stone flakes III

June 22, 2014
By

(This article was first published on Wiekvoet, and kindly contributed to R-bloggers)

Stone flakes are waste products from the tool making process in the stone age. This is the second post, first post was clustering, second linking to hominid type. The data also contains a more or less continuous age variable, which gives possibility to use regression, which is the topic of this week.

Data

Data source see first post. Regarding age especially: 'in millenia (not to be taken too seriously) ... mode of dating (geological=more accurate, typological)'. On inspection, it seems most of the typological dates are 200k, hence it seemed an idea to ignore typological. In  addition, age is negative. Since at some point I want to use a Box-Cox transformation, for which positive is required, -age is added.
r2 <- read.table('StoneFlakes.txt',header=TRUE,na.strings='?')
r1 <- read.table('annotation.txt',header=TRUE,na.strings='?')
r12 <- merge(r1,r2)
r12$Group <- factor(r12$group,labels=c('Lower Paleolithic',
        'Levallois technique',
        'Middle Paleolithic',
        'Homo Sapiens'))
r12$mAge <- -r12$age
r12c <- r12[complete.cases(r12),]
table(r12$age ,r1$dating )
       geo typo
  -400   2    0
  -300   8    1
  -200  13   12
  -130   1    0
  -120  12    0
  -80   23    2
  -40    3    0

Regression

The tool to start is linear regression. This shows there is a relation, mostly age with FSF and LBI. It is not a very good model, the standard error is at least 55 thousand years.
l1 <- lm(age ~ LBI + RTI + WDI + FLA + PSF + FSF + ZDF1 + PROZD,
    data=r12c[r12c$dating=='geo',])
summary(l1)
Call:
lm(formula = age ~ LBI + RTI + WDI + FLA + PSF + FSF + ZDF1 + 
    PROZD, data = r12c[r12c$dating == "geo", ])

Residuals:
     Min       1Q   Median       3Q      Max 
-127.446  -30.646   -7.889   27.790  159.471 

Coefficients:
             Estimate Std. Error t value Pr(>|t|)  
(Intercept) -328.8260   310.6756  -1.058   0.2953  
LBI          149.1334    65.8323   2.265   0.0281 *
RTI           -0.8196     2.8498  -0.288   0.7749  
WDI           16.2067    20.1351   0.805   0.4249  
FLA           -1.6769     1.8680  -0.898   0.3739  
PSF           -0.9222     1.0706  -0.861   0.3934  
FSF            1.9496     0.8290   2.352   0.0229 *
ZDF1           0.9537     1.1915   0.800   0.4275  
PROZD          1.2245     2.0068   0.610   0.5447  
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 55.09 on 47 degrees of freedom
Multiple R-squared:  0.7062, Adjusted R-squared:  0.6562 
F-statistic: 14.12 on 8 and 47 DF,  p-value: 3.23e-10
Some model validation can be made through the car package. It gives the impression that the error increases with age. It is not a particular strong effect, but then, the age range is not that large either, 40 to 400, which is a factor 10.
library(car)
par(mfrow=c(2,2))
plot(l1,ask=FALSE)
Since I know of no theoretical basis to chose a transformation, Box-Cox is my method of choice to proceed. Lambda zero, or log transformation, is certainly a choice which seems reasonable, hence it has been selected.
r12cx <- r12c[r12c$dating=='geo',]
summary(p1 <- powerTransform(
        mAge ~ LBI + RTI + WDI + FLA + PSF + FSF + ZDF1 + PROZD, 
        r12cx))
bcPower Transformation to Normality 

   Est.Power Std.Err. Wald Lower Bound Wald Upper Bound
Y1    0.1211   0.1839          -0.2394           0.4816

Likelihood ratio tests about transformation parameters
                             LRT df         pval
LR test, lambda = (0)  0.4343012  1 5.098859e-01
LR test, lambda = (1) 21.3406407  1 3.844933e-06

Linear regression, step 2

Having chosen a transformation, it is time to rerun the model. It is now clear that FSF is most important and LBI a bit less.
r12cx$lAge <- log(-r12cx$age)
l1 <- lm(lAge ~ LBI + RTI + WDI + FLA + PSF + FSF + ZDF1 + PROZD,
    data=r12cx)
summary(l1)
Call:
lm(formula = lAge ~ LBI + RTI + WDI + FLA + PSF + FSF + ZDF1 + 
    PROZD, data = r12cx)

Residuals:
     Min       1Q   Median       3Q      Max 
-1.04512 -0.18333  0.07013  0.21085  0.58648 

