Reputation: 23898
I need to get the coefficients along with their SEs, t-values and p-values from gls output in R.
library(nlme)
fm1 <- gls(follicles ~ sin(2*pi*Time) + cos(2*pi*Time), Ovary,
correlation = corAR1(form = ~ 1 | Mare))
summary(fm1)
Generalized least squares fit by REML
Model: follicles ~ sin(2 * pi * Time) + cos(2 * pi * Time)
Data: Ovary
AIC BIC logLik
1571.455 1590.056 -780.7273
Correlation Structure: AR(1)
Formula: ~1 | Mare
Parameter estimate(s):
Phi
0.7532079
Coefficients:
Value Std.Error t-value p-value
(Intercept) 12.216398 0.6646437 18.380373 0.0000
sin(2 * pi * Time) -2.774712 0.6450478 -4.301561 0.0000
cos(2 * pi * Time) -0.899605 0.6975383 -1.289685 0.1981
Correlation:
(Intr) s(*p*T
sin(2 * pi * Time) 0.000
cos(2 * pi * Time) -0.294 0.000
Standardized residuals:
Min Q1 Med Q3 Max
-2.41180365 -0.75405234 -0.02923628 0.63156880 3.16247697
Residual standard error: 4.616172
Degrees of freedom: 308 total; 305 residual
I'd highly appreciate if someone help me to figure out this. Thanks in advance.
Upvotes: 4
Views: 6968
Reputation: 9503
Assuming that you want the values above for some kind of table, a solution is relatively simple.
sumfm1 <- summary(fm1)
sumfm1$tTable
Value Std.Error t-value p-value
(Intercept) 12.2163982 0.6646437 18.380373 2.618737e-51
sin(2 * pi * Time) -2.7747122 0.6450478 -4.301561 2.286284e-05
cos(2 * pi * Time) -0.8996047 0.6975383 -1.289685 1.981371e-01
More generally, if you call the str()
function on any R object, you can normally (with a bit of trial and error) figure out how to extract the results you need.
EDIT: if you need it to go into a sweave file, then call xtable on the object above, and all should be good.
Upvotes: 2
Reputation: 66852
try this:
> cs <- as.data.frame(summary(fm1)$tTable)
> cs
Value Std.Error t-value p-value
(Intercept) 12.2163982 0.6646437 18.380373 2.618737e-51
sin(2 * pi * Time) -2.7747122 0.6450478 -4.301561 2.286284e-05
cos(2 * pi * Time) -0.8996047 0.6975383 -1.289685 1.981371e-01
> cs$t
[1] 18.380373 -4.301561 -1.289685
> cs$p
[1] 2.618737e-51 2.286284e-05 1.981371e-01
Upvotes: 11