calib: Calculation of qPCR efficiency using dilution curves and...
In qpcR: Modelling and Analysis of Real-Time PCR Data
Description
Usage
Arguments
Details
Value
Author(s)
Examples
Description
This function calculates the PCR efficiency from a classical qPCR dilution experiment. The threshold cycles are plotted against the logarithmized concentration (or dilution) values, a linear regression line is fit and the efficiency calculated by E = 10^{\frac{-1}{slope}}. A graph is displayed with the raw values plotted with the threshold cycle and the linear regression curve. The threshold cycles are calculated either by some arbitrary fluorescence value (i.e. as given by the qPCR software) or calculated from the second derivative maximum of the dilution curves. If values to be predicted are given, they are calculated from the curve and also displayed within. calib2 uses a bootstrap approach if replicates for the dilutions are supplied. See 'Details'.
Usage
1
2
Arguments
refcurve
a 'modlist' containing the curves for calibration.
predcurve
an (optional) 'modlist' containing the curves for prediction.
thresh
the fluorescence value from which the threshold cycles are defined. Either "cpD2" or a numeric value.
dil
a vector with the concentration (or dilution) values corresponding to the calibration curves.
group
a factor defining the group membership for the replicates. See 'Examples'.
plot
logical. Should the fitting (bootstrapping) be displayed? If FALSE, only values are returned.
conf
the confidence interval. Defaults to 95%, can be omitted with NULL.
B
the number of bootstraps.
Details
calib2 calculates confidence intervals for efficiency, AICc, adjusted R^2_{adj} and the prediction curve concentrations. If single replicates per dilution are supplied by the user, confidence intervals for the prediction curves are calculated based on asymptotic normality. If multiple replicates are supplied, the regression curves are calculated by randomly sampling one of the replicates from each dilution group. The confidence intervals are then calculated from the bootstraped results.
Value
A list with the following components:
eff
the efficiency.
AICc
the second-order corrected AIC.
Rsq.ad
the adjusted R^2_{adj}.
predconc
the (log) concentration of the predicted curves.
conf.boot
a list containing the confidence intervals for the efficiency, the AICc, Rsq.ad and the predicted concentrations.
A plot is also supplied for efficiency, AICc, Rsq.ad and predicted concentrations including confidence intervals in red.
Author(s)
Andrej-Nikolai Spiess
Examples
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
## Define calibration curves,
## dilutions (or copy numbers)
## and curves to be predicted.
## Do background subtraction using
## average of first 8 cycles. No replicates.
CAL <- modlist(reps, fluo = c(2, 6, 10, 14, 18, 22),
baseline = "mean", basecyc = 1:8)
COPIES <- c(100000, 10000, 1000, 100, 10, 1)
PRED <- modlist(reps, fluo = c(3, 7, 11),
baseline = "mean", basecyc = 1:8)
## Conduct normal quantification using
## the second derivative maximum of first curve.
calib(refcurve = CAL, predcurve = PRED, thresh = "cpD2",
dil = COPIES, plot = FALSE)
## Using a defined treshold value.
#calib(refcurve = CAL, predcurve = PRED, thresh = 0.5, dil = COPIES)
## Using six dilutions with four replicates/dilution.
## Not run:
#CAL2 <- modlist(reps, fluo = 2:25)
#calib(refcurve = CAL2, predcurve = PRED, thresh = "cpD2",
# dil = COPIES, group = gl(6,4))
## End(Not run)
Example output
Loading required package: MASS
Loading required package: minpack.lm
Loading required package: rgl
Loading required package: robustbase
Loading required package: Matrix
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE
3: .onUnload failed in unloadNamespace() for 'rgl', details:
call: fun(...)
error: object 'rgl_quit' not found
Making model for F1.1 (l4)
=> Fitting passed...
Making model for F2.1 (l4)
=> Fitting passed...
Making model for F3.1 (l4)
=> Fitting passed...
Making model for F4.1 (l4)
=> Fitting passed...
Making model for F5.1 (l4)
=> Fitting passed...
Making model for F6.1 (l4)
=> Fitting passed...
Calculating delta of first/second derivative maxima...
......
Making model for F1.2 (l4)
=> Fitting passed...
Making model for F2.2 (l4)
=> Fitting passed...
Making model for F3.2 (l4)
=> Fitting passed...
Calculating delta of first/second derivative maxima...
...
[1] "Calculating threshold cycles of reference curves..."
[1] "Calculating threshold cycles of prediction curves..."
