/usr/lib/R/site-library/lsmeans/NAMESPACE is in r-cran-lsmeans 2.27-61-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 | # Namespace for lsmeans package
# Imports
# From default packages (new req from CRAN, July 2015)
importFrom("graphics", "pairs", "plot")
importFrom("stats", "as.formula", "coef", "complete.cases", "confint", "cov",
"cov2cor", "delete.response", "deriv", "family", "lm", "make.link",
"model.frame", "model.matrix", "na.omit", "na.pass", "p.adjust",
"p.adjust.methods", "pchisq", "pf", "poly", "predict", "pt", "ptukey",
"qbeta", "qf", "qt", "qtukey", "reformulate", "terms", "uniroot",
"update", "vcov")
importFrom("utils", "head", "installed.packages", "str")
importFrom("nlme", "fixef")
# Others
import(methods)
import(mvtnorm)
import(estimability)
# 'requireNamespace' block below allows me to put multcomp in
# Imports instead of Depends.
if (requireNamespace("multcomp", quietly = TRUE)) {
importFrom(multcomp, cld, glht, modelparm)
export(cld) # needed so that cld is visible even when multcomp not attached
S3method(cld, ref.grid)
S3method(cld, lsm.list)
S3method(glht, lsmlf)
S3method(glht, ref.grid)
S3method(modelparm, lsmwrap)
}
if (requireNamespace("plyr", quietly = TRUE)) {
importFrom(plyr, alply)
}
if (requireNamespace("coda", quietly = TRUE)) {
importFrom(coda, as.mcmc, as.mcmc.list)
S3method(as.mcmc, ref.grid)
S3method(as.mcmc.list, ref.grid)
}
### If rstan ever implements an as.stanfit generic, we need to move rstan
### from Suggests to Imports and do something more like we do for coda::as.mcmc
#if (requireNamespace("rstan", quietly = TRUE)) {
export(as.stanfit)
#}
if (requireNamespace("xtable", quietly = TRUE)) {
importFrom(xtable, xtable, xtableList)
}
# Visible exports
exportPattern("*.lsmc") #all contrast fcns
export(
add_grouping,
as.glht,
contrast,
defaults.lsm,
get.lsm.option,
get.pmm.option,
lsm,
lsm.basis,
lsmeans,
lsmeans.character,
lsmobj,
lsmip,
lsm.options,
lstrends,
make.tran,
pmm,
pmmeans,
pmmobj,
pmmip,
pmm.options,
pmtrends,
###rbind, # my own version that overrides one in methods
recover.data,
ref.grid,
regrid,
test
)
# hidden functions of possible use to other package developers
export(
.all.vars,
.aovlist.dffun,
.diag,
.get.offset,
.my.vcov
)
# S3 methods for recover.data and lsm.basis that are needed by other packages
S3method(recover.data, call)
S3method(recover.data, aovlist)
S3method(lsm.basis, aovlist)
S3method(recover.data, lm)
S3method(lsm.basis, lm)
S3method(recover.data, lme)
S3method(lsm.basis, lme)
S3method(recover.data, merMod)
S3method(lsm.basis, merMod)
S3method(lsm.basis, mlm) # recover.data for mlm uses lm
# S3 methods -
# For clarity, I'm showing them all
# but commenting out the ones used only interally
S3method("[", ref.grid)
S3method(as.glht, ref.grid)
S3method(as.glht, lsm.list)
S3method(coef, ref.grid)
S3method(coef, lsm.list)
S3method(confint, ref.grid)
S3method(confint, lsm.list)
S3method(contrast, ref.grid)
S3method(contrast, lsm.list)
#S3method(glht, lsmlf) # in namespace block above
#S3method(glht, ref.grid)
S3method(lsmeans, character)
S3method(lsmeans.character, default)
S3method(lsmeans.character, ref.grid)
S3method(lsmeans, default)
S3method(lsmeans, formula)
S3method(lsmeans, list)
S3method(lsmip, default)
#S3method(modelparm, lsmwrap) # in namespace block above
S3method(pairs, ref.grid)
S3method(pairs, lsm.list)
S3method(plot, lsmobj)
S3method(plot, summary.ref.grid)
S3method(predict, ref.grid)
S3method(print, ref.grid)
S3method(print, summary.ref.grid)
S3method(print, lsm.list)
S3method(print, xtable.lsm)
S3method(rbind, ref.grid)
S3method(str, ref.grid)
S3method(str, lsm.list)
S3method(summary, ref.grid)
S3method(summary, lsm.list)
S3method(test, ref.grid)
S3method(test, lsm.list)
S3method(update, ref.grid)
S3method(vcov, ref.grid)
S3method(xtable, ref.grid)
S3method(xtable, summary.ref.grid)
# Support for my glht.list objects (cede to Torsten if he wants 'em in multcomp)
# DOESN'T WORK: S3method(cld, glht.list)
S3method(coef, glht.list)
S3method(confint, glht.list)
S3method(plot, glht.list)
# NOT NEEDED: S3method(print, glht.list)
S3method(summary, glht.list)
S3method(vcov, glht.list)
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