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other_software
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Analysis in R
lm function
fixed-effect model, specify clusters using factor command (e.g., factor(mouseid))
library(gee)
gee function
marginal model, specify clusters with the id sub-command in the model statment (e.g., id=mouseid)
The gee package is a user-contributed package: https://cran.r-project.org/web/packages/gee/index.html
library(lme4)
lmer function, for basic clustering the notation of (1|mouseid) in the model statement is used to specify that observations are clustered within the 'mouseid' variable.
mixed-effect model
The lme4 package is a user-contributed package: https://cran.r-project.org/web/packages/lme4/index.html
Analysis in Matlab
fitlm function
fixed-effects, use the categorical function before running fitlm to inform Matlab that seperate coefficients are to be estimated for each level of the cluster variable
GEEQBOX toolbox
marginal model, the cluster variable is specified with the id input in the model statement.
GEEQBOX is not part of the statistical module of Matlab but is a user-contributed package: see more at http://www.jstatsoft.org/article/view/v025i14
fitlme function
mixed-effect model, for basic clustering the notation of (1|mouseid) in the model statement is used to specify that observations are clustered within the 'mouseid' variable.
Analysis in SAS
PROC GLM
fixed-effect model, use class statement to identify the cluster variable as categorical and list variable as per normal in the model statement
PROC GENMOD
marginal model, use class statement to identify the cluster variable as categorical and the repeated command to specify that multiple observations are made on that variable
PRsOC MIXED
mixed-effect model, use class statement to identify the cluster variable as categorical and the RANDOM sub-command to indicate that its effects are treated as random
Note: these packages and functions were not specifically implemented in our manuscript. Rather, this serves as a starting point for a reseracher who prefers using a statistical software other than Stata. Each of these functions contain addition options and outputs that the software will provide.