$eff
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,9] [,10] [,11] [,12] [,13] [,14] [,15] [,16]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,25] [,26] [,27] [,28] [,29] [,30] [,31] [,32]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,33] [,34] [,35] [,36] [,37] [,38] [,39] [,40]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,41] [,42] [,43] [,44] [,45] [,46] [,47] [,48]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,49] [,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,57] [,58] [,59] [,60] [,61] [,62] [,63] [,64]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,65] [,66] [,67] [,68] [,69] [,70] [,71] [,72]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,73] [,74] [,75] [,76] [,77] [,78] [,79] [,80]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,81] [,82] [,83] [,84] [,85] [,86] [,87] [,88]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,89] [,90] [,91] [,92] [,93] [,94] [,95] [,96]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,97] [,98] [,99] [,100] [,101] [,102] [,103] [,104]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,105] [,106] [,107] [,108] [,109] [,110] [,111] [,112]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,113] [,114] [,115] [,116] [,117] [,118] [,119] [,120]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,121] [,122] [,123] [,124] [,125] [,126] [,127] [,128]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,129] [,130] [,131] [,132] [,133] [,134] [,135] [,136]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,137] [,138] [,139] [,140] [,141] [,142] [,143] [,144]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,145] [,146] [,147] [,148] [,149] [,150] [,151] [,152]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,153] [,154] [,155] [,156] [,157] [,158] [,159] [,160]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,161] [,162] [,163] [,164] [,165] [,166] [,167] [,168]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,169] [,170] [,171] [,172] [,173] [,174] [,175] [,176]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,177] [,178] [,179] [,180] [,181] [,182] [,183] [,184]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,185] [,186] [,187] [,188] [,189] [,190] [,191] [,192]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,193] [,194] [,195] [,196] [,197] [,198] [,199] [,200]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
$AICc
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,99] [,100] [,101] [,102] [,103] [,104] [,105]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,106] [,107] [,108] [,109] [,110] [,111] [,112]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,113] [,114] [,115] [,116] [,117] [,118] [,119]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,120] [,121] [,122] [,123] [,124] [,125] [,126]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,127] [,128] [,129] [,130] [,131] [,132] [,133]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,134] [,135] [,136] [,137] [,138] [,139] [,140]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,141] [,142] [,143] [,144] [,145] [,146] [,147]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,148] [,149] [,150] [,151] [,152] [,153] [,154]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,155] [,156] [,157] [,158] [,159] [,160] [,161]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,162] [,163] [,164] [,165] [,166] [,167] [,168]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,169] [,170] [,171] [,172] [,173] [,174] [,175]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,176] [,177] [,178] [,179] [,180] [,181] [,182]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,183] [,184] [,185] [,186] [,187] [,188] [,189]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,190] [,191] [,192] [,193] [,194] [,195] [,196]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,197] [,198] [,199] [,200]
[1,] -1.212265 -1.212265 -1.212265 -1.212265
$Rsq.ad
