Linear Mixed Model for Tumor Growth Data
Usage
lmm(
tumr_obj = NULL,
formula = NULL,
data = NULL,
id = NULL,
time = NULL,
measure = NULL,
group = NULL,
...
)Arguments
- tumr_obj
takes tumr_obj created by tumr()
- formula
linear mixed model formula
- data
tumor growth data
- id
Column of subject ID's
- time
Column of repeated time measurements
- measure
Column of repeated measurements of tumor
- group
Column specifying the treatment group for each measurement
- ...
Further arguments to
lme4::lmer()
Examples
data(melanoma1)
mel1 <- tumr(melanoma1, ID, Day, Volume, Treatment)
lmm(mel1)
#> Warning: Model failed to converge with max|grad| = 0.3043 (tol = 0.002, component 1)
#> See ?lme4::convergence and ?lme4::troubleshooting.
#> Linear mixed model fit by REML. t-tests use Satterthwaite's method [
#> lmerModLmerTest]
#> Formula: log1p(Volume) ~ Treatment * Day + (Day | ID)
#> Data: data
#>
#> REML criterion at convergence: 2057.9
#>
#> Scaled residuals:
#> Min 1Q Median 3Q Max
#> -2.7388 -0.4455 0.0897 0.5194 3.2523
#>
#> Random effects:
#> Groups Name Variance Std.Dev. Corr
#> ID (Intercept) 0.1006944 0.31732
#> Day 0.0005492 0.02344 -0.29
#> Residual 1.4496878 1.20403
#> Number of obs: 600, groups: ID, 35
#>
#> Fixed effects:
#> Estimate Std. Error df t value Pr(>|t|)
#> (Intercept) 3.803278 0.241055 63.696770 15.778 < 2e-16 ***
#> TreatmentB -2.077289 0.311809 44.850653 -6.662 3.29e-08 ***
#> TreatmentC -0.151380 0.336695 58.812300 -0.450 0.65465
#> TreatmentD -1.482092 0.315893 42.320462 -4.692 2.84e-05 ***
#> Day 0.064163 0.010131 58.005388 6.333 3.82e-08 ***
#> TreatmentB:Day -0.042430 0.013049 41.175964 -3.252 0.00229 **
#> TreatmentC:Day -0.003019 0.014348 55.455508 -0.210 0.83412
#> TreatmentD:Day -0.081544 0.013289 39.417584 -6.136 3.21e-07 ***
#> ---
#> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
#>
#> Correlation of Fixed Effects:
#> (Intr) TrtmnB TrtmnC TrtmnD Day TrtB:D TrtC:D
#> TreatmentB -0.773
#> TreatmentC -0.716 0.553
#> TreatmentD -0.763 0.590 0.546
#> Day -0.567 0.438 0.406 0.432
#> TretmntB:Dy 0.440 -0.489 -0.315 -0.336 -0.776
#> TretmntC:Dy 0.400 -0.309 -0.559 -0.305 -0.706 0.548
#> TretmntD:Dy 0.432 -0.334 -0.309 -0.475 -0.762 0.592 0.538
#> optimizer (nloptwrap) convergence code: 0 (OK)
#> Model failed to converge with max|grad| = 0.3043 (tol = 0.002, component 1)
#> See ?lme4::convergence and ?lme4::troubleshooting.
#>
lmm(
tumr_obj = mel1,
formula = "Volume ~ Day + (1 | ID)"
)
#> Linear mixed model fit by REML. t-tests use Satterthwaite's method [
#> lmerModLmerTest]
#> Formula: Volume ~ Day + (1 | ID)
#> Data: data
#>
#> REML criterion at convergence: 8821.3
#>
#> Scaled residuals:
#> Min 1Q Median 3Q Max
#> -1.5481 -0.5180 -0.1911 0.2727 7.0346
#>
#> Random effects:
#> Groups Name Variance Std.Dev.
#> ID (Intercept) 90118 300.2
#> Residual 125177 353.8
#> Number of obs: 600, groups: ID, 35
#>
#> Fixed effects:
#> Estimate Std. Error df t value Pr(>|t|)
#> (Intercept) 127.342 56.728 42.665 2.245 0.03 *
#> Day 3.665 0.435 584.726 8.427 2.77e-16 ***
#> ---
#> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
#>
#> Correlation of Fixed Effects:
#> (Intr)
#> Day -0.351
data(breast)
lmm(
data = breast,
id = "ID",
group = "Treatment",
time = "Week",
measure = "Volume"
)
#> boundary (singular) fit: see help('isSingular')
#> Linear mixed model fit by REML. t-tests use Satterthwaite's method [
#> lmerModLmerTest]
#> Formula: log1p(Volume) ~ Treatment * Week + (Week | ID)
#> Data: data
#>
#> REML criterion at convergence: 1425.4
#>
#> Scaled residuals:
#> Min 1Q Median 3Q Max
#> -2.55646 -0.38793 0.01298 0.56080 2.09235
#>
#> Random effects:
#> Groups Name Variance Std.Dev. Corr
#> ID (Intercept) 2.4895 1.5778
#> Week 0.3673 0.6061 -1.00
#> Residual 3.8081 1.9514
#> Number of obs: 319, groups: ID, 28
#>
#> Fixed effects:
#> Estimate Std. Error df t value Pr(>|t|)
#> (Intercept) -2.6356 0.5345 28.9902 -4.931 3.07e-05 ***
#> TreatmentVEH 0.5622 0.7588 29.3956 0.741 0.465
#> Week 0.8822 0.1686 25.4077 5.233 1.95e-05 ***
#> TreatmentVEH:Week -0.1595 0.2391 25.6613 -0.667 0.511
#> ---
#> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
#>
#> Correlation of Fixed Effects:
#> (Intr) TrtVEH Week
#> TreatmntVEH -0.704
#> Week -0.908 0.640
#> TrtmntVEH:W 0.640 -0.909 -0.705
#> optimizer (nloptwrap) convergence code: 0 (OK)
#> boundary (singular) fit: see help('isSingular')
#>