Anyone know how to get p-values for the t-values from the coefficients
produced in vglm?
Attached is the code and output ? see comment added to output to show
where I need p-values
+ print(paste("********** Using VGAM function gamma2
**********"))
+ modl2<-
vglm(MidPoint~Count,gamma2,data=modl.subset,trace=TRUE,crit="c")
+ print(coef(modl2,matrix=TRUE))
+ print(summary(modl2))
[1] "********** Using VGAM function gamma2 **********"
VGLM linear loop 1 : coefficients 0.408464609241, 3.255887520104,
-0.000220585671
VGLM linear loop 2 : coefficients 2.34723239e-01, 1.28969691e+00,
-4.52393778e-05
VGLM linear loop 3 : coefficients 2.19500481e-01, 1.92534895e+00,
-3.02160949e-05
VGLM linear loop 4 : coefficients 2.19383151e-01, 2.26845910e+00,
-3.00838664e-05
VGLM linear loop 5 : coefficients 2.19383045e-01, 2.34645688e+00,
-3.00836087e-05
VGLM linear loop 6 : coefficients 2.19383045e-01, 2.34977070e+00,
-3.00836082e-05
VGLM linear loop 7 : coefficients 2.19383045e-01, 2.34977637e+00,
-3.00836082e-05
VGLM linear loop 8 : coefficients 2.19383045e-01, 2.34977637e+00,
-3.00836082e-05
log(mu) log(shape)
(Intercept) 2.193830e-01 2.349776
Count -3.008361e-05 0.000000
Call:
vglm(formula = MidPoint ~ Count, family = gamma2, data = modl.subset,
trace = TRUE, crit = "c")
Pearson Residuals:
Min 1Q Median 3Q Max
log(mu) -1.7037 -0.82997 0.072275 0.78520 1.72834
log(shape) -2.5152 -0.32448 0.254698 0.58772 0.70678
######### NEED P-VALUES HERE #########
Coefficients:
Value Std. Error t value
(Intercept):1 2.1938e-01 5.2679e-02 4.16455
(Intercept):2 2.3498e+00 1.7541e-01 13.39574
Count -3.0084e-05 8.9484e-05 -0.33619
Number of linear predictors: 2
Names of linear predictors: log(mu), log(shape)
Dispersion Parameter for gamma2 family: 1
Log-likelihood: -26.39268 on 123 degrees of freedom
Number of Iterations: 8
Steven Matthew Anderson
Anderson Research, LLC
Statistical Programming and Analysis
SAS (R) Certified Professional
AdAstra69 at mac.com
Ad Astra per Aspera
???????
On Jun 5, 2009, at 3:15 PM, Steven Matthew Anderson wrote:> Anyone know how to get p-values for the t-values from the > coefficients produced in vglm? > Attached is the code and output ? see comment added to output to > show where I need p-values > > > + print(paste("********** Using VGAM function gamma2 > **********")) > + modl2<- > vglm(MidPoint~Count,gamma2,data=modl.subset,trace=TRUE,crit="c") > + print(coef(modl2,matrix=TRUE)) > + print(summary(modl2)) > > > [1] "********** Using VGAM function gamma2 **********" > VGLM linear loop 1 : coefficients > 0.408464609241, 3.255887520104, -0.000220585671 > VGLM linear loop 2 : coefficients > 2.34723239e-01, 1.28969691e+00, -4.52393778e-05 > VGLM linear loop 3 : coefficients > 2.19500481e-01, 1.92534895e+00, -3.02160949e-05 > VGLM linear loop 4 : coefficients > 2.19383151e-01, 2.26845910e+00, -3.00838664e-05 > VGLM linear loop 5 : coefficients > 2.19383045e-01, 2.34645688e+00, -3.00836087e-05 > VGLM linear loop 6 : coefficients > 2.19383045e-01, 2.34977070e+00, -3.00836082e-05 > VGLM linear loop 7 : coefficients > 2.19383045e-01, 2.34977637e+00, -3.00836082e-05 > VGLM linear loop 8 : coefficients > 2.19383045e-01, 2.34977637e+00, -3.00836082e-05 > log(mu) log(shape) > (Intercept) 2.193830e-01 2.349776 > Count -3.008361e-05 0.000000 > > Call: > vglm(formula = MidPoint ~ Count, family = gamma2, data = modl.subset, > trace = TRUE, crit = "c") > > Pearson Residuals: > Min 1Q Median 3Q Max > log(mu) -1.7037 -0.82997 0.072275 0.78520 1.72834 > log(shape) -2.5152 -0.32448 0.254698 0.58772 0.70678 > > > ######### NEED P-VALUES HERE #########Perhaps: dt(summary( modl2 )@coef3[ , 3], 1)> > > Coefficients: > Value Std. Error t value > (Intercept):1 2.1938e-01 5.2679e-02 4.16455 > (Intercept):2 2.3498e+00 1.7541e-01 13.39574 > Count -3.0084e-05 8.9484e-05 -0.33619 > > Number of linear predictors: 2 > > Names of linear predictors: log(mu), log(shape) > > Dispersion Parameter for gamma2 family: 1 > > Log-likelihood: -26.39268 on 123 degrees of freedom > > Number of Iterations: 8 > > > Steven Matthew Anderson > > Anderson Research, LLC > Statistical Programming and Analysis > SAS (R) Certified Professional > AdAstra69 at mac.com-- David Winsemius, MD Heritage Laboratories West Hartford, CT