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,99] [,100] [,101] [,102] [,103] [,104] [,105]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,106] [,107] [,108] [,109] [,110] [,111] [,112]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,113] [,114] [,115] [,116] [,117] [,118] [,119]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,120] [,121] [,122] [,123] [,124] [,125] [,126]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,127] [,128] [,129] [,130] [,131] [,132] [,133]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,134] [,135] [,136] [,137] [,138] [,139] [,140]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,141] [,142] [,143] [,144] [,145] [,146] [,147]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,148] [,149] [,150] [,151] [,152] [,153] [,154]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,155] [,156] [,157] [,158] [,159] [,160] [,161]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,162] [,163] [,164] [,165] [,166] [,167] [,168]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,169] [,170] [,171] [,172] [,173] [,174] [,175]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,176] [,177] [,178] [,179] [,180] [,181] [,182]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,183] [,184] [,185] [,186] [,187] [,188] [,189]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,190] [,191] [,192] [,193] [,194] [,195] [,196]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,197] [,198] [,199] [,200]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353
$predconc
[,1] [,2] [,3]
[1,] 5.058594 4.021451 3.057951
[2,] 5.058594 4.021451 3.057951
[3,] 5.058594 4.021451 3.057951
[4,] 5.058594 4.021451 3.057951
[5,] 5.058594 4.021451 3.057951
[6,] 5.058594 4.021451 3.057951
[7,] 5.058594 4.021451 3.057951
[8,] 5.058594 4.021451 3.057951
[9,] 5.058594 4.021451 3.057951
[10,] 5.058594 4.021451 3.057951
[11,] 5.058594 4.021451 3.057951
[12,] 5.058594 4.021451 3.057951
[13,] 5.058594 4.021451 3.057951
[14,] 5.058594 4.021451 3.057951
[15,] 5.058594 4.021451 3.057951
[16,] 5.058594 4.021451 3.057951
[17,] 5.058594 4.021451 3.057951
[18,] 5.058594 4.021451 3.057951
[19,] 5.058594 4.021451 3.057951
[20,] 5.058594 4.021451 3.057951
[21,] 5.058594 4.021451 3.057951
[22,] 5.058594 4.021451 3.057951
[23,] 5.058594 4.021451 3.057951
[24,] 5.058594 4.021451 3.057951
[25,] 5.058594 4.021451 3.057951
[26,] 5.058594 4.021451 3.057951
[27,] 5.058594 4.021451 3.057951
[28,] 5.058594 4.021451 3.057951
[29,] 5.058594 4.021451 3.057951
[30,] 5.058594 4.021451 3.057951
[31,] 5.058594 4.021451 3.057951
[32,] 5.058594 4.021451 3.057951
[33,] 5.058594 4.021451 3.057951
[34,] 5.058594 4.021451 3.057951
[35,] 5.058594 4.021451 3.057951
[36,] 5.058594 4.021451 3.057951
[37,] 5.058594 4.021451 3.057951
[38,] 5.058594 4.021451 3.057951
[39,] 5.058594 4.021451 3.057951
[40,] 5.058594 4.021451 3.057951
[41,] 5.058594 4.021451 3.057951
[42,] 5.058594 4.021451 3.057951
[43,] 5.058594 4.021451 3.057951
[44,] 5.058594 4.021451 3.057951
[45,] 5.058594 4.021451 3.057951
[46,] 5.058594 4.021451 3.057951
[47,] 5.058594 4.021451 3.057951
[48,] 5.058594 4.021451 3.057951
[49,] 5.058594 4.021451 3.057951
[50,] 5.058594 4.021451 3.057951
[51,] 5.058594 4.021451 3.057951
[52,] 5.058594 4.021451 3.057951
[53,] 5.058594 4.021451 3.057951
[54,] 5.058594 4.021451 3.057951
[55,] 5.058594 4.021451 3.057951
[56,] 5.058594 4.021451 3.057951
[57,] 5.058594 4.021451 3.057951
[58,] 5.058594 4.021451 3.057951
[59,] 5.058594 4.021451 3.057951
[60,] 5.058594 4.021451 3.057951
[61,] 5.058594 4.021451 3.057951
[62,] 5.058594 4.021451 3.057951
[63,] 5.058594 4.021451 3.057951
[64,] 5.058594 4.021451 3.057951
[65,] 5.058594 4.021451 3.057951
[66,] 5.058594 4.021451 3.057951
[67,] 5.058594 4.021451 3.057951
[68,] 5.058594 4.021451 3.057951
[69,] 5.058594 4.021451 3.057951
[70,] 5.058594 4.021451 3.057951
[71,] 5.058594 4.021451 3.057951
[72,] 5.058594 4.021451 3.057951
[73,] 5.058594 4.021451 3.057951
[74,] 5.058594 4.021451 3.057951
[75,] 5.058594 4.021451 3.057951
[76,] 5.058594 4.021451 3.057951
[77,] 5.058594 4.021451 3.057951
[78,] 5.058594 4.021451 3.057951
[79,] 5.058594 4.021451 3.057951
[80,] 5.058594 4.021451 3.057951
[81,] 5.058594 4.021451 3.057951
[82,] 5.058594 4.021451 3.057951
[83,] 5.058594 4.021451 3.057951
[84,] 5.058594 4.021451 3.057951
[85,] 5.058594 4.021451 3.057951
[86,] 5.058594 4.021451 3.057951
