Mixor-package: Mixed-Effects Ordinal Regression Analysis
In mixor: Mixed-Effects Ordinal Regression Analysis
Description
Details
Author(s)
References
See Also
Examples
Description
This package provides a function mixor for fitting mixed-effects ordinal and binary response models and associated methods for printing, summarizing, extracting estimated coefficients and the variance-covariance matrix, and estimating contrasts for the fitted models.
Details
This package was not yet installed at build time.
Index: This package was not yet installed at build time.
This package provides a function mixor for fitting mixed-effects ordinal and binary response models and associated methods for printing, summarizing, extracting estimated coefficients and the variance-covariance matrix, and estimating contrasts for the fitted models.
Author(s)
Kellie J. Archer, Donald Hedeker, Rachel Nordgren, Robert D. Gibbons Kellie J. Archer, Donald Hedeker, Rachel Nordgren, Robert D. Gibbons
Maintainer: Kellie J. Archer <archer.43@osu.edu> Kellie J. Archer <archer.43@osu.edu>
References
Hedeker D. and Gibbons R.D. (1996) A computer program for mixed-effects ordinal regression analysis. Computer Methods and Programs in Biomedicine 49, 157-176.
See Also
See also mixor, and examples in norcag, irt.data, concen, SmokeOnset, schizophrenia
Examples
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library("mixor")
data("SmokingPrevention")
# data frame must be sorted by id variable
SmokingPrevention<-SmokingPrevention[order(SmokingPrevention$class),]
# school model
Fitted.school<-mixor(thksord~thkspre+cc+tv+cctv, data=SmokingPrevention,
id=school, link="logit")
summary(Fitted.school)
vcov(Fitted.school)
# students in classrooms analysis
Fitted.students<-mixor(thksord~thkspre+cc+tv+cctv, data=SmokingPrevention,
id=class, link="logit", nAGQ=11)
summary(Fitted.students)
coef(Fitted.students)
vcov(Fitted.students)
cm<-matrix(c(-1,-1,-1,0,0,0,0,0,
0,0,0,0,0,0,0,0,
0,0,0,1,0,0,0,1),
ncol=3,byrow=TRUE)
Contrasts(Fitted.students, contrast.matrix=cm)
Example output
Loading required package: survival
Call:
mixor(formula = thksord ~ thkspre + cc + tv + cctv, data = SmokingPrevention,
id = school, link = "logit")
Deviance = 4239.486
Log-likelihood = -2119.743
RIDGEMAX = 0.2
AIC = -2127.743
SBC = -2133.072
Estimate Std. Error z value P(>|z|)
(Intercept) 0.088180 0.313111 0.2816 0.77823
thkspre 0.403280 0.042928 9.3944 < 2e-16 ***
cc 0.924101 0.371345 2.4885 0.01283 *
tv 0.275213 0.315155 0.8733 0.38252
cctv -0.466194 0.406211 -1.1477 0.25111
Random.(Intercept) 0.073498 0.049480 1.4854 0.13743
Threshold2 1.241768 0.088310 14.0614 < 2e-16 ***
Threshold3 2.420359 0.083617 28.9456 < 2e-16 ***
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
(Intercept) thkspre cc tv
(Intercept) 0.098038380 -0.0016292741 -0.0927395980 -0.085558825
thkspre -0.001629274 0.0018427733 -0.0004062879 -0.003222260
cc -0.092739598 -0.0004062879 0.1378968669 0.086972881
tv -0.085558825 -0.0032222604 0.0869728815 0.099322570
cctv 0.091733417 0.0015967494 -0.1384613619 -0.099993295
Random.(Intercept) 0.001493140 0.0009901739 -0.0033952610 -0.004351205
Threshold2 0.012913169 0.0010487855 -0.0124376451 -0.011246805
Threshold3 0.009452837 0.0016778290 -0.0087083931 -0.010787624
cctv Random.(Intercept) Threshold2 Threshold3
(Intercept) 0.091733417 0.0014931404 0.012913169 0.009452837
thkspre 0.001596749 0.0009901739 0.001048786 0.001677829
cc -0.138461362 -0.0033952610 -0.012437645 -0.008708393
tv -0.099993295 -0.0043512047 -0.011246805 -0.010787624
cctv 0.165007083 0.0045724987 0.012871837 0.009753890
