This question is about how to remove a part of the string from S4 lme model summary object.
Suppose this is my model.
# ----preliminaries-------------------------------------------------------
library("lme4")
library("lattice")
library("minqa")
library("nlme")
##-------------------------------------------------------------------------
data("sleepstudy")
##-------------------------------------------------------------------------
sleepstudy$Days[sleepstudy$Days == "0"] <- "Zero"
sleepstudy$Days[sleepstudy$Days == "1"] <- "One"
sleepstudy$Days[sleepstudy$Days == "2"] <- "Two"
sleepstudy$Days[sleepstudy$Days == "3"] <- "Three"
sleepstudy$Days[sleepstudy$Days == "4"] <- "Four"
sleepstudy$Days[sleepstudy$Days == "5"] <- "Five"
sleepstudy$Days[sleepstudy$Days == "6"] <- "Six"
sleepstudy$Days[sleepstudy$Days == "7"] <- "Seven"
## Model
##-------------------------------------------------------------------------
fm1 <- lme(fixed = Reaction ~ Days ,
random = ~1 | Days,
data = sleepstudy)
summary(fm1)
Linear mixed-effects model fit by REML
Data: sleepstudy
AIC BIC logLik
1855.854 1893.483 -915.9268
Random effects:
Formula: ~1 | Days
(Intercept) Residual
StdDev: 30.55409 48.61125
Fixed effects: Reaction ~ Days
Value Std.Error DF t-value p-value
(Intercept) 336.6295 32.63178 170 10.316003 0
Days9 14.2217 46.14830 0 0.308174 NaN
DaysFive -28.1110 46.14830 0 -0.609146 NaN
DaysFour -47.9801 46.14830 0 -1.039693 NaN
DaysOne -72.1337 46.14830 0 -1.563086 NaN
DaysSeven -17.8789 46.14830 0 -0.387423 NaN
DaysSix -24.4512 46.14830 0 -0.529841 NaN
DaysThree -53.6375 46.14830 0 -1.162285 NaN
DaysTwo -71.2676 46.14830 0 -1.544317 NaN
DaysZero -79.9777 46.14830 0 -1.733058 NaN
I like to remove the word "Day" at the beginning of the fixed effects model summary
Expecting my fixed effects summary terms to look like this.
Fixed effects: Reaction ~ Days
Value Std.Error DF t-value p-value
(Intercept) 336.6295 32.63178 170 10.316003 0
9 14.2217 46.14830 0 0.308174 NaN
Five -28.1110 46.14830 0 -0.609146 NaN
Four -47.9801 46.14830 0 -1.039693 NaN
One -72.1337 46.14830 0 -1.563086 NaN
Seven -17.8789 46.14830 0 -0.387423 NaN
Six -24.4512 46.14830 0 -0.529841 NaN
Three -53.6375 46.14830 0 -1.162285 NaN
Two -71.2676 46.14830 0 -1.544317 NaN
Zero -79.9777 46.14830 0 -1.733058 NaN
I have tried
summary(fm1) <- gsub("Days", "", summary(fm1))
I received an error saying, this object fm1 is of class S4 and gsub will not work. So any suggestion for how to exclude the word "Days" from the model summary terms is appreciated. Thanks.
Most summary() functions return a result that you can modify before printing. So instead of running summary(fm1), save the result of that call using
summ <- summary(fm1)
and edit the names before printing. You can look at ?summary.lme to find the names of the components to edit, or just look at names(summ) and guess. This works for me:
rownames(summ$tTable) <- sub("Days", "", rownames(summ$tTable))
rownames(summ$corFixed) <- sub("Days", "", rownames(summ$corFixed))
colnames(summ$corFixed) <- sub("Days", "", colnames(summ$corFixed))
summ