[87,] 5.058594 4.021451 3.057951
[88,] 5.058594 4.021451 3.057951
[89,] 5.058594 4.021451 3.057951
[90,] 5.058594 4.021451 3.057951
[91,] 5.058594 4.021451 3.057951
[92,] 5.058594 4.021451 3.057951
[93,] 5.058594 4.021451 3.057951
[94,] 5.058594 4.021451 3.057951
[95,] 5.058594 4.021451 3.057951
[96,] 5.058594 4.021451 3.057951
[97,] 5.058594 4.021451 3.057951
[98,] 5.058594 4.021451 3.057951
[99,] 5.058594 4.021451 3.057951
[100,] 5.058594 4.021451 3.057951
[101,] 5.058594 4.021451 3.057951
[102,] 5.058594 4.021451 3.057951
[103,] 5.058594 4.021451 3.057951
[104,] 5.058594 4.021451 3.057951
[105,] 5.058594 4.021451 3.057951
[106,] 5.058594 4.021451 3.057951
[107,] 5.058594 4.021451 3.057951
[108,] 5.058594 4.021451 3.057951
[109,] 5.058594 4.021451 3.057951
[110,] 5.058594 4.021451 3.057951
[111,] 5.058594 4.021451 3.057951
[112,] 5.058594 4.021451 3.057951
[113,] 5.058594 4.021451 3.057951
[114,] 5.058594 4.021451 3.057951
[115,] 5.058594 4.021451 3.057951
[116,] 5.058594 4.021451 3.057951
[117,] 5.058594 4.021451 3.057951
[118,] 5.058594 4.021451 3.057951
[119,] 5.058594 4.021451 3.057951
[120,] 5.058594 4.021451 3.057951
[121,] 5.058594 4.021451 3.057951
[122,] 5.058594 4.021451 3.057951
[123,] 5.058594 4.021451 3.057951
[124,] 5.058594 4.021451 3.057951
[125,] 5.058594 4.021451 3.057951
[126,] 5.058594 4.021451 3.057951
[127,] 5.058594 4.021451 3.057951
[128,] 5.058594 4.021451 3.057951
[129,] 5.058594 4.021451 3.057951
[130,] 5.058594 4.021451 3.057951
[131,] 5.058594 4.021451 3.057951
[132,] 5.058594 4.021451 3.057951
[133,] 5.058594 4.021451 3.057951
[134,] 5.058594 4.021451 3.057951
[135,] 5.058594 4.021451 3.057951
[136,] 5.058594 4.021451 3.057951
[137,] 5.058594 4.021451 3.057951
[138,] 5.058594 4.021451 3.057951
[139,] 5.058594 4.021451 3.057951
[140,] 5.058594 4.021451 3.057951
[141,] 5.058594 4.021451 3.057951
[142,] 5.058594 4.021451 3.057951
[143,] 5.058594 4.021451 3.057951
[144,] 5.058594 4.021451 3.057951
[145,] 5.058594 4.021451 3.057951
[146,] 5.058594 4.021451 3.057951
[147,] 5.058594 4.021451 3.057951
[148,] 5.058594 4.021451 3.057951
[149,] 5.058594 4.021451 3.057951
[150,] 5.058594 4.021451 3.057951
[151,] 5.058594 4.021451 3.057951
[152,] 5.058594 4.021451 3.057951
[153,] 5.058594 4.021451 3.057951
[154,] 5.058594 4.021451 3.057951
[155,] 5.058594 4.021451 3.057951
[156,] 5.058594 4.021451 3.057951
[157,] 5.058594 4.021451 3.057951
[158,] 5.058594 4.021451 3.057951
[159,] 5.058594 4.021451 3.057951
[160,] 5.058594 4.021451 3.057951
[161,] 5.058594 4.021451 3.057951
[162,] 5.058594 4.021451 3.057951
[163,] 5.058594 4.021451 3.057951
[164,] 5.058594 4.021451 3.057951
[165,] 5.058594 4.021451 3.057951
[166,] 5.058594 4.021451 3.057951
[167,] 5.058594 4.021451 3.057951
[168,] 5.058594 4.021451 3.057951
[169,] 5.058594 4.021451 3.057951
[170,] 5.058594 4.021451 3.057951
[171,] 5.058594 4.021451 3.057951
[172,] 5.058594 4.021451 3.057951
[173,] 5.058594 4.021451 3.057951
[174,] 5.058594 4.021451 3.057951
[175,] 5.058594 4.021451 3.057951
[176,] 5.058594 4.021451 3.057951
[177,] 5.058594 4.021451 3.057951
[178,] 5.058594 4.021451 3.057951
[179,] 5.058594 4.021451 3.057951
[180,] 5.058594 4.021451 3.057951
[181,] 5.058594 4.021451 3.057951
[182,] 5.058594 4.021451 3.057951
[183,] 5.058594 4.021451 3.057951
[184,] 5.058594 4.021451 3.057951
[185,] 5.058594 4.021451 3.057951
[186,] 5.058594 4.021451 3.057951
[187,] 5.058594 4.021451 3.057951
[188,] 5.058594 4.021451 3.057951
[189,] 5.058594 4.021451 3.057951
[190,] 5.058594 4.021451 3.057951
[191,] 5.058594 4.021451 3.057951
[192,] 5.058594 4.021451 3.057951
[193,] 5.058594 4.021451 3.057951
[194,] 5.058594 4.021451 3.057951
[195,] 5.058594 4.021451 3.057951
[196,] 5.058594 4.021451 3.057951
[197,] 5.058594 4.021451 3.057951
[198,] 5.058594 4.021451 3.057951
[199,] 5.058594 4.021451 3.057951
[200,] 5.058594 4.021451 3.057951
$conf.boot
$conf.boot$conf.eff
2.5% 97.5%
2.027388 2.027388
$conf.boot$conf.AICc
2.5% 97.5%
-1.212265 -1.212265
$conf.boot$conf.Rsq.ad
2.5% 97.5%
0.9996353 0.9996353
$conf.boot$conf.predconc
[,1] [,2] [,3]
2.5% 4.989290 3.969923 3.017477
97.5% 5.127899 4.072979 3.098424
qpcR documentation built on May 2, 2019, 5:17 a.m.
