Pint007

1

library("tidyverse")

── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
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✔ forcats   1.0.0     ✔ stringr   1.5.1
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✔ lubridate 1.9.3     ✔ tidyr     1.3.1
✔ purrr     1.0.2     
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
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✖ dplyr::lag()    masks stats::lag()
ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors

library("survival")
library("ggfortify")
pint007 <- read.csv("/Users/chloebelton/Desktop/Pint007.csv")
pint007$AdultDays <- as.integer(pint007$AdultDays)

Warning: NAs introduced by coercion

str(pint007)

'data.frame':   228 obs. of  11 variables:
 $ Experiment   : chr  "Pint007" "Pint007" "Pint007" "Pint007" ...
 $ PairID       : int  1 1 2 2 3 3 4 4 5 5 ...
 $ PairType     : chr  "FemalePair" "FemalePair" "FemalePair" "FemalePair" ...
 $ IndividualID : chr  "A" "B" "A" "B" ...
 $ SampleID     : chr  "001A" "001B" "002A" "002B" ...
 $ Sex          : chr  "Female" "Female" "Female" "Female" ...
 $ EclosionDate : chr  "2024-05-24" "2024-05-24" "2024-05-24" "2024-05-24" ...
 $ DeathDate    : chr  "2024-06-05" "2024-06-05" "2024-06-07" "2024-06-05" ...
 $ LarvaObserved: logi  NA NA NA NA TRUE NA ...
 $ AdultDays    : int  12 12 14 12 13 8 10 13 NA 8 ...
 $ Comment      : chr  "" "" "" "" ...

boxplot(AdultDays ~ Sex, data = pint007, col = c("firebrick2", "dodgerblue"))

boxplot(AdultDays~PairType, data = pint007, col = c("firebrick2", "dodgerblue", "yellow"))

boxplot(AdultDays ~ LarvaObserved, data = pint007, col = c("firebrick2", "dodgerblue"))

breaksBy1 <- 2:17
par(mfrow = c(1,2))
hist(pint007$AdultDays[pint007$Sex == "Female"], col = "firebrick2",  breaks = breaksBy1, xlab = "Adult Age", main = "Female")
hist(pint007$AdultDays[pint007$Sex == "Male"], col="dodgerblue", breaks = breaksBy1, xlab = "Adult Age", main = "Male")

par(mfrow = c(2,2))
hist(pint007$AdultDays[pint007$PairType == "FemalePair"], col = "firebrick2", breaks = breaksBy1, xlab = "Pair Type", main = "FemalePair")
hist(pint007$AdultDays[pint007$PairType == "MixedPair"], col = "dodgerblue", breaks = breaksBy1, xlab = "Pair Type", main = "MixedPair")
hist(pint007$AdultDays[pint007$PairType == "MalePair"], col = "yellow", breaks = breaksBy1, xlab = "Pair Type", main = "MalePair")
hist(pint007$AdultDays[pint007$PairType == "Singleton"], col = "green", breaks = breaksBy1, xlab = "Pair Type", main = "Singleton")

par(mfrow = c(1,2))
hist(pint007$AdultDays[pint007$LarvaObserved == "TRUE"], col = "firebrick2", breaks = breaksBy1, xlab = "Larva Observed", main = "TRUE")
hist(pint007$AdultDays[pint007$LarvaObserved == "FALSE"], col="dodgerblue", breaks = breaksBy1, xlab = "Larva Observed", main = "FALSE")

tapply(X=pint007$AdultDays, INDEX=pint007$LarvaObserved,
FUN=summary)

$`FALSE`
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   9.00   10.00   11.00   11.46   13.00   14.00 

$`TRUE`
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  6.000   9.000   9.000   9.568  10.250  14.000 

survPint007 <- Surv(time = pint007$AdultDays, event = rep(1, nrow(pint007)))
survPint007.diff <- survdiff(survPint007 ~ pint007$LarvaObserved)
print(survPint007.diff)

Call:
survdiff(formula = survPint007 ~ pint007$LarvaObserved)

n=57, 171 observations deleted due to missingness.

                             N Observed Expected (O-E)^2/E (O-E)^2/V
pint007$LarvaObserved=FALSE 13       13     20.4      2.68       6.8
pint007$LarvaObserved=TRUE  44       44     36.6      1.50       6.8

 Chisq= 6.8  on 1 degrees of freedom, p= 0.009 

survPint007.diff$pvalue

[1] 0.009100094

survPint007.fit <- survfit(survPint007 ~ pint007$LarvaObserved)
print(survPint007.fit)

Call: survfit(formula = survPint007 ~ pint007$LarvaObserved)

   171 observations deleted due to missingness 
                             n events median 0.95LCL 0.95UCL
pint007$LarvaObserved=FALSE 13     13     11      10      NA
pint007$LarvaObserved=TRUE  44     44      9       9      10

autoplot(survPint007.fit) + scale_fill_manual(values=c("firebrick2", 
"dodgerblue")) +
theme_classic() + 
labs(title = "Plodia bFog Survivorship", x="Days", y="Survival")