**Setup 

cd "/Users/kristenaiemjoy/Box Sync/_Teaching/Biostat 212/Biostat212.2018/Assignments/Assignment 2" //modify filepath to your directory


capture log close //close any open log files


quietly log using biostat212_assignment2_name.smcl, replace //using "quietly" will stop print out in your smcl file making a nicer looking .pdf when you use markdown



/***
#Biostat 212: 2018
#Assignment 2: Data cleaning
## Your Name

---

#Instructions   
In this assignment we will be cleaning a subset of the NHANES data set "nhanes_raw.csv"
We will import the data from a .csv file and export a clean data set. 

* Download "nhanes_raw.csv" and "nhanes_vegan.dta" from the course website and save in your working directory
* Fill in the answer and include the command in the space below the question 
* Turn in the PDF, docX or html you generate from this .do file using MarkDoc
* Round numeric answers to 2 decimal points   




###43 points total


---
***/


/***
###1. Import the "nhanes_raw.csv" file from the course website
***/



/***
###2. How many observations are there?  
__Answer=XX__
***/


/***
###3. How many variables are there?   
__Answer=XX__
***/


/***
#DUPLICATES

###4. List and drop duplicate observations
***/




/***
#REFORMAT VARIABLES

###5. What format is age? (string(character), numerical, categorical)    
__Answer=XX__  
hint: try the describe command
***/


/***
###6. Replace the value of age that is currently "sixty one" with 61.
hint: try [replace varname = "value", if varname == "value"] (you will need to use the person's id)
***/


/***
###7. Transform age into a numeric variable. 
hint: "help destring"
***/


/***
###8. What is the mean age?
__Answer=XX__
***/



/***
#REMOVE OUTLIERS

###9. Use the spikeplot command to visualize outliers for age
remember to use "img" after the command to include the plot in your markdoc 
***/


/***
###10. What is the highest age in this dataset?
__Answer=XX__
***/



/***
###11. Replace any values of age greater than 100 as missing ("."). 
***/


/***
###12. Now what is the mean age?
__Answer=XX__
***/



/***
#MISSING DATA

###13. Use the mvdecode command to change -99 values to missing
age, height and weight all have "-99" values
***/



/***
###14. Now what is the mean age?
__Answer=XX__
***/



/***
#LABELS

###15. Create value labels for the variable sex. 0=female 1=male
***/



/***
###16. How many males in this sample?
__Answer=XX__
***/



/***
#GENERATING NEW VARIABLES

###17. Generate a categorical variable for race
hint: "help encode"
***/



/***
####18. What percentage of the population is "other"?
__Answer=XX__
***/



/*** 
###19. Create variable for bmi, from weight and height
hint: bmi = weight/((height/100)^2)
***/



/***
###20. What is the mean bmi?
__Answer=XX__
***/


/*** 
###21. Create a categorical variable for hypertension from systolic blood pressure (sbp)
(0/119=no hypertension & 120/max=1)
hint: "help recode"
***/



/***
###22. How many people have hypertension?
__Answer=XX__
***/




/***
###23. Create a new variable that is quintiles of hdl. 
hint: "help xtile"
***/



/***
###24. How many people are in the second quintile?
__Answer=XX__
***/


/***
#DATES
###25. Reformat "dob" as a date format
***/




/***
#MERGE

You sent out a nutritional survey to study participants and want to merge it with this data set.   

###26. Merge this data set with "nhanes_vegan.dta" on the course website
hint: merge 1:1 idvariable using "dataset name", update replace
***/



/***
###27. What percent of study participants are vegan?
__Answer=XX__
***/


/***
###28. What is the mean BMI among participants who are vegan and those who are not vegan?
__Answer=XX__
***/




/*** 
#SAVE CLEAN DATA
###29. Save the clean data set as nhanes_clean.dta
***/








qui log close //close log (quietly so it wont appear in markdown document


*Generate MarkDoc
markdoc biostat212_assignment2_name, replace statax  export(html)  
markdoc biostat212_assignment2_name, replace statax  export(docx)