R Package Documentation
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Description Usage Arguments Details Value Author(s) Examples
Description
This function calculates the PCR efficiency from a classical qPCR dilution experiment. The threshold cycles are plotted against the logarithmized concentration (or dilution) values, a linear regression line is fit and the efficiency calculated by E = 10^{\frac{-1}{slope}}. A graph is displayed with the raw values plotted with the threshold cycle and the linear regression curve. The threshold cycles are calculated either by some arbitrary fluorescence value (i.e. as given by the qPCR software) or calculated from the second derivative maximum of the dilution curves. If values to be predicted are given, they are calculated from the curve and also displayed within. calib2 uses a bootstrap approach if replicates for the dilutions are supplied. See 'Details'.
Usage
1 2 |
Arguments
refcurve |
a 'modlist' containing the curves for calibration. |
predcurve |
an (optional) 'modlist' containing the curves for prediction. |
thresh |
the fluorescence value from which the threshold cycles are defined. Either "cpD2" or a numeric value. |
dil |
a vector with the concentration (or dilution) values corresponding to the calibration curves. |
group |
a factor defining the group membership for the replicates. See 'Examples'. |
plot |
logical. Should the fitting (bootstrapping) be displayed? If |
conf |
the confidence interval. Defaults to 95%, can be omitted with |
B |
the number of bootstraps. |
Details
calib2 calculates confidence intervals for efficiency, AICc, adjusted R^2_{adj} and the prediction curve concentrations. If single replicates per dilution are supplied by the user, confidence intervals for the prediction curves are calculated based on asymptotic normality. If multiple replicates are supplied, the regression curves are calculated by randomly sampling one of the replicates from each dilution group. The confidence intervals are then calculated from the bootstraped results.
Value
A list with the following components:
eff |
the efficiency. |
AICc |
the second-order corrected AIC. |
Rsq.ad |
the adjusted R^2_{adj}. |
predconc |
the (log) concentration of the predicted curves. |
conf.boot |
a list containing the confidence intervals for the efficiency, the AICc, Rsq.ad and the predicted concentrations. |
A plot is also supplied for efficiency, AICc, Rsq.ad and predicted concentrations including confidence intervals in red.
Author(s)
Andrej-Nikolai Spiess
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 | ## Define calibration curves,
## dilutions (or copy numbers)
## and curves to be predicted.
## Do background subtraction using
## average of first 8 cycles. No replicates.
CAL <- modlist(reps, fluo = c(2, 6, 10, 14, 18, 22),
baseline = "mean", basecyc = 1:8)
COPIES <- c(100000, 10000, 1000, 100, 10, 1)
PRED <- modlist(reps, fluo = c(3, 7, 11),
baseline = "mean", basecyc = 1:8)
## Conduct normal quantification using
## the second derivative maximum of first curve.
calib(refcurve = CAL, predcurve = PRED, thresh = "cpD2",
dil = COPIES, plot = FALSE)
## Using a defined treshold value.
#calib(refcurve = CAL, predcurve = PRED, thresh = 0.5, dil = COPIES)
## Using six dilutions with four replicates/dilution.
## Not run:
#CAL2 <- modlist(reps, fluo = 2:25)
#calib(refcurve = CAL2, predcurve = PRED, thresh = "cpD2",
# dil = COPIES, group = gl(6,4))
## End(Not run)
|
Example output
Loading required package: MASS
Loading required package: minpack.lm
Loading required package: rgl
Loading required package: robustbase
Loading required package: Matrix
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE
3: .onUnload failed in unloadNamespace() for 'rgl', details:
call: fun(...)
error: object 'rgl_quit' not found
Making model for F1.1 (l4)
=> Fitting passed...
Making model for F2.1 (l4)
=> Fitting passed...
Making model for F3.1 (l4)
=> Fitting passed...
Making model for F4.1 (l4)
=> Fitting passed...
Making model for F5.1 (l4)
=> Fitting passed...
Making model for F6.1 (l4)
=> Fitting passed...
Calculating delta of first/second derivative maxima...
......
Making model for F1.2 (l4)
=> Fitting passed...
Making model for F2.2 (l4)
=> Fitting passed...
Making model for F3.2 (l4)
=> Fitting passed...
Calculating delta of first/second derivative maxima...
...
[1] "Calculating threshold cycles of reference curves..."
[1] "Calculating threshold cycles of prediction curves..."
