summary.lmcal: Summarizing fitted calibration curves

Description Usage Arguments Details Value Note Author(s) See Also Examples

Description

A 'summary' class for 'lmcal' and 'nlscal' objects.

Usage

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## S3 method for class 'lmcal'
summary(object, sort.models = FALSE, ...)
## S3 method for class 'nlscal'
summary(object, sort.models = FALSE, ...)

Arguments

object

an object of class 'lmcal' or 'nlscal'

sort.models

should the tables be sorted by models (TRUE) or variables (FALSE).

...

additional arguments, currently ignored.

Details

The function performs summarizing of fitted calibration models and produces several tables (see below). The are printed in appropriate form, and their list is returned invisibly.

Value

A list, consisting of following items:

coefficients

Estimated coefficients, their standard error, significance (t) and p-value

residuals

Quantiles of residuals and Shapiro-Wilk test of their normality

variances

Quantiles of variances (without transform, with log-log, and with Box-Cox on y) ond Bartlett test for therir heteroscedascity. Calculated only, if there are at least 2 replicates for each x

fit

R-squared, adjusted R-squared, AIC, residual standard error, sum of squared residuals, sum of pure error and Lack-of-Fit ANOVA test

sensitivity

sensitivity, limit of detection and quantitation, autocorrelation of residuals, Durbin-Watson test for autocorrelation

Note

The p-value of Durbin-Watson statistic is *only* approximated using normal transform algorhitm! This is not critical criterion and *always* residual plot should be visually examined.

Some of values given above are not computed for 'nlscal' models.

Author(s)

Lukasz Komsta, with portion by Achim Zeileis (from dwtest())

See Also

lmcal, nlscal

Examples

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set.seed(1234)
x=rep(1:8,5)
y=jitter(sqrt(x))
fit=lmcal(x,y)
fit
summary(fit)

Example output

Loading required package: MASS
Loading required package: outliers
------------------------------------------
If you use this package, please cite the recent paper containing description of this software:
Komsta, L. Chemometric and statistical evaluation of calibration curves in pharmaceutical analysis 
           - a short review on trends and recommendations. J. AOAC Int. 2012, 95, 3, 669-672.
------------------------------------------
There were 12 warnings (use warnings() to see them)

Optimal Box-Cox power on x: 0.4737
Optimal Box-Cox power on y: 2.0234

Optimal power of weighting on x: -2.3
Optimal power of weighting on y: -4
Better weighting on y: FALSE 

Coefficients:
           x0         x1         x2         x3     x4
p1  0.8921822  0.2540093         NA         NA     NA
p2  0.6234089  0.4152733 -0.0179182         NA     NA
p3  0.4910853  0.5529433 -0.0540065  0.0026732     NA
p4  0.4342341  0.6364974 -0.0904238  0.0087029 -3e-04
P1  0.7019934  0.3084108         NA         NA     NA
P2  0.5445987  0.4703910 -0.0245821         NA     NA
P3  0.4563520  0.5925888 -0.0651559  0.0035413     NA
P4  0.3960184  0.6955026 -0.1173771  0.0133395 -6e-04
l1 -0.0030650  0.5037472         NA         NA     NA
l2 -0.0054354  0.5220794 -0.0198106         NA     NA
bx  0.9885017  0.5170598         NA         NA     NA
by -0.5112502  0.5063314         NA         NA     NA
r1  1.0262661  0.2317381         NA         NA     NA
r2  0.6221464  0.4163627 -0.0180644         NA     NA
r3  0.4857868  0.5584750 -0.0554785  0.0027792     NA
r4  0.4327170  0.6370596 -0.0899461  0.0085171 -3e-04
R1  1.0644338  0.2277410         NA         NA     NA
R2  0.7204687  0.3791276 -0.0148678         NA     NA
R3  0.4461184  0.5980542 -0.0659036  0.0035650     NA
R4  0.3824829  0.7051641 -0.1190629  0.0133534 -6e-04