Random.(Intercept) 0.004572499 0.0024482246 0.000995455 0.001304427
Threshold2 0.012871837 0.0009954550 0.007798735 0.005784051
Threshold3 0.009753890 0.0013044269 0.005784051 0.006991873
Call:
mixor(formula = thksord ~ thkspre + cc + tv + cctv, data = SmokingPrevention,
id = class, nAGQ = 11, link = "logit")
Deviance = 4230.766
Log-likelihood = -2115.383
RIDGEMAX = 0
AIC = -2123.383
SBC = -2135.004
Estimate Std. Error z value P(>|z|)
(Intercept) 0.075750 0.153514 0.4934 0.621701
thkspre 0.414797 0.040822 10.1612 < 2.2e-16 ***
cc 0.861324 0.187239 4.6001 4.222e-06 ***
tv 0.205859 0.168025 1.2252 0.220510
cctv -0.301123 0.251755 -1.1961 0.231660
Random.(Intercept) 0.188630 0.066243 2.8476 0.004406 **
Threshold2 1.273406 0.062949 20.2293 < 2.2e-16 ***
Threshold3 2.478912 0.080216 30.9029 < 2.2e-16 ***
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
(Intercept) thkspre cc tv
0.07575035 0.41479744 0.86132413 0.20585925
cctv Random.(Intercept) Threshold2 Threshold3
-0.30112255 0.18862954 1.27340629 2.47891177
(Intercept) thkspre cc tv
(Intercept) 2.356667e-02 -0.0033425314 -0.016115374 -1.554730e-02
thkspre -3.342531e-03 0.0016664078 0.000215435 -1.005232e-04
cc -1.611537e-02 0.0002154350 0.035058258 1.558126e-02
tv -1.554730e-02 -0.0001005232 0.015581257 2.823231e-02
cctv 1.425335e-02 0.0009160829 -0.033842031 -2.793812e-02
Random.(Intercept) -8.011787e-05 0.0002697499 0.001749551 -1.948124e-03
Threshold2 -1.793964e-04 0.0008120776 0.001349416 8.913283e-04
Threshold3 2.950014e-04 0.0010213593 0.000698184 4.116407e-05
cctv Random.(Intercept) Threshold2 Threshold3
(Intercept) 0.0142533511 -8.011787e-05 -0.0001793964 2.950014e-04
thkspre 0.0009160829 2.697499e-04 0.0008120776 1.021359e-03
cc -0.0338420310 1.749551e-03 0.0013494164 6.981840e-04
tv -0.0279381163 -1.948124e-03 0.0008913283 4.116407e-05
cctv 0.0633804946 1.241640e-03 -0.0003811800 1.260757e-03
Random.(Intercept) 0.0012416404 4.388076e-03 0.0006060819 1.702859e-03
Threshold2 -0.0003811800 6.060819e-04 0.0039625142 3.838976e-03
Threshold3 0.0012607567 1.702859e-03 0.0038389758 6.434629e-03
1 2 3
(Intercept) -1 -1 -1
thkspre 0 0 0
cc 0 0 0
tv 0 0 0
cctv 0 0 0
Random.(Intercept) 0 0 0
Threshold2 0 1 0
Threshold3 0 0 1
Estimate Std. Error z value P(>|z|)
1 -0.07575 0.15351 -0.4934 0.6217
2 1.19766 0.16700 7.1717 7.405e-13 ***
3 2.40316 0.17150 14.0128 < 2.2e-16 ***
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
mixor documentation built on May 2, 2019, 5:56 a.m.
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Description Details Author(s) References See Also Examples
Description
This package provides a function mixor for fitting mixed-effects ordinal and binary response models and associated methods for printing, summarizing, extracting estimated coefficients and the variance-covariance matrix, and estimating contrasts for the fitted models.
Details
This package was not yet installed at build time.
Index: This package was not yet installed at build time.
This package provides a function mixor for fitting mixed-effects ordinal and binary response models and associated methods for printing, summarizing, extracting estimated coefficients and the variance-covariance matrix, and estimating contrasts for the fitted models.
Author(s)
Kellie J. Archer, Donald Hedeker, Rachel Nordgren, Robert D. Gibbons Kellie J. Archer, Donald Hedeker, Rachel Nordgren, Robert D. Gibbons Maintainer: Kellie J. Archer <archer.43@osu.edu> Kellie J. Archer <archer.43@osu.edu>
References
Hedeker D. and Gibbons R.D. (1996) A computer program for mixed-effects ordinal regression analysis. Computer Methods and Programs in Biomedicine 49, 157-176.