Coefficients:
             Estimate Std. Error t value Pr(>|t|)   
(Intercept)  5.071224   2.030941   2.497  0.01609 * 
LBI         -0.953462   0.430357  -2.216  0.03161 * 
RTI          0.005561   0.018630   0.298  0.76664   
WDI         -0.041576   0.131627  -0.316  0.75350   
FLA          0.018477   0.012211   1.513  0.13695   
PSF          0.002753   0.006999   0.393  0.69580   
FSF         -0.015956   0.005419  -2.944  0.00502 **
ZDF1        -0.004485   0.007789  -0.576  0.56748   
PROZD       -0.009941   0.013119  -0.758  0.45236   
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 0.3601 on 47 degrees of freedom
Multiple R-squared:  0.6882, Adjusted R-squared:  0.6351 
F-statistic: 12.97 on 8 and 47 DF,  p-value: 1.217e-09

Plot of regression

With two independent variables, it is easy to make a nice plot:
l2 <- lm(lAge ~ LBI + FSF ,
    data=r12cx)
par(mfrow=c(1,1))
incont <- list(x=seq(min(r12cx$LBI),max(r12cx$LBI),length.out=12),
    y=seq(min(r12cx$FSF),max(r12cx$FSF),length.out=13))
topred <- expand.grid(LBI=incont$x,
    FSF=incont$y)
topred$p1 <- predict(l2,topred)        
incont$z <- matrix(-exp(topred$p1),nrow=length(incont$x))
contour(incont,xlab='LBI',ylab='FSF')
cols <- colorRampPalette(c('violet','gold','seagreen'))(4) 
with(r12cx,text(x=LBI,y=FSF,ID,col=cols[group]))

Predictions

I started in data analysis as a chemometrician, my method of choice for a predictive model with correlated independent variables is PLS. In this case one component seems enough (lowest cross validation RMSEP), but the model explains 60% of log(age) variability, which is not impressive.
library(pls)
p1 <- mvr(lAge ~ LBI + RTI + WDI + FLA + PSF + FSF + ZDF1 + PROZD,
    data=r12cx,
    method='simpls',
    validation='LOO',
    scale=TRUE,
    ncomp=5)
summary(p1)
Data: X dimension: 56 8 
Y dimension: 56 1
Fit method: simpls
Number of components considered: 5

VALIDATION: RMSEP
Cross-validated using 56 leave-one-out segments.
       (Intercept)  1 comps  2 comps  3 comps  4 comps  5 comps
CV          0.6016   0.3714   0.3812   0.3864   0.3915   0.3983
adjCV       0.6016   0.3713   0.3808   0.3859   0.3910   0.3976

TRAINING: % variance explained
      1 comps  2 comps  3 comps  4 comps  5 comps
X       51.07    64.11    76.81    83.13    89.44
lAge    64.62    67.94    68.70    68.78    68.81
A plot shows there are a number of odd points, which are removed in the next section.
r12c$plspred <- -exp(predict(p1,r12c,ncomp=1))
plot(plspred ~age,ylab='PLS prediction',type='n',data=r12c)
text(x=r12c$age,y=r12c$plspred,r12c$ID,col=cols[r12c$group])
In an email from Thomas Weber, it was also indicated that there might be reasons to doubt the homonid group of a few inventories (rows); reasons include few flakes, changing insight and misfit from "impressionist technological" point of view. All inventories mentioned in that email are now removed. As can be seen, a two component PLS model is now preferred, and 80% of variance is explained.
p2 <- mvr(lAge ~ LBI + RTI + WDI + FLA + PSF + FSF + ZDF1 + PROZD,
    data=r12cx,
    method='simpls',
    validation='LOO',
    scale=TRUE,
    ncomp=5,
    subset= !(ID %in% c('ms','c','roe','sz','va','arn')))
summary(p2)

Data: X dimension: 53 8 
Y dimension: 53 1
Fit method: simpls
Number of components considered: 5

VALIDATION: RMSEP
Cross-validated using 53 leave-one-out segments.
       (Intercept)  1 comps  2 comps  3 comps  4 comps  5 comps
CV          0.6088   0.3127   0.3057   0.3062   0.3070   0.3153
adjCV       0.6088   0.3126   0.3054   0.3059   0.3065   0.3140

TRAINING: % variance explained
      1 comps  2 comps  3 comps  4 comps  5 comps
X       52.14    63.94    77.05    79.82    84.77
lAge    75.44    79.66    80.31    81.00    81.56

Plot 

The plot below shows age in data versus the model predictions. It should be noted that after all steps, it is to be expected the data used to fit the model is predicted better than the other data. This is especially true for the suspected outliers which were removed, but also for inventories with dating method typological.
Having said that, the model really does not find inventories v1 and v2 to be as old as the data states. Perhaps there was no or less or different technological change, which is not picked by the model. In addition, the step between middle paleolithic and homo sapiens is not picked by the model. It is my personal suspicion that getting more homo sapiens data would improve all of the models which I have made in these three blog posts. As it is, the regression tree was the best tool to detect these inventories, which is a bit odd.
r12c$plspred2 <- -exp(predict(p2,r12c,ncomp=2))
plot(plspred2 ~age,ylab='PLS prediction',type='n',data=r12c)
text(x=r12c$age,y=r12c$plspred2,r12c$ID,col=cols[r12c$group])

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