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I have fitted a negative binomial regression model to my data, and the summary of this compares latency of 3 resources to that of burrows:

NegativeBinomalLatencyModel <- glm.nb(Latency_s ~ Resource, data = Cricket)

summary(NegativeBinomalLatencyModel)
Coefficients:
           Estimate Std. Error z value Pr(>|z|)    
(Intercept)      4.9416     0.3055  16.178   <2e-16 ***
ResourceFemale   0.3292     0.4895   0.672    0.501    
ResourceFood     0.1878     0.4228   0.444    0.657    
ResourceNone    -0.2179     0.4231  -0.515    0.606

I was wondering how to produce a pairwise comparison of this, comparing each resource to all the other resources.

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You could do it using the emmeans package.

Then simply do:

m_means <- emmeans(NegativeBinomalLatencyModel, ~ Resource)
#TO GET PAIRWISE COMPARISONS WITH DIFFERENCES INDICATED AS LETTERS
cld(m_means, Letters = letters)

The emmeans package has a very good documentation (see link above).

Edit to address OPs comments:

If you want to plot the data, you can do it simply via the emmip() function (from the emmeans package). Have look at ?emmip for details. Using your specific example a basic plot could be generated like this:

#BASIC PLOT
emmip(m_means, ~ Resource) 
#BASIC PLOT WITH CONFIDENCE LIMITS
emmip(m_means, ~ Resource, CIs=T) 
#BASIC PLOT WITH CONFIDENCE LIMITS ON THE RESPONSE SCALE
emmip(m_means, ~ Resource, CIs=T, type="response")

Another way of plotting can be achieved by simply using the plot() function. For that have a look at ?plot.emmGrid.

If you want more control, you can store the output of cld() in an object such as this:

m_means_table <- cld(m_means, Letters = letters)

This can then be used in ggplot2 for example:

require(ggplot2)
ggplot(m_means_table, aes(x=Resource, y=emmean)) + geom_point() + 
       geom_errorbar(aes(ymin=emmean-SE, ymax=emmean+SE))

If you want upper and lower confidence limits, you can simply replace emmean-SE with asymp.LCL and emmean+SE with asymp.UCL, respectively (from the m_means_table object).

Also have a look at my answer on poisson and glm.nb models here: poisson glm to observe whether effects of artificial light on the number of bat passes in each location were significant

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  • $\begingroup$ Thanks, I'm having some trouble interpreting the output. It looks like this Resource emmean SE df asymp.LCL asymp.UCL .group 4 None 4.723694 0.2927040 Inf 4.150004 5.297383 a 1 Burrow 4.941642 0.3054607 Inf 4.342951 5.540334 a 3 Food 5.129405 0.2922820 Inf 4.556543 5.702268 a 2 Female 5.270799 0.3825413 Inf 4.521032 6.020567 a Is there a way to plot this? $\endgroup$ – Harry Mar 9 '18 at 11:40
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    $\begingroup$ @Harry I added some more detail. Have a look and see if this answers you questions. $\endgroup$ – Stefan Mar 9 '18 at 13:12
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    $\begingroup$ that's exactly what I needed. Thank you very much for your help. $\endgroup$ – Harry Mar 9 '18 at 13:37

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