Blundering Ecologist - 1 year ago 161

R Question

Another user asked How do I add confidence intervals to odds ratios in stargazer table? and outlined their solution to the problem (I've included the relevant lines of code here)

`OR.vector <- exp(mylogit$coef)`

CI.vector <- exp(confint(mylogit))

p.values <- summary(mylogit)$coefficients[, 4]

# Table with ORs and CIs`

stargazer(mylogit, coef = list(OR.vector), ci = T,

ci.custom = list(CI.vector), p = list(p.values),

single.row = T, type = "text")

When I try to run the same code for my own model, I receive the following error

`Error in summary(ml.TatC)$coefficients[, 4] :`

incorrect number of dimensions

Might anyone know why this is happening? Thank you in advance for your help!

UPDATE: Here is a link to the .txt file used.

The code I have used is as follows:

`tattoo <- read.table("https://ndownloader.figshare.com/files/6920972",`

header=TRUE, na.strings=c("unk", "NA"))

library(mlogit)

Tat<-mlogit.data(tattoo, varying=NULL, shape="wide", choice="size", id.var="date")

ml.Tat<-mlogit(size~1|age+sex+yy, Tat, reflevel="small", id.var="date")

library(stargazer)

OR.vector<-exp(ml.Tat$coef)

CI.vector<-exp(confint(ml.Tat))

p.values<-summary(ml.Tat)$coefficients[,4] #incorrect # of dimensions, how am I supposed to determine dimensions?

stargazer(ml.Tat, coef=list(OR.vector), ci=TRUE, ci.custom=list(CI.vector), single.row=T, type="text", star.cutoffs=c(0.05,0.01,0.001), out="table1.txt", digits=4)

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Answer Source

The `mlogit`

package stores p-values through the function `summary.mlogit`

in `$CoefTable`

, not in `$coefficients`

, as with `summary.glm`

. You can see this:

```
> str(summary(ml.Tat)$coefficients)
atomic [1:8] -4.45e+02 -1.88e+02 2.51e-02 8.04e-03 1.38 ...
```

`summary(ml.Tat)$coefficients`

is an atomic vector, so has only one dimension. That's why you are getting the error.

Use `summary(ml.Tat)$CoefTable[,4]`

to extract the p-values you want:

```
> summary(ml.Tat)$CoefTable[,4]
large:(intercept) medium:(intercept) large:age medium:age large:sexM medium:sexM
0.000000e+00 0.000000e+00 8.536121e-10 1.731441e-03 0.000000e+00 0.000000e+00
large:yy medium:yy
0.000000e+00 0.000000e+00
```

So your code should read:

```
library(stargazer)
OR.vector<-exp(ml.Tat$coef)
CI.vector<-exp(confint(ml.Tat))
p.values<-summary(ml.Tat)$CoefTable[,4]
stargazer(ml.Tat, coef=list(OR.vector), ci=TRUE, ci.custom=list(CI.vector),
p = p.values, single.row=T, type="text",
star.cutoffs=c(0.05,0.01,0.001),
out="table1.txt", digits=4)
```

Your table:

```
================================================
Dependent variable:
-----------------------------
size
------------------------------------------------
large:(intercept) 0.0000*** (0.0000, 0.0000)
medium:(intercept) 0.0000 (0.0000, 0.0000)
large:age 1.0254 (1.0172, 1.0336)
medium:age 1.0081 (1.0030, 1.0132)
large:sexM 3.9821 (3.5355, 4.4851)
medium:sexM 2.0886 (1.9576, 2.2284)
large:yy 1.2455 (1.2189, 1.2726)
medium:yy 1.0976 (1.0849, 1.1105)
------------------------------------------------
Observations 18,162
R2 0.0410
Log Likelihood -15,882.7000
LR Test 1,357.1140*** (df = 8)
================================================
Note: *p<0.05; **p<0.01; ***p<0.001
```

Good to know (if you are new to R) that packages deploy the `summary`

function differently, so always good to explore the object to see what is going on.

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