11-example_cancer.Rmd

# Intro: Cancer Experiemnt {#cancerprep}

```{r, message=FALSE, error=FALSE}
library(tidyverse)       # super helpful everything!
library(haven)           # inporting SPSS, SAS, & Stata data files
library(psych)           # lots of nice tidbits 
```



## Source of Data 

Mid-Michigan Medical Center, Midland, Michigan, 1999: A  study of oral condition of cancer patients.

## Description of the Study 

The data set contains part of the data for a study of **oral condition** of cancer patients conducted at the Mid-Michigan Medical Center.  The oral conditions of the patients were measured and recorded at the *initial* stage, at the end of the *second week*, at the end of the *fourth week*, and at the end of the *sixth week*.  The variables age, initial weight and initial cancer stage of the patients were recorded.  Patients were divided into two groups **at random**:  One group received a placebo and the other group received aloe juice treatment.


> Sample size n = 25 patients with neck cancer. 
>
> The treatment is Aloe Juice. 

## Variables 

* `ID` patient identification number

* `trt` treatment group 
    + `0` *placebo* 
    + `1` *aloe juice*

* `age` patient's age, *in years*

* `weightin` patient's weight *(pounds)* at the initial stage

* `stage`	initial cancer stage
    + coded `1` through `4`

* `totalcin` oral condition at the *initial stage*
* `totalcw2` oral condition at the end of *week 2*
* `totalcw4` oral condition at the end of *week 4*
* `totalcw6` oral condition at the end of *week 6*





## Import Data

The `Cancer` dataset is saved in SPSS format, which is evident from the `.sav` ending on the file name.

The `haven` package is downloaded as part of the `tidyverse` set of packages, but is not automatically loaded.  It must have its own `library()` function call *(see above)*.  The `haven::read_spss()` function works very simarly to the `readxl::read_excel()` function we used last chapter [@R-haven].

* Make sure the **dataset** is saved in the same *folder* as this file
* Make sure the that *folder* is the **working directory**

```{r}
cancer_raw <- haven::read_spss("https://github.com/CEHS-research/PSY-6600_students/raw/master/Data/Cancer.sav")
```


```{r}
tibble::glimpse(cancer_raw)
```


## Wrangle Data

```{r}
cancer_clean <- cancer_raw %>% 
  dplyr::rename_all(tolower) %>% 
  dplyr::mutate(id = factor(id)) %>% 
  dplyr::mutate(trt = factor(trt,
                             labels = c("Placebo", 
                                        "Aloe Juice"))) %>% 
  dplyr::mutate(stage = factor(stage))
```


## Overview


### Dimentions (size) of the dataset


```{r}
dim(cancer_clean)
```

### Variable Names

```{r}
names(cancer_clean)
```

### Quick Glimpse

```{r}
tibble::glimpse(cancer_clean)
```


### Top and Bottom Rows

```{r}
psych::headTail(cancer_clean)
```