See Also
See also mixor, and examples in norcag, irt.data, concen, SmokeOnset, schizophrenia
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | library("mixor")
data("SmokingPrevention")
# data frame must be sorted by id variable
SmokingPrevention<-SmokingPrevention[order(SmokingPrevention$class),]
# school model
Fitted.school<-mixor(thksord~thkspre+cc+tv+cctv, data=SmokingPrevention,
id=school, link="logit")
summary(Fitted.school)
vcov(Fitted.school)
# students in classrooms analysis
Fitted.students<-mixor(thksord~thkspre+cc+tv+cctv, data=SmokingPrevention,
id=class, link="logit", nAGQ=11)
summary(Fitted.students)
coef(Fitted.students)
vcov(Fitted.students)
cm<-matrix(c(-1,-1,-1,0,0,0,0,0,
0,0,0,0,0,0,0,0,
0,0,0,1,0,0,0,1),
ncol=3,byrow=TRUE)
Contrasts(Fitted.students, contrast.matrix=cm)
|
Example output
Loading required package: survival
Call:
mixor(formula = thksord ~ thkspre + cc + tv + cctv, data = SmokingPrevention,
id = school, link = "logit")
Deviance = 4239.486
Log-likelihood = -2119.743
RIDGEMAX = 0.2
AIC = -2127.743
SBC = -2133.072
Estimate Std. Error z value P(>|z|)
(Intercept) 0.088180 0.313111 0.2816 0.77823
thkspre 0.403280 0.042928 9.3944 < 2e-16 ***
cc 0.924101 0.371345 2.4885 0.01283 *
tv 0.275213 0.315155 0.8733 0.38252
cctv -0.466194 0.406211 -1.1477 0.25111
Random.(Intercept) 0.073498 0.049480 1.4854 0.13743
Threshold2 1.241768 0.088310 14.0614 < 2e-16 ***
Threshold3 2.420359 0.083617 28.9456 < 2e-16 ***
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
(Intercept) thkspre cc tv
(Intercept) 0.098038380 -0.0016292741 -0.0927395980 -0.085558825
thkspre -0.001629274 0.0018427733 -0.0004062879 -0.003222260
cc -0.092739598 -0.0004062879 0.1378968669 0.086972881
tv -0.085558825 -0.0032222604 0.0869728815 0.099322570
cctv 0.091733417 0.0015967494 -0.1384613619 -0.099993295
Random.(Intercept) 0.001493140 0.0009901739 -0.0033952610 -0.004351205
Threshold2 0.012913169 0.0010487855 -0.0124376451 -0.011246805
Threshold3 0.009452837 0.0016778290 -0.0087083931 -0.010787624
cctv Random.(Intercept) Threshold2 Threshold3
(Intercept) 0.091733417 0.0014931404 0.012913169 0.009452837
thkspre 0.001596749 0.0009901739 0.001048786 0.001677829
cc -0.138461362 -0.0033952610 -0.012437645 -0.008708393
tv -0.099993295 -0.0043512047 -0.011246805 -0.010787624
cctv 0.165007083 0.0045724987 0.012871837 0.009753890
Random.(Intercept) 0.004572499 0.0024482246 0.000995455 0.001304427
Threshold2 0.012871837 0.0009954550 0.007798735 0.005784051
Threshold3 0.009753890 0.0013044269 0.005784051 0.006991873
Call:
mixor(formula = thksord ~ thkspre + cc + tv + cctv, data = SmokingPrevention,
id = class, nAGQ = 11, link = "logit")
Deviance = 4230.766
Log-likelihood = -2115.383
RIDGEMAX = 0
AIC = -2123.383
SBC = -2135.004
Estimate Std. Error z value P(>|z|)
(Intercept) 0.075750 0.153514 0.4934 0.621701
thkspre 0.414797 0.040822 10.1612 < 2.2e-16 ***
cc 0.861324 0.187239 4.6001 4.222e-06 ***
tv 0.205859 0.168025 1.2252 0.220510
cctv -0.301123 0.251755 -1.1961 0.231660
Random.(Intercept) 0.188630 0.066243 2.8476 0.004406 **
Threshold2 1.273406 0.062949 20.2293 < 2.2e-16 ***
Threshold3 2.478912 0.080216 30.9029 < 2.2e-16 ***
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
(Intercept) thkspre cc tv
0.07575035 0.41479744 0.86132413 0.20585925
cctv Random.(Intercept) Threshold2 Threshold3
-0.30112255 0.18862954 1.27340629 2.47891177
(Intercept) thkspre cc tv
(Intercept) 2.356667e-02 -0.0033425314 -0.016115374 -1.554730e-02
thkspre -3.342531e-03 0.0016664078 0.000215435 -1.005232e-04
cc -1.611537e-02 0.0002154350 0.035058258 1.558126e-02
tv -1.554730e-02 -0.0001005232 0.015581257 2.823231e-02
cctv 1.425335e-02 0.0009160829 -0.033842031 -2.793812e-02
Random.(Intercept) -8.011787e-05 0.0002697499 0.001749551 -1.948124e-03
Threshold2 -1.793964e-04 0.0008120776 0.001349416 8.913283e-04
Threshold3 2.950014e-04 0.0010213593 0.000698184 4.116407e-05
cctv Random.(Intercept) Threshold2 Threshold3
(Intercept) 0.0142533511 -8.011787e-05 -0.0001793964 2.950014e-04
thkspre 0.0009160829 2.697499e-04 0.0008120776 1.021359e-03
cc -0.0338420310 1.749551e-03 0.0013494164 6.981840e-04
tv -0.0279381163 -1.948124e-03 0.0008913283 4.116407e-05
cctv 0.0633804946 1.241640e-03 -0.0003811800 1.260757e-03
Random.(Intercept) 0.0012416404 4.388076e-03 0.0006060819 1.702859e-03
Threshold2 -0.0003811800 6.060819e-04 0.0039625142 3.838976e-03
Threshold3 0.0012607567 1.702859e-03 0.0038389758 6.434629e-03
1 2 3
(Intercept) -1 -1 -1
thkspre 0 0 0
cc 0 0 0
tv 0 0 0
cctv 0 0 0
Random.(Intercept) 0 0 0
Threshold2 0 1 0
Threshold3 0 0 1
Estimate Std. Error z value P(>|z|)
1 -0.07575 0.15351 -0.4934 0.6217
2 1.19766 0.16700 7.1717 7.405e-13 ***
3 2.40316 0.17150 14.0128 < 2.2e-16 ***
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
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