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I have a reviewer that wants me to analyze my data along the lines:
Con_Ratio ~ Range * Latitude * Longitude + (1 | Genotype/Pair).

But I'm not sure if this can be done and how. My experimental design is where a caterpillar was given a choice of two genotypes of plant tissue- one from the native range and one from the invasive range. I have 38 genotypes divided between the two ranges. I calculated the Con_Ratio from the amount of that genotype consumed divided by the total amount of leaf consumed so I have a proportion. Each pair was replicated 5 times (except for one). The genotypes were not used an equal number of times and can appear in more than one pair. I want to answer if caterpillars prefer leaf tissue from one range over the other.

The reviewer was concerned that because some of my genotypes were close to each other this may have an effect and wanted the latitude and longitude included. They were also concerned because I use the Con_Ratio from both genotypes and want a Pair factor also. This means that I have 84 pairs.

I needed a starting point so this is what I ran but I'm concerned that I have proportion data and that there are so many factors for the Pair variable

PrefData <- read.csv("pref_data_18Jan2019.csv")
PrefData$Plate <- as.factor(PrefData$Plate)
PrefData$Pair <- as.factor(PrefData$Pair)
PrefDataCut <- subset(PrefData, Con_Ratio > 0)
PrefDataCut <- subset(PrefDataCut, Con_Ratio < 1) # This removes 28 points of user error
hist(PrefDataCut$Con_Ratio)
m1 <- lmer(Con_Ratio ~ Range * Latitude * Longitude  + (1 + Range|Genotype/Pair), data = PrefDataCut)
plot(m1,type=c("p","smooth"))
plot(m1,sqrt(abs(resid(.)))~fitted(.), type=c("p","smooth"))
qqnorm(resid(m1))
qqline(resid(m1))

This gives a warning. Warning messages: 1: Some predictor variables are on very different scales: consider rescaling 2: Some predictor variables are on very different scales: consider rescaling

I read about using the logit function to transform the response variable so I tried that but the warning was the same and I also read it was better to use a glmer with the binomial and logit function. But I don't know how to do that because my data can't be transformed into 0 and 1. I also read about applying the weights option to include the number of counts but I was confused how to apply it based on my dataset.

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  • $\begingroup$ You don't seem to have count data, so binomial (logistic) model is not appropriate. See stats.stackexchange.com/questions/233366. $\endgroup$
    – amoeba
    Commented Jan 19, 2019 at 23:55
  • $\begingroup$ Regarding your specific dataset, I am not quite sure what Pair means. Why is it nested in Genotype (as Genotype/Pair suggests)? $\endgroup$
    – amoeba
    Commented Jan 19, 2019 at 23:57
  • $\begingroup$ Do I understand correctly that for each pair you have two ratios in your data table that add up to 1? $\endgroup$
    – amoeba
    Commented Jan 20, 2019 at 0:00
  • $\begingroup$ It is not clear which random effects you want to use. Note that random effects are used to model correlation in the outcome data. That is, if you put a random effect for Genotype, you assume that measurements for your outcome variable Con_Ratio from the same genotype are correlated. Is this a reasonable assumption? $\endgroup$ Commented Jan 20, 2019 at 20:41
  • $\begingroup$ @amoeba. each genotype in the pair adds to 1. Here is the reviewer comment: a t-test is not an appropriate method to analyse these data. The t-test does not account for pseudo-replication within genotypes (each pair was replicated in 5 petri dishes). If you did not use genotype means but data on the petri dish level, you should rather fit a Mixed Effects Model with the respective random effect Have you used both plants from each of the petri dishes or only one plant per petri dish to build the data set? If you used both, you need an additional random factor for petri dish nested in genotype $\endgroup$
    – CJ123
    Commented Jan 21, 2019 at 0:30

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