$eff
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,9] [,10] [,11] [,12] [,13] [,14] [,15] [,16]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,25] [,26] [,27] [,28] [,29] [,30] [,31] [,32]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,33] [,34] [,35] [,36] [,37] [,38] [,39] [,40]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,41] [,42] [,43] [,44] [,45] [,46] [,47] [,48]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,49] [,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,57] [,58] [,59] [,60] [,61] [,62] [,63] [,64]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,65] [,66] [,67] [,68] [,69] [,70] [,71] [,72]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,73] [,74] [,75] [,76] [,77] [,78] [,79] [,80]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,81] [,82] [,83] [,84] [,85] [,86] [,87] [,88]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,89] [,90] [,91] [,92] [,93] [,94] [,95] [,96]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,97] [,98] [,99] [,100] [,101] [,102] [,103] [,104]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,105] [,106] [,107] [,108] [,109] [,110] [,111] [,112]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,113] [,114] [,115] [,116] [,117] [,118] [,119] [,120]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,121] [,122] [,123] [,124] [,125] [,126] [,127] [,128]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,129] [,130] [,131] [,132] [,133] [,134] [,135] [,136]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,137] [,138] [,139] [,140] [,141] [,142] [,143] [,144]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,145] [,146] [,147] [,148] [,149] [,150] [,151] [,152]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,153] [,154] [,155] [,156] [,157] [,158] [,159] [,160]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,161] [,162] [,163] [,164] [,165] [,166] [,167] [,168]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,169] [,170] [,171] [,172] [,173] [,174] [,175] [,176]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,177] [,178] [,179] [,180] [,181] [,182] [,183] [,184]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,185] [,186] [,187] [,188] [,189] [,190] [,191] [,192]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
[,193] [,194] [,195] [,196] [,197] [,198] [,199] [,200]
[1,] 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388 2.027388
$AICc
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,99] [,100] [,101] [,102] [,103] [,104] [,105]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,106] [,107] [,108] [,109] [,110] [,111] [,112]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,113] [,114] [,115] [,116] [,117] [,118] [,119]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,120] [,121] [,122] [,123] [,124] [,125] [,126]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,127] [,128] [,129] [,130] [,131] [,132] [,133]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,134] [,135] [,136] [,137] [,138] [,139] [,140]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,141] [,142] [,143] [,144] [,145] [,146] [,147]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,148] [,149] [,150] [,151] [,152] [,153] [,154]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,155] [,156] [,157] [,158] [,159] [,160] [,161]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,162] [,163] [,164] [,165] [,166] [,167] [,168]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,169] [,170] [,171] [,172] [,173] [,174] [,175]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,176] [,177] [,178] [,179] [,180] [,181] [,182]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,183] [,184] [,185] [,186] [,187] [,188] [,189]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,190] [,191] [,192] [,193] [,194] [,195] [,196]
[1,] -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265 -1.212265
[,197] [,198] [,199] [,200]
[1,] -1.212265 -1.212265 -1.212265 -1.212265
$Rsq.ad
