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GitHub Repo
https://github.com/AdekoyaOlatolokikiAyomide/How-to-share-data-
AdekoyaOlatolokikiAyomide/How-to-share-data-
How to share data with a statistician This is a guide for anyone who needs to share data with a statistician or data scientist. The target audiences I have in mind are: Collaborators who need statisticians or data scientists to analyze data for them Students or postdocs in various disciplines looking for consulting advice Junior statistics students whose job it is to collate/clean/wrangle data sets The goals of this guide are to provide some instruction on the best way to share data to avoid the most common pitfalls and sources of delay in the transition from data collection to data analysis. The Leek group works with a large number of collaborators and the number one source of variation in the speed to results is the status of the data when they arrive at the Leek group. Based on my conversations with other statisticians this is true nearly universally. My strong feeling is that statisticians should be able to handle the data in whatever state they arrive. It is important to see the raw data, understand the steps in the processing pipeline, and be able to incorporate hidden sources of variability in one's data analysis. On the other hand, for many data types, the processing steps are well documented and standardized. So the work of converting the data from raw form to directly analyzable form can be performed before calling on a statistician. This can dramatically speed the turnaround time, since the statistician doesn't have to work through all the pre-processing steps first. What you should deliver to the statistician To facilitate the most efficient and timely analysis this is the information you should pass to a statistician: The raw data. A tidy data set A code book describing each variable and its values in the tidy data set. An explicit and exact recipe you used to go from 1 -> 2,3 Let's look at each part of the data package you will transfer. The raw data It is critical that you include the rawest form of the data that you have access to. This ensures that data provenance can be maintained throughout the workflow. Here are some examples of the raw form of data: The strange binary file your measurement machine spits out The unformatted Excel file with 10 worksheets the company you contracted with sent you The complicated JSON data you got from scraping the Twitter API The hand-entered numbers you collected looking through a microscope You know the raw data are in the right format if you: Ran no software on the data Did not modify any of the data values You did not remove any data from the data set You did not summarize the data in any way If you made any modifications of the raw data it is not the raw form of the data. Reporting modified data as raw data is a very common way to slow down the analysis process, since the analyst will often have to do a forensic study of your data to figure out why the raw data looks weird. (Also imagine what would happen if new data arrived?) The tidy data set The general principles of tidy data are laid out by Hadley Wickham in this paper and this video. While both the paper and the video describe tidy data using R, the principles are more generally applicable: Each variable you measure should be in one column Each different observation of that variable should be in a different row There should be one table for each "kind" of variable If you have multiple tables, they should include a column in the table that allows them to be joined or merged While these are the hard and fast rules, there are a number of other things that will make your data set much easier to handle. First is to include a row at the top of each data table/spreadsheet that contains full row names. So if you measured age at diagnosis for patients, you would head that column with the name AgeAtDiagnosis instead of something like ADx or another abbreviation that may be hard for another person to understand. Here is an example of how this would work from genomics. Suppose that for 20 people you have collected gene expression measurements with RNA-sequencing. You have also collected demographic and clinical information about the patients including their age, treatment, and diagnosis. You would have one table/spreadsheet that contains the clinical/demographic information. It would have four columns (patient id, age, treatment, diagnosis) and 21 rows (a row with variable names, then one row for every patient). You would also have one spreadsheet for the summarized genomic data. Usually this type of data is summarized at the level of the number of counts per exon. Suppose you have 100,000 exons, then you would have a table/spreadsheet that had 21 rows (a row for gene names, and one row for each patient) and 100,001 columns (one row for patient ids and one row for each data type). If you are sharing your data with the collaborator in Excel, the tidy data should be in one Excel file per table. They should not have multiple worksheets, no macros should be applied to the data, and no columns/cells should be highlighted. Alternatively share the data in a CSV or TAB-delimited text file. (Beware however that reading CSV files into Excel can sometimes lead to non-reproducible handling of date and time variables.) The code book For almost any data set, the measurements you calculate will need to be described in more detail than you can or should sneak into the spreadsheet. The code book contains this information. At minimum it should contain: Information about the variables (including units!) in the data set not contained in the tidy data Information about the summary choices you made Information about the experimental study design you used In our genomics example, the analyst would want to know what the unit of measurement for each clinical/demographic variable is (age in years, treatment by name/dose, level of diagnosis and how heterogeneous). They would also want to know how you picked the exons you used for summarizing the genomic data (UCSC/Ensembl, etc.). They would also want to know any other information about how you did the data collection/study design. For example, are these the first 20 patients that walked into the clinic? Are they 20 highly selected patients by some characteristic like age? Are they randomized to treatments? A common format for this document is a Word file. There should be a section called "Study design" that has a thorough description of how you collected the data. There is a section called "Code book" that describes each variable and its units. How to code variables When you put variables into a spreadsheet there are several main categories you will run into depending on their data type: Continuous Ordinal Categorical Missing Censored Continuous variables are anything measured on a quantitative scale that could be any fractional number. An example would be something like weight measured in kg. Ordinal data are data that have a fixed, small (< 100) number of levels but are ordered. This could be for example survey responses where the choices are: poor, fair, good. Categorical data