Goodness of fit:
         R-Sq   Adj-R-Sq        AIC  Sigma
p1    0.97779    0.97720  -75.17266 0.0900
p2    0.99725    0.99710 -156.73694 0.0321
p3    0.99878    0.99868 -187.30302 0.0217
p4    0.99886    0.99872 -187.78518 0.0213
P1    0.97223    0.97150  -49.12746 0.0271
P2    0.99677    0.99660 -133.19178 0.0094
P3    0.99841    0.99828 -159.55685 0.0067
P4    0.99854    0.99837 -160.96813 0.0065
l1    0.99899    0.99896 -311.23094 0.0047
l2    0.99910    0.99905 -313.93331 0.0045
bx    0.99887    0.99884 -194.39086 0.0203
by    0.99836    0.99832 -125.07729 0.0482
r1         NA         NA  -59.29057 0.0615
r2         NA         NA -156.70646 0.0320
r3         NA         NA -187.12089 0.0215
r4         NA         NA -187.61104 0.0205
R1         NA         NA   64.48967 0.0085
R2         NA         NA  -24.33253 0.0057
R3         NA         NA -155.83682 0.0045
R4         NA         NA -156.95371 0.0043

Optimal Box-Cox power on x: 0.4737
Optimal Box-Cox power on y: 2.0234

Optimal power of weighting on x: -2.3
Optimal power of weighting on y: -4

Mean relative error:
 0.09029114 on x
 0.09076084 on y
 0.1257794 unweighted

Better weighting on y: FALSE 

Coefficients:
      Estimate Std. Error  t value  Pr(>|t|)    
x0 P1   0.7020     0.0168  41.7097 < 2.2e-16 ***
x0 P2   0.5446     0.0110  49.3165 < 2.2e-16 ***
x0 P3   0.4564     0.0165  27.7091 < 2.2e-16 ***
x0 P4   0.3960     0.0377  10.4928 2.372e-12 ***
x0 R1   1.0644     0.0046 230.0240 < 2.2e-16 ***
x0 R2   0.7205     0.0054 132.5575 < 2.2e-16 ***
x0 R3   0.4461     0.0119  37.4066 < 2.2e-16 ***
x0 R4   0.3825     0.0269  14.2125 < 2.2e-16 ***
x0 bx   0.9885     0.0065 151.0407 < 2.2e-16 ***
x0 by  -0.5113     0.0168 -30.4193 < 2.2e-16 ***
x0 l1  -0.0031     0.0017  -1.8309 0.0749584 .  
x0 l2  -0.0054     0.0019  -2.7971 0.0081341 ** 
x0 p1   0.8922     0.0314  28.4481 < 2.2e-16 ***
x0 p2   0.6234     0.0200  31.1352 < 2.2e-16 ***
x0 p3   0.4911     0.0239  20.5802 < 2.2e-16 ***
x0 p4   0.4342     0.0446   9.7271 1.740e-11 ***
x0 r1   1.0263     0.0226  45.4684 < 2.2e-16 ***
x0 r2   0.6221     0.0225  27.6610 < 2.2e-16 ***
x0 r3   0.4858     0.0259  18.7704 < 2.2e-16 ***
x0 r4   0.4327     0.0492   8.7876 < 2.2e-16 ***
x1 P1   0.3084     0.0085  36.4721 < 2.2e-16 ***
x1 P2   0.4704     0.0101  46.6070 < 2.2e-16 ***
x1 P3   0.5926     0.0213  27.8313 < 2.2e-16 ***
x1 P4   0.6955     0.0619  11.2422 3.633e-13 ***
x1 R1   0.2277     0.0023  97.9542 < 2.2e-16 ***
x1 R2   0.3791     0.0050  76.3223 < 2.2e-16 ***
x1 R3   0.5981     0.0154  38.7879 < 2.2e-16 ***
x1 R4   0.7052     0.0441  15.9854 < 2.2e-16 ***
x1 bx   0.5171     0.0028 183.4632 < 2.2e-16 ***
x1 by   0.5063     0.0033 152.1319 < 2.2e-16 ***
x1 l1   0.5037     0.0026 193.4081 < 2.2e-16 ***
x1 l2   0.5221     0.0089  58.7366 < 2.2e-16 ***
x1 p1   0.2540     0.0062  40.8996 < 2.2e-16 ***
x1 p2   0.4153     0.0102  40.6796 < 2.2e-16 ***
x1 p3   0.5529     0.0216  25.6092 < 2.2e-16 ***
x1 p4   0.6365     0.0597  10.6582 1.558e-12 ***
x1 r1   0.2317     0.0045  51.8462 < 2.2e-16 ***
x1 r2   0.4164     0.0115  36.3088 < 2.2e-16 ***
x1 r3   0.5585     0.0234  23.8481 < 2.2e-16 ***
x1 r4   0.6371     0.0659   9.6711 < 2.2e-16 ***
x2 P2  -0.0246     0.0015 -16.7676 < 2.2e-16 ***
x2 P3  -0.0652     0.0067  -9.6712 1.506e-11 ***
x2 P4  -0.1174     0.0303  -3.8738 0.0004490 ***
x2 R2  -0.0149     0.0007 -20.6049 < 2.2e-16 ***
x2 R3  -0.0659     0.0049 -13.5086 < 2.2e-16 ***
x2 R4  -0.1191     0.0216  -5.5108 3.572e-08 ***
x2 l2  -0.0198     0.0092  -2.1484 0.0382946 *  
x2 p2  -0.0179     0.0011 -16.1825 < 2.2e-16 ***
x2 p3  -0.0540     0.0054  -9.9718 6.700e-12 ***
x2 p4  -0.0904     0.0249  -3.6308 0.0008948 ***
x2 r2  -0.0181     0.0012 -14.5236 < 2.2e-16 ***
x2 r3  -0.0555     0.0059  -9.4446 < 2.2e-16 ***
x2 r4  -0.0899     0.0275  -3.2742 0.0010595 ** 
x3 P3   0.0035     0.0006   6.0959 5.175e-07 ***
