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iccCounts (version 1.1.2)

Intraclass Correlation Coefficient for Count Data

Description

Estimates the intraclass correlation coefficient (ICC) for count data to assess repeatability (intra-methods concordance) and concordance (between-method concordance). In the concordance setting, the ICC is equivalent to the concordance correlation coefficient estimated by variance components. The ICC is estimated using the estimates from generalized linear mixed models. The within-subjects distributions considered are: Poisson; Negative Binomial with additive and proportional extradispersion; Zero-Inflated Poisson; and Zero-Inflated Negative Binomial with additive and proportional extradispersion. The statistical methodology used to estimate the ICC with count data can be found in Carrasco (2010) .

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Version

Install

install.packages('iccCounts')

Monthly Downloads

233

Version

1.1.2

License

GPL (>= 2)

Maintainer

Josep Carrasco

Last Published

February 28th, 2024

Functions in iccCounts (1.1.2)

r_est_rep_zi

ICC repeatability for zero-inflated models
plot_BA

Bland-Altman plot
r_ZINB2_2

ICC for Zero-Inflated Negative Binomial with proportional extradispersion. Concordance setting
r_ZIP2

ICC Zero-Inflated Poisson model. Concordance setting
r_NB1

ICC for Negative Binomial with additive extradispersion. Repeatability setting
r_est_con

ICC concordance
se_r_ZIP

ICC standard error for Zero-Inflated Poisson model. Repeatability setting
se_r_NB1

ICC standard error for Negative Binomial with a additive extradispersion. Repeatability setting
rqr_zinb1

RQR for ZINB1 GLMM Computes the randomized quantile residuals for ZINB1 GLMM
se_r_ZIP2

ICC standard error for Zero-Inflated Poisson model. Concordance setting
se_r_NB1_2

ICC standard error for Negative Binomial with additive extradispersion. Repeatability setting
se_r_ZINB1

ICC standard error for Zero-Inflated Negative Binomial with a additive extradispersion. Repeatability setting
rqr_pois

RQR for Poisson GLMM Computes the randomized quantile residuals for Poisson GLMM
se_r_NB2_2

ICC standard error for Negative Binomial with proportional extradispersion. Repeatability setting
rqr

RQR for GLMM Computes the randomized quantile residuals for GLMM
se_r_ZINB2_2

ICC standard error for Zero-Inflated Negative Binomial with proportional extradispersion. Repeatability setting
r_NB2_2

ICC for Negative Binomial with proportional extradispersion. Concordance setting
r_ZIP

ICC Zero-Inflated Poisson model. Repeatability setting
se_r_ZINB2

ICC standard error for Zero-Inflated Negative Binomial with proportional extradispersion. Repeatability setting
rqr_zinb2

RQR for ZINB2 GLMM Computes the randomized quantile residuals for ZINB2 GLMM
se_r_Pois2

ICC standard error for Poisson model. Concordance setting
se_r_NB2

ICC standard error for Negative Binomial with proportional extradispersion. Repeatability setting
se_r_Pois

ICC standard error for Poisson model. Repeatability setting
rqr_zip

RQR for ZIP GLMM Computes the randomized quantile residuals for ZIP GLMM
se_r_ZINB1_2

ICC standard error for Zero-Inflated Negative Binomial with additive extradispersion. Repeatability setting
r_ZINB1_2

ICC for Zero-Inflated Negative Binomial with additive extradispersion. Concordance setting
r_Pois

ICC Poisson model. Repeatability setting
rqr_nb1

RQR for NegBin1 GLMM Computes the randomized quantile residuals for NegBin1 GLMM
rqr_nb2

RQR for NegBin2 GLMM Computes the randomized quantile residuals for NegBin2 GLMM
r_ZINB2

ICC for Zero-Inflated Negative Binomial with proportional extradispersion. Repeatability setting
EPP

Sparrow fledglings paternity data
GOF_check

Goodness of fit for GLMM
ICC

Prints the intraclass correlation coefficient
DispersionTest

Dispersion test for GLMM
ZeroTest

Zero-Inflation test for GLMM
VarComp

GLMM variance components
icc_counts

Intraclass correlation coefficient (ICC) for count data
plot.GOF

Goodness of fit plots
fit_model_rep

Estimates GLMM. Repeatability setting.
r_NB2

ICC for Negative Binomial with proportional extradispersion. Repeatability setting
Grimso

Tick counts data
r_NB1_2

ICC for Negative Binomial with additive extradispersion. Concordance setting
AF

CD34+ count cell data
fit_model_con

Estimates GLMM. Concordance setting.
r_est_con_zi

ICC concordance for zero-inflated models
r_est_rep

ICC repeatability
r_Pois2

ICC Poisson model. Concordance setting
r_ZINB1

ICC for Zero-Inflated Negative Binomial with additive extradispersion. Repeatability setting