictors that are transformations of the variable 'kelvin',we can also check the model for collinearity with the car package vif function:

# examine collinearity with the vif (variance inflation factors)
> car::vif(fm1)
kelvin     I(kelvin^-1) I(log10(kelvin))     I(kelvin^-2) 
716333          9200929          7688348          1224275

These vif values suggest the fm1 model suffers from high collinearity.

We can try to drop the some of those predictors, to examine a simpler model:

fm1_b <- lme4::lmer(Log_Ca_Mg ~ 1 + kelvin + I(kelvin^-1) + (1|FIELD) +(1|DepthID),data=dat1)

When we run the code, we still get a warning about the predictors being on different scales:

Warning message: Some predictor variables are on very different scales: consider rescaling

At the same time the vif values are much smaller:

# examine collinearity with the vif (variance inflation factors)
  > car::vif(fm1_b)
kelvin I(kelvin^-1) 
46.48406     46.48406

Following gung's suggestion that I mentioned in the comments, we can see what happens when we center our kelvin variables:

dat1$kelvin_centered <- as.vector(scale(dat1$kelvin, center= TRUE, scale = FALSE ))
# Make a power transformation on the kelvin_centered variable
dat1$kelvin_centered_pwr <- dat1$kelvin_centered^-1

And check to see if they are correlated

# check the correlation of the centered vars
cor(dat1$kelvin_centered, dat1$kelvin_centered_pwr)
> cor(dat1$kelvin_centered, dat1$kelvin_centered_pwr)
[1] 0.08056641

And construct a different model with the centered variables:

# construct a modifed model
fm1_c <- lme4::lmer(Log_Ca_Mg ~ 1 + kelvin_centered + kelvin_centered_pwr + (1|FIELD) +(1|DepthID),data=dat1)

Notably, we don' see any warnings when we run the code with this model. And the vif values are quite low:

car::vif(fm1_c)

> car::vif(fm1_c)
    kelvin_centered kelvin_centered_pwr 
           1.005899            1.005899

Conclusion

The original model has a high degree of collinearity. Collinearity can make models unstable, which could account for why fm1 failed to converge, and why you are seeing weird predictions in the plots. Model fm1_c may or may not be the correct model for your purpose. It at least provides a lens to understand the issue with your original model.

user_12500315 · Answer

I think you are going about this the wrong way. It sounds like you are trying to estimate the parameters A, B, C, D and E in the Maier-Kelley equation. You can do this by using non-linear least squares rather than a linear mixed effects model.

Start by defining a function that replicates the formula:

MK_eq <- function(A, B, C, D, E, Temp)
{
  A + B * Temp + C / Temp + D * log10(Temp) + E / (Temp^2)
}

Now we use the nls function to get an estimate for A to E:

mod1 <- nls(Log_Ca_Mg ~ MK_eq(A, B, C, D, E, kelvin), 
            start = list(A = 1, B = 1, C = 1, D = 1, E = 2), data = dat1)

coef(mod1)
#>             A             B             C             D             E 
#>  4.802008e+03  6.538166e-01 -2.818917e+05 -1.717040e+03  1.755566e+07

and we can create a "regression line" by getting a prediction for every value of Kelvin between, say, 275 and 400 in increments of 0.1:

new_data <- data.frame(kelvin = seq(275, 400, 0.1))
new_data$Log_Ca_Mg <- predict(mod1, newdata = new_data)

and we can demonstrate that this is a good approximation by plotting our prediction over the sample:

ggplot(dat1, aes(x = kelvin, y = Log_Ca_Mg)) + 
  geom_point() + 
  geom_line(data = new_data, linetype = 2, colour = "red", size = 2)

Note that for simplicity I have avoided discussion of the random effects - it is possible to do mixed effects non-linear least squares using the nlme package, but it is more involved and the discussion here describes how to do it in more detail than I can here.

Regression equation produces model outside of all data

2 Answers