x3 P4   0.0133     0.0056   2.3908 0.0223237 *  
x3 R3   0.0036     0.0004   8.4746 < 2.2e-16 ***
x3 R4   0.0134     0.0040   3.3564 0.0007896 ***
x3 p3   0.0027     0.0004   6.7277 7.494e-08 ***
x3 p4   0.0087     0.0040   2.1504 0.0385083 *  
x3 r3   0.0028     0.0004   6.4489 1.127e-10 ***
x3 r4   0.0085     0.0045   1.9079 0.0564016 .  
x4 P4  -0.0006     0.0003  -1.7652 0.0862588 .  
x4 R4  -0.0006     0.0002  -2.4375 0.0147881 *  
x4 p4  -0.0003     0.0002  -1.4969 0.1433852    
x4 r4  -0.0003     0.0002  -1.2974 0.1944866    
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residuals:
        0%     25%     50%     75%    100%       W    Pr(<W)    
p1 -0.1743 -0.0630  0.0173  0.0661  0.1220  0.9128 0.0045977 ** 
p2 -0.0536 -0.0314  0.0034  0.0268  0.0545  0.9524 0.0918667 .  
p3 -0.0320 -0.0173 -0.0036  0.0182  0.0493  0.9600 0.1678323    
p4 -0.0297 -0.0140 -0.0034  0.0147  0.0418  0.9504 0.0783601 .  
P1 -0.3743 -0.1468 -0.0242  0.0817  0.1189  0.8853 0.0007354 ***
P2 -0.0677 -0.0242 -0.0053  0.0232  0.1185  0.9368 0.0269511 *  
P3 -0.0453 -0.0133 -0.0017  0.0131  0.0551  0.9827 0.7879913    
P4 -0.0367 -0.0153 -0.0031  0.0146  0.0349  0.9484 0.0668441 .  
l1 -0.0093 -0.0035 -0.0014  0.0037  0.0088  0.9440 0.0472662 *  
l2 -0.0070 -0.0034 -0.0005  0.0033  0.0107  0.9686 0.3246200    
bx -0.0312 -0.0158 -0.0013  0.0136  0.0408  0.9527 0.0936788 .  
by -0.0841 -0.0335 -0.0038  0.0267  0.1096  0.9655 0.2562434    
r1 -0.2861 -0.0694 -0.0091  0.0337  0.0774  0.8121 1.220e-05 ***
r2 -0.0536 -0.0310  0.0026  0.0265  0.0561  0.9539 0.1031173    
r3 -0.0310 -0.0162 -0.0038  0.0200  0.0516  0.9626 0.2060758    
r4 -0.0296 -0.0130 -0.0029  0.0150  0.0444  0.9548 0.1110577    
R1 -0.3203 -0.0852 -0.0220  0.0177  0.0592  0.7953 5.422e-06 ***
R2 -0.1129 -0.0249 -0.0043  0.0158  0.0510  0.8993 0.0018284 ** 
R3 -0.0431 -0.0123  0.0013  0.0152  0.0556  0.9847 0.8550521    
R4 -0.0351 -0.0136 -0.0005  0.0152  0.0365  0.9506 0.0794619 .  
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Variances:
           Min Median    Max       K  Pr(>K)  
Pure    0.0002 0.0004 0.0008  3.1911 0.86678  
Log     0.0000 0.0000 0.0000  1.5023 0.98223  
Box-Cox 0.0002 0.0021 0.0058 14.4723 0.04339 *
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Goodness of fit:
         R-Sq   Adj-R-Sq        AIC  Sigma    SSR   SSPE         F    Pr(>F)
p1    0.97779    0.97720  -75.17266 0.0900 0.3078 0.0149 104.68406 < 2.2e-16
p2    0.99725    0.99710 -156.73694 0.0321 0.0381 0.0149   9.94387 8.267e-06
p3    0.99878    0.99868 -187.30302 0.0217 0.0169 0.0149   1.05072  0.396727
p4    0.99886    0.99872 -187.78518 0.0213 0.0159 0.0149   0.67488  0.573800
P1    0.97223    0.97150  -49.12746 0.0271 0.0280 0.0149   4.67027  0.001624
P2    0.99677    0.99660 -133.19178 0.0094 0.0033 0.0149        NA        NA
P3    0.99841    0.99828 -159.55685 0.0067 0.0016 0.0149        NA        NA
P4    0.99854    0.99837 -160.96813 0.0065 0.0015 0.0149        NA        NA
l1    0.99899    0.99896 -311.23094 0.0047 0.0008 0.0007   1.02249  0.428657
l2    0.99910    0.99905 -313.93331 0.0045 0.0007 0.0007   0.38106  0.857990
bx    0.99887    0.99884 -194.39086 0.0203 0.0156 0.0149   0.25222  0.954790
by    0.99836    0.99832 -125.07729 0.0482 0.0884 0.0851   0.20616  0.972329
r1         NA         NA  -59.29057 0.0615 0.4578 0.0149        NA        NA
r2         NA         NA -156.70646 0.0320 0.0381 0.0149        NA        NA
r3         NA         NA -187.12089 0.0215 0.0170 0.0149        NA        NA
r4         NA         NA -187.61104 0.0205 0.0159 0.0149        NA        NA
R1         NA         NA   64.48967 0.0085 0.4792 0.0149        NA        NA
R2         NA         NA  -24.33253 0.0057 0.0495 0.0149        NA        NA
R3         NA         NA -155.83682 0.0045 0.0018 0.0149        NA        NA
R4         NA         NA -156.95371 0.0043 0.0016 0.0149        NA        NA
      