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,99] [,100] [,101] [,102] [,103] [,104] [,105]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,106] [,107] [,108] [,109] [,110] [,111] [,112]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,113] [,114] [,115] [,116] [,117] [,118] [,119]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,120] [,121] [,122] [,123] [,124] [,125] [,126]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,127] [,128] [,129] [,130] [,131] [,132] [,133]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,134] [,135] [,136] [,137] [,138] [,139] [,140]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,141] [,142] [,143] [,144] [,145] [,146] [,147]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,148] [,149] [,150] [,151] [,152] [,153] [,154]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,155] [,156] [,157] [,158] [,159] [,160] [,161]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,162] [,163] [,164] [,165] [,166] [,167] [,168]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,169] [,170] [,171] [,172] [,173] [,174] [,175]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,176] [,177] [,178] [,179] [,180] [,181] [,182]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,183] [,184] [,185] [,186] [,187] [,188] [,189]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,190] [,191] [,192] [,193] [,194] [,195] [,196]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353 0.9996353
[,197] [,198] [,199] [,200]
[1,] 0.9996353 0.9996353 0.9996353 0.9996353
$predconc
[,1] [,2] [,3]
[1,] 5.058594 4.021451 3.057951
[2,] 5.058594 4.021451 3.057951
[3,] 5.058594 4.021451 3.057951
[4,] 5.058594 4.021451 3.057951
[5,] 5.058594 4.021451 3.057951
[6,] 5.058594 4.021451 3.057951
[7,] 5.058594 4.021451 3.057951
[8,] 5.058594 4.021451 3.057951
[9,] 5.058594 4.021451 3.057951
[10,] 5.058594 4.021451 3.057951
[11,] 5.058594 4.021451 3.057951
[12,] 5.058594 4.021451 3.057951
[13,] 5.058594 4.021451 3.057951
[14,] 5.058594 4.021451 3.057951
[15,] 5.058594 4.021451 3.057951
[16,] 5.058594 4.021451 3.057951
[17,] 5.058594 4.021451 3.057951
[18,] 5.058594 4.021451 3.057951
[19,] 5.058594 4.021451 3.057951
[20,] 5.058594 4.021451 3.057951
[21,] 5.058594 4.021451 3.057951
[22,] 5.058594 4.021451 3.057951
[23,] 5.058594 4.021451 3.057951
[24,] 5.058594 4.021451 3.057951
[25,] 5.058594 4.021451 3.057951
[26,] 5.058594 4.021451 3.057951
[27,] 5.058594 4.021451 3.057951
[28,] 5.058594 4.021451 3.057951
[29,] 5.058594 4.021451 3.057951
[30,] 5.058594 4.021451 3.057951
[31,] 5.058594 4.021451 3.057951
[32,] 5.058594 4.021451 3.057951
[33,] 5.058594 4.021451 3.057951
[34,] 5.058594 4.021451 3.057951
[35,] 5.058594 4.021451 3.057951
[36,] 5.058594 4.021451 3.057951
[37,] 5.058594 4.021451 3.057951
[38,] 5.058594 4.021451 3.057951
[39,] 5.058594 4.021451 3.057951
[40,] 5.058594 4.021451 3.057951
[41,] 5.058594 4.021451 3.057951
[42,] 5.058594 4.021451 3.057951
[43,] 5.058594 4.021451 3.057951
[44,] 5.058594 4.021451 3.057951
[45,] 5.058594 4.021451 3.057951
[46,] 5.058594 4.021451 3.057951
[47,] 5.058594 4.021451 3.057951
[48,] 5.058594 4.021451 3.057951
[49,] 5.058594 4.021451 3.057951
[50,] 5.058594 4.021451 3.057951
[51,] 5.058594 4.021451 3.057951
[52,] 5.058594 4.021451 3.057951
[53,] 5.058594 4.021451 3.057951
[54,] 5.058594 4.021451 3.057951
[55,] 5.058594 4.021451 3.057951
[56,] 5.058594 4.021451 3.057951
[57,] 5.058594 4.021451 3.057951
[58,] 5.058594 4.021451 3.057951
[59,] 5.058594 4.021451 3.057951
[60,] 5.058594 4.021451 3.057951
[61,] 5.058594 4.021451 3.057951
[62,] 5.058594 4.021451 3.057951
[63,] 5.058594 4.021451 3.057951
[64,] 5.058594 4.021451 3.057951
[65,] 5.058594 4.021451 3.057951
[66,] 5.058594 4.021451 3.057951
[67,] 5.058594 4.021451 3.057951
[68,] 5.058594 4.021451 3.057951
[69,] 5.058594 4.021451 3.057951
[70,] 5.058594 4.021451 3.057951
[71,] 5.058594 4.021451 3.057951
[72,] 5.058594 4.021451 3.057951
[73,] 5.058594 4.021451 3.057951
[74,] 5.058594 4.021451 3.057951
[75,] 5.058594 4.021451 3.057951
[76,] 5.058594 4.021451 3.057951
[77,] 5.058594 4.021451 3.057951
[78,] 5.058594 4.021451 3.057951
[79,] 5.058594 4.021451 3.057951
[80,] 5.058594 4.021451 3.057951
[81,] 5.058594 4.021451 3.057951
[82,] 5.058594 4.021451 3.057951
[83,] 5.058594 4.021451 3.057951
[84,] 5.058594 4.021451 3.057951
[85,] 5.058594 4.021451 3.057951
[86,] 5.058594 4.021451 3.057951