?str It's a pretty fundamental function for understanding R objects. > str(summary(vglm.D93)) Formal class 'summary.vglm' [package "VGAM"] with 43 slots ..@ coef3 : num [1:5, 1:3] 3.04 -4.54e-01 -2.93e-01 1.00e-15 9.33e-16 ... .. ..- attr(*, "dimnames")=List of 2 .. .. ..$ : chr [1:5] "(Intercept)" "outcome2" "outcome3" "treatment2" ... .. .. ..$ : chr [1:3] "Value" "Std. Error" "t value" ..@ cov.unscaled : num [1:5, 1:5] 0.0292 -0.0159 -0.0159 -0.02 -0.02 ... .. ..- attr(*, "dimnames")=List of 2 .. .. ..$ : chr [1:5] "(Intercept)" "outcome2" "outcome3" "treatment2" ... .. .. ..$ : chr [1:5] "(Intercept)" "outcome2" "outcome3" "treatment2" ... <snipped about three pages of further output> On Jun 5, 2009, at 7:28 PM, Steven Matthew Anderson wrote:> Thank you for your reply. Related question ... how do you know the > matrix of values in the summary(modl2) was called coef3? Is there a > function for extracting that information? > > dt(summary( modl2 )@coef3[ , 3], 1) > > Thank you, > > Steve > > > > > > > > On Jun 5, 2009, at 2:18 PM, David Winsemius wrote: > >> >> On Jun 5, 2009, at 3:15 PM, Steven Matthew Anderson wrote: >> >>> Anyone know how to get p-values for the t-values from the >>> coefficients produced in vglm? >>> Attached is the code and output ? see comment added to output to >>> show where I need p-values >>> >>> >>> + print(paste("********** Using VGAM function gamma2 >>> **********")) >>> + modl2<- >>> vglm(MidPoint~Count,gamma2,data=modl.subset,trace=TRUE,crit="c") >>> + print(coef(modl2,matrix=TRUE)) >>> + print(summary(modl2)) >>> >>> >>> [1] "********** Using VGAM function gamma2 **********" >>> VGLM linear loop 1 : coefficients >>> 0.408464609241, 3.255887520104, -0.000220585671 >>> VGLM linear loop 2 : coefficients >>> 2.34723239e-01, 1.28969691e+00, -4.52393778e-05 >>> VGLM linear loop 3 : coefficients >>> 2.19500481e-01, 1.92534895e+00, -3.02160949e-05 >>> VGLM linear loop 4 : coefficients >>> 2.19383151e-01, 2.26845910e+00, -3.00838664e-05 >>> VGLM linear loop 5 : coefficients >>> 2.19383045e-01, 2.34645688e+00, -3.00836087e-05 >>> VGLM linear loop 6 : coefficients >>> 2.19383045e-01, 2.34977070e+00, -3.00836082e-05 >>> VGLM linear loop 7 : coefficients >>> 2.19383045e-01, 2.34977637e+00, -3.00836082e-05 >>> VGLM linear loop 8 : coefficients >>> 2.19383045e-01, 2.34977637e+00, -3.00836082e-05 >>> log(mu) log(shape) >>> (Intercept) 2.193830e-01 2.349776 >>> Count -3.008361e-05 0.000000 >>> >>> Call: >>> vglm(formula = MidPoint ~ Count, family = gamma2, data = >>> modl.subset, >>> trace = TRUE, crit = "c") >>> >>> Pearson Residuals: >>> Min 1Q Median 3Q Max >>> log(mu) -1.7037 -0.82997 0.072275 0.78520 1.72834 >>> log(shape) -2.5152 -0.32448 0.254698 0.58772 0.70678 >>> >>> >>> ######### NEED P-VALUES HERE ######### >> >> Perhaps: >> >> dt(summary( modl2 )@coef3[ , 3], 1) >> >> >>> >>> >>> Coefficients: >>> Value Std. Error t value >>> (Intercept):1 2.1938e-01 5.2679e-02 4.16455 >>> (Intercept):2 2.3498e+00 1.7541e-01 13.39574 >>> Count -3.0084e-05 8.9484e-05 -0.33619 >>> >>> Number of linear predictors: 2 >>> >>> Names of linear predictors: log(mu), log(shape) >>> >>> Dispersion Parameter for gamma2 family: 1 >>> >>> Log-likelihood: -26.39268 on 123 degrees of freedom >>> >>> Number of Iterations: 8 >>> >>> >>> Steven Matthew Anderson >>> >>> Anderson Research, LLC >>> Statistical Programming and Analysis >>> SAS (R) Certified Professional >>> AdAstra69 at mac.com >> -- >> David Winsemius, MD >> Heritage Laboratories >> West Hartford, CT >> > > Steven Matthew Anderson > > Anderson Research, LLC > Statistical Programming and Analysis > SAS (R) Certified Professional > AdAstra69 at mac.com > > Ad Astra per Aspera > > ??????? > > > >David Winsemius, MD Heritage Laboratories West Hartford, CT