Hi
I am a new R user and I did try elrm package to do Exact Logistic
regression for my dataset ( about 170 patients with a binary dependent
variable against age and 6 other binary covariates), I did not have n column
because it was about individuals, I made n column with 1 for each
individual, here is my code and result:
>
> #### Libraries needed ####
>
> library("elrm")
Loading required package: coda
Loading required package: lattice
>
>
> #### Indicate your default directory ####
>
>
> my.directory <- "C:/Users/Masoud/Desktop/r/"
> #my.directory <- "C:/Documents and Settings/laurent/My
> Documents/Bioinfo_workshop/"
> setwd("C:/Users/Masoud/Desktop/r/")
>
> #### Read data ####
>
>
>
> PAD1 <- read.delim("C:/Users/Masoud/Desktop/r/PAD.txt", header=TRUE)
>
> attach(PAD1)
>
> head(PAD1)
Code PAD Age High_ratio Smoke DM1_2 HT HxVasc PI_NonPI n
1 EE-001 0 46 0 1 0 0 0 1 1
2 SK-002 0 56 1 0 0 1 1 1 1
3 EP-003 0 52 0 0 0 0 0 1 1
4 TS-004 0 48 0 0 1 1 0 1 1
5 XS-005 1 65 0 1 1 1 1 1 1
6 UG-006 1 51 0 1 1 1 1 1 1
>
> PAD ~ Age + High_ratio + DM1_2 + HT + HxVasc + PI_NonPI + Smoke
PAD ~ Age + High_ratio + DM1_2 + HT + HxVasc + PI_NonPI + Smoke
>
> simPAD.elrm <- elrm(PAD/n ~ Age + High_ratio + DM1_2 + HT + HxVasc +
> PI_NonPI + Smoke, interest = ~Age + High_ratio + DM1_2 + HT + HxVasc +
> PI_NonPI + Smoke, iter = 700000, burnIn = 800, alpha = 0.05, dataset =
> PAD1)
Generating the Markov chain ...
Progress: 100%
Generation of the Markov Chain required 9.7667 mins
Conducting inference ...
Inference required 1.2167 mins
Warning messages:
1: 'Age' conditional distribution of the sufficient statistic was found to
be degenerate
2: 'High_ratio' conditional distribution of the sufficient statistic was
found to be degenerate
3: 'DM1_2' conditional distribution of the sufficient statistic was found to
be degenerate
4: 'HT' conditional distribution of the sufficient statistic was found to be
degenerate
5: 'HxVasc' conditional distribution of the sufficient statistic was found
to be degenerate
6: 'PI_NonPI' conditional distribution of the sufficient statistic was found
to be degenerate
7: 'Smoke' conditional distribution of the sufficient statistic was found to
be degenerate
>
> summary(simPAD.elrm)
Call:
[[1]]
elrm(formula = PAD/n ~ Age + High_ratio + DM1_2 + HT + HxVasc +
PI_NonPI + Smoke, interest = ~Age + High_ratio + DM1_2 +
HT + HxVasc + PI_NonPI + Smoke, iter = 7e+05, dataset = PAD1,
burnIn = 800, alpha = 0.05)
Results:
estimate p-value p-value_se mc_size
joint NA 0.18251 0.01144 699200
Age NA NA NA 553
High_ratio NA NA NA 553
DM1_2 NA NA NA 553
HT NA NA NA 553
HxVasc NA NA NA 553
PI_NonPI NA NA NA 553
Smoke NA NA NA 553
95% Confidence Intervals for Parameters
lower upper
Age NA NA
High_ratio NA NA
DM1_2 NA NA
HT NA NA
HxVasc NA NA
PI_NonPI NA NA
Smoke NA NA
I did use update command a couple of times yet no better result, do you know
what I need to do for getting confidence intervals for my covariates?
--
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