[87,] 5.058594 4.021451 3.057951
[88,] 5.058594 4.021451 3.057951
[89,] 5.058594 4.021451 3.057951
[90,] 5.058594 4.021451 3.057951
[91,] 5.058594 4.021451 3.057951
[92,] 5.058594 4.021451 3.057951
[93,] 5.058594 4.021451 3.057951
[94,] 5.058594 4.021451 3.057951
[95,] 5.058594 4.021451 3.057951
[96,] 5.058594 4.021451 3.057951
[97,] 5.058594 4.021451 3.057951
[98,] 5.058594 4.021451 3.057951
[99,] 5.058594 4.021451 3.057951
[100,] 5.058594 4.021451 3.057951
[101,] 5.058594 4.021451 3.057951
[102,] 5.058594 4.021451 3.057951
[103,] 5.058594 4.021451 3.057951
[104,] 5.058594 4.021451 3.057951
[105,] 5.058594 4.021451 3.057951
[106,] 5.058594 4.021451 3.057951
[107,] 5.058594 4.021451 3.057951
[108,] 5.058594 4.021451 3.057951
[109,] 5.058594 4.021451 3.057951
[110,] 5.058594 4.021451 3.057951
[111,] 5.058594 4.021451 3.057951
[112,] 5.058594 4.021451 3.057951
[113,] 5.058594 4.021451 3.057951
[114,] 5.058594 4.021451 3.057951
[115,] 5.058594 4.021451 3.057951
[116,] 5.058594 4.021451 3.057951
[117,] 5.058594 4.021451 3.057951
[118,] 5.058594 4.021451 3.057951
[119,] 5.058594 4.021451 3.057951
[120,] 5.058594 4.021451 3.057951
[121,] 5.058594 4.021451 3.057951
[122,] 5.058594 4.021451 3.057951
[123,] 5.058594 4.021451 3.057951
[124,] 5.058594 4.021451 3.057951
[125,] 5.058594 4.021451 3.057951
[126,] 5.058594 4.021451 3.057951
[127,] 5.058594 4.021451 3.057951
[128,] 5.058594 4.021451 3.057951
[129,] 5.058594 4.021451 3.057951
[130,] 5.058594 4.021451 3.057951
[131,] 5.058594 4.021451 3.057951
[132,] 5.058594 4.021451 3.057951
[133,] 5.058594 4.021451 3.057951
[134,] 5.058594 4.021451 3.057951
[135,] 5.058594 4.021451 3.057951
[136,] 5.058594 4.021451 3.057951
[137,] 5.058594 4.021451 3.057951
[138,] 5.058594 4.021451 3.057951
[139,] 5.058594 4.021451 3.057951
[140,] 5.058594 4.021451 3.057951
[141,] 5.058594 4.021451 3.057951
[142,] 5.058594 4.021451 3.057951
[143,] 5.058594 4.021451 3.057951
[144,] 5.058594 4.021451 3.057951
[145,] 5.058594 4.021451 3.057951
[146,] 5.058594 4.021451 3.057951
[147,] 5.058594 4.021451 3.057951
[148,] 5.058594 4.021451 3.057951
[149,] 5.058594 4.021451 3.057951
[150,] 5.058594 4.021451 3.057951
[151,] 5.058594 4.021451 3.057951
[152,] 5.058594 4.021451 3.057951
[153,] 5.058594 4.021451 3.057951
[154,] 5.058594 4.021451 3.057951
[155,] 5.058594 4.021451 3.057951
[156,] 5.058594 4.021451 3.057951
[157,] 5.058594 4.021451 3.057951
[158,] 5.058594 4.021451 3.057951
[159,] 5.058594 4.021451 3.057951
[160,] 5.058594 4.021451 3.057951
[161,] 5.058594 4.021451 3.057951
[162,] 5.058594 4.021451 3.057951
[163,] 5.058594 4.021451 3.057951
[164,] 5.058594 4.021451 3.057951
[165,] 5.058594 4.021451 3.057951
[166,] 5.058594 4.021451 3.057951
[167,] 5.058594 4.021451 3.057951
[168,] 5.058594 4.021451 3.057951
[169,] 5.058594 4.021451 3.057951
[170,] 5.058594 4.021451 3.057951
[171,] 5.058594 4.021451 3.057951
[172,] 5.058594 4.021451 3.057951
[173,] 5.058594 4.021451 3.057951
[174,] 5.058594 4.021451 3.057951
[175,] 5.058594 4.021451 3.057951
[176,] 5.058594 4.021451 3.057951
[177,] 5.058594 4.021451 3.057951
[178,] 5.058594 4.021451 3.057951
[179,] 5.058594 4.021451 3.057951
[180,] 5.058594 4.021451 3.057951
[181,] 5.058594 4.021451 3.057951
[182,] 5.058594 4.021451 3.057951
[183,] 5.058594 4.021451 3.057951
[184,] 5.058594 4.021451 3.057951
[185,] 5.058594 4.021451 3.057951
[186,] 5.058594 4.021451 3.057951
[187,] 5.058594 4.021451 3.057951
[188,] 5.058594 4.021451 3.057951
[189,] 5.058594 4.021451 3.057951
[190,] 5.058594 4.021451 3.057951
[191,] 5.058594 4.021451 3.057951
[192,] 5.058594 4.021451 3.057951
[193,] 5.058594 4.021451 3.057951
[194,] 5.058594 4.021451 3.057951
[195,] 5.058594 4.021451 3.057951
[196,] 5.058594 4.021451 3.057951
[197,] 5.058594 4.021451 3.057951
[198,] 5.058594 4.021451 3.057951
[199,] 5.058594 4.021451 3.057951
[200,] 5.058594 4.021451 3.057951
$conf.boot
$conf.boot$conf.eff
2.5% 97.5%
2.027388 2.027388
$conf.boot$conf.AICc
2.5% 97.5%
-1.212265 -1.212265
$conf.boot$conf.Rsq.ad
2.5% 97.5%
0.9996353 0.9996353
$conf.boot$conf.predconc
[,1] [,2] [,3]
2.5% 4.989290 3.969923 3.017477
97.5% 5.127899 4.072979 3.098424
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