preprocess.qmd

---
title: "Preprocessing"
description: "Load and format experimental data for analysis."
format:
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```{=html}
<style type="text/css">

body, td {
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## Libraries
```{r, warning=FALSE, message=FALSE}
library(tidyverse)
library(INLA)
library(here)
library(pals)
```

## Custom Functions
```{r}
source(here("R/utilities.R"))
source_dir(here("R"))
```

## Read Data  
```{r warning=FALSE, message=FALSE}
antem_df <- read_csv(here("local/bov_antemortem_2024.csv"))

# minimum date
min_date <- min(antem_df$date)
min_date # date of donor inoculation

# add variables 
antem_df <- antem_df %>%
  mutate(hpdi = as.numeric(difftime(date, min_date, units = "hours")), # hours post donor inoculation 
         hpe = dpe*24, # convert dpe to hpe
         exp_type = if_else(group == "donor", "inoc", "cont"), # exposed by inoculation or direct contact
         fever = if_else(temp >= 104, "fever", "no_fever"), # temp >= 104 constitutes fever
         censor_status = if_else(group == "Group 1" | animal == "BR23-24", 0, 1), # No obs symptoms (0) in these 
  )

dim(antem_df)
```


## Plots to Check Data  

### Donors  
```{r fig.width=8, fig.height=8, warning=FALSE, message=FALSE}
plot_donors(antem_df)
```



### Contact Groups
```{r fig.width=8, fig.height=8, warning=FALSE, message=FALSE}
plot_contact_groups(antem_df)
```
  
## ANOVA  
To evaluate the differences in nasal, serum, and lesion score among groups and over time, repeated measures ANOVAs were applied using the *ezANOVA()* function from the **ez** R-package. The analyses included within-subjects (days post-exposure, dpe) and between-subjects (group) factors, with nasal, serum, and lesion scores as the dependent variables. Mauchly's test was conducted to test the assumption of sphericity. Where violations were found, Greenhouse-Geisser and Huynh-Feldt corrections were applied.  
  
The repeated measures ANOVA results for nasal, serum, and lesion scores were significant. For nasal virus quantity, there were significant main effects of group (F(2, 9) = 9.22, p = 0.0066) and days post-exposure (dpe) (F(6, 54) = 33.99, p < 0.0001), as well as a significant interaction between group and dpe (F(12, 54) = 5.53, p < 0.0001), suggesting that nasal virus quantity varied significantly across groups and time, with different temporal patterns among groups. For serum virus quantity, no significant main effect of group was found (F(2, 9) = 2.79, p = 0.114), but there were significant effects of dpe (F(6, 54) = 25.18, p < 0.0001) and the group by dpe interaction (F(12, 54) = 7.95, p < 0.0001), indicating significant changes over time and different temporal patterns among groups. Lesion scores showed significant main effects of group (F(2, 9) = 5.86, p = 0.023) and dpe (F(6, 54) = 45.87, p < 0.0001), and a significant interaction between group and dpe (F(12, 54) = 3.04, p = 0.0025), indicating significant differences in lesion severity across groups and over time, with varying temporal patterns among the groups.    

**Prepare Data**    
```{r}
contact_groups <- antem_df %>%
  filter(group %in% c("Group 2", "Group 3", "Group 4")) %>%
  select(animal, group, nasal, serum, dpe, score) %>%
  mutate(
    score = replace_na(score, 0)) %>%
  drop_na() %>%
  mutate(
    score = replace_na(score, 0),          
    nasal = replace(nasal, nasal == 45, 0), 
    serum = replace(serum, serum == 45, 0),
    dpe = as.factor(dpe),                   
    animal = as.factor(animal),            
    group = as.factor(group)                
  ) %>%
  as.data.frame()
```

::: panel-tabset

## Nasal  
Results indicate that nasal virus quantity differed significantly between the groups and across the days post-exposure, with an interaction effect suggesting that the temporal pattern of virus quantity varied among the groups.
```{r}
nasal_anova <- ez::ezANOVA(data = contact_groups, dv = .(nasal), wid = .(animal), within = .(dpe), between = .(group))
nasal_anova
```

## Serum  
Results suggest that while there were no significant differences between groups, there were significant changes over time, and the pattern of these changes differed significantly among the groups.
```{r}
serum_anova <- ez::ezANOVA(data = contact_groups, dv = .(serum), wid = .(animal), within = .(dpe), between = .(group))
serum_anova
```

## Score  
Results indicate that lesion scores differed significantly between the groups and across the days post-exposure, with an interaction effect suggesting that the temporal pattern of lesion severity varied among the groups. 
```{r}
score_anova <- ez::ezANOVA(data = contact_groups, dv = .(score), wid = .(animal), within = .(dpe), between = .(group))
score_anova
```

:::