p1 ***
p2 ***
p3    
p4    
P1 ** 
P2    
P3    
P4    
l1    
l2    
bx    
by    
r1    
r2    
r3    
r4    
R1    
R2    
R3    
R4    
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Sensitivity and autocorrelation:
      Sens     LOD     LOQ    Auto      DW   Pr(<DW)    
p1  0.3543  1.1692  3.5432  0.5100 0.86374 8.822e-05 ***
p2  0.0773  0.2550  0.7728 -0.0259 1.91823 0.3247223    
p3  0.0392  0.1292  0.3916  0.0324 1.87568 0.2780457    
p4  0.0334  0.1104  0.3345  0.0524 1.82833 0.2365706    
P1  0.0880  0.2904  0.8800  0.5840 0.73389 1.520e-05 ***
P2  0.0199  0.0658  0.1994  0.2005 1.42637 0.0213064 *  
P3  0.0113  0.0371  0.1126  0.0391 1.90373 0.3083886    
P4  0.0093  0.0308  0.0932  0.0547 1.81244 0.2217909    
l1      NA      NA      NA  0.0518 1.78172 0.2204653    
l2      NA      NA      NA  0.0329 1.83520 0.2465011    
bx      NA      NA      NA  0.0692 1.78306 0.2196654    
by      NA      NA      NA  0.0962 1.72460 0.1667593    
r1  0.2654  0.8759  2.6542  0.4137 0.99185 0.0004245 ***
r2  0.0768  0.2535  0.7682 -0.0361 1.93427 0.3433829    
r3  0.0384  0.1268  0.3842  0.0393 1.86204 0.2638388    
r4  0.0322  0.1061  0.3215  0.0570 1.81606 0.2251145    
R1  0.0374  0.1233  0.3738  0.4592 0.89922 0.0001385 ***
R2  0.0150  0.0494  0.1498 -0.0470 1.87082 0.2722074    
R3  0.0076  0.0251  0.0759  0.0263 1.93379 0.3424243    
R4  0.0060  0.0200  0.0605  0.0553 1.82233 0.2309266    
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

quantchem documentation built on May 30, 2017, 5:28 a.m.