---

title: “Frequency of Blast Exposure and PTSD” author: “Agnes WHite” date: “2021-01-23” output: prettydoc::html_pretty: theme: leonids highlight: github

Import Your Data

nb <- read_xlsx ("Blastexposure.xlsx")

summary(nb)

##     PartNum          Rank             HighRank             Ref           
##  Min.   :  1.0   Length:1008        Length:1008        Length:1008       
##  1st Qu.:215.8   Class :character   Class :character   Class :character  
##  Median :425.0   Mode  :character   Mode  :character   Mode  :character  
##  Mean   :434.8                                                           
##  3rd Qu.:649.2                                                           
##  Max.   :892.0                                                           
##                                                                          
##    NumBlasts        DiagA          
##  Min.   :0.000   Length:1008       
##  1st Qu.:1.000   Class :character  
##  Median :2.000   Mode  :character  
##  Mean   :1.637                     
##  3rd Qu.:2.000                     
##  Max.   :2.000                     
##  NA's   :309

```r
nb %>% 
    pull(DiagA) %>% 
    unique() %>% 
    sort()  

## [1] "OTHER" "PTSD"

nb2 <- 
    nb %>% 
    rename(diagnosis = DiagA) %>% 
    mutate(blast_exposure = case_when(
      NumBlasts == 0 ~ "0 blasts",
      NumBlasts == 1 ~ "1 blast",
      NumBlasts == 2 ~ "2+ blasts"
    )) %>% 
    mutate(blast_exposure = factor(
      blast_exposure,
      levels = c("0 blasts", "1 blast", "2+ blasts")
    ))

```r
nb2 %>%
drop_na(blast_exposure, diagnosis) %>% 
group_by(blast_exposure) %>% 
summarize(
  PTSD = sum(diagnosis == "PTSD"),
  total = n(),
  percent = PTSD / total
)  
```

```
## # A tibble: 3 x 4
##   blast_exposure  PTSD total percent
## * <fct>          <int> <int>   <dbl>
## 1 0 blasts          15    56   0.268
## 2 1 blast           69   116   0.595
## 3 2+ blasts        331   439   0.754
```

chisqtestGC(
    ~ blast_exposure + diagnosis,
    data = nb2)

## Pearson's Chi-squared test 
## 
## Observed Counts:
##               diagnosis
## blast_exposure OTHER PTSD
##      0 blasts     41   15
##      1 blast      47   69
##      2+ blasts   108  331
## 
## Counts Expected by Null:
##               diagnosis
## blast_exposure  OTHER   PTSD
##      0 blasts   17.96  38.04
##      1 blast    37.21  78.79
##      2+ blasts 140.82 298.18
## 
## Contributions to the chi-square statistic:
##               diagnosis
## blast_exposure OTHER  PTSD
##      0 blasts  29.54 13.95
##      1 blast    2.58  1.22
##      2+ blasts  7.65  3.61
## 
## 
## Chi-Square Statistic = 58.5475 
## Degrees of Freedom of the table = 2 
## P-Value = 0