are data where there are multiple categories, but they aren't ordered. One example would be sex: male or female. This coding is attractive because it is self-documenting. Missing data are data that are unobserved and you don't know the mechanism. You should code missing values as NA. Censored data are data where you know the missingness mechanism on some level. Common examples are a measurement being below a detection limit or a patient being lost to follow-up. They should also be coded as NA when you don't have the data. But you should also add a new column to your tidy data called, "VariableNameCensored" which should have values of TRUE if censored and FALSE if not. In the code book you should explain why those values are missing. It is absolutely critical to report to the analyst if there is a reason you know about that some of the data are missing. You should also not impute/make up/ throw away missing observations. In general, try to avoid coding categorical or ordinal variables as numbers. When you enter the value for sex in the tidy data, it should be "male" or "female". The ordinal values in the data set should be "poor", "fair", and "good" not 1, 2 ,3. This will avoid potential mixups about which direction effects go and will help identify coding errors. Always encode every piece of information about your observations using text. For example, if you are storing data in Excel and use a form of colored text or cell background formatting to indicate information about an observation ("red variable entries were observed in experiment 1.") then this information will not be exported (and will be lost!) when the data is exported as raw text. Every piece of data should be encoded as actual text that can be exported. The instruction list/script You may have heard this before, but reproducibility is a big deal in computational science. That means, when you submit your paper, the reviewers and the rest of the world should be able to exactly replicate the analyses from raw data all the way to final results. If you are trying to be efficient, you will likely perform some summarization/data analysis steps before the data can be considered tidy. The ideal thing for you to do when performing summarization is to create a computer script (in R, Python, or something else) that takes the raw data as input and produces the tidy data you are sharing as output. You can try running your script a couple of times and see if the code produces the same output. In many cases, the person who collected the data has incentive to make it tidy for a statistician to speed the process of collaboration. They may not know how to code in a scripting language. In that case, what you should provide the statistician is something called pseudocode. It should look something like: Step 1 - take the raw file, run version 3.1.2 of summarize software with parameters a=1, b=2, c=3 Step 2 - run the software separately for each sample Step 3 - take column three of outputfile.out for each sample and that is the corresponding row in the output data set You should also include information about which system (Mac/Windows/Linux) you used the software on and whether you tried it more than once to confirm it gave the same results. Ideally, you will run this by a fellow student/labmate to confirm that they can obtain the same output file you did. What you should expect from the analyst When you turn over a properly tidied data set it dramatically decreases the workload on the statistician. So hopefully they will get back to you much sooner. But most careful statisticians will check your recipe, ask questions about steps you performed, and try to confirm that they can obtain the same tidy data that you did with, at minimum, spot checks. You should then expect from the statistician: An analysis script that performs each of the analyses (not just instructions) The exact computer code they used to run the analysis All output files/figures they generated. This is the information you will use in the supplement to establish reproducibility and precision of your results. Each of the steps in the analysis should be clearly explained and you should ask questions when you don't understand what the analyst did. It is the responsibility of both the statistician and the scientist to understand the statistical analysis. You may not be able to perform the exact analyses without the statistician's code, but you should be able to explain why the statistician performed each step to a labmate/your principal investigator. Contributors Jeff Leek - Wrote the initial version. L. Collado-Torres - Fixed typos, added links. Nick Reich - Added tips on storing data as text. Nick Horton - Minor wording suggestions.
GitHub Repo
https://github.com/ManojKumarPatnaik/Major-project-list
ManojKumarPatnaik/Major-project-list
A list of practical projects that anyone can solve in any programming language (See solutions). These projects are divided into multiple categories, and each category has its own folder. To get started, simply fork this repo. CONTRIBUTING See ways of contributing to this repo. You can contribute solutions (will be published in this repo) to existing problems, add new projects, or remove existing ones. Make sure you follow all instructions properly. Solutions You can find implementations of these projects in many other languages by other users in this repo. Credits Problems are motivated by the ones shared at: Martyr2’s Mega Project List Rosetta Code Table of Contents Numbers Classic Algorithms Graph Data Structures Text Networking Classes Threading Web Files Databases Graphics and Multimedia Security Numbers Find PI to the Nth Digit - Enter a number and have the program generate PI up to that many decimal places. Keep a limit to how far the program will go. Find e to the Nth Digit - Just like the previous problem, but with e instead of PI. Enter a number and have the program generate e up to that many decimal places. Keep a limit to how far the program will go. Fibonacci Sequence - Enter a number and have the program generate the Fibonacci sequence to that number or to the Nth number. Prime Factorization - Have the user enter a number and find all Prime Factors (if there are any) and display them. Next Prime Number - Have the program find prime numbers until the user chooses to stop asking for the next one. Find Cost of Tile to Cover W x H Floor - Calculate the total cost of the tile it would take to cover a floor plan of width and height, using a cost entered by the user. Mortgage Calculator - Calculate the monthly payments of a fixed-term mortgage over given Nth terms at a given interest rate. Also, figure out how long it will take the user to pay back the loan. For added complexity, add an option for users to select the compounding interval (Monthly, Weekly, Daily, Continually). Change Return Program - The user enters a cost and then the amount of money given. The program will figure out the change and the number of quarters, dimes, nickels, pennies needed for the change. Binary to Decimal and Back Converter - Develop a converter to convert a decimal number to binary or a binary number to its decimal equivalent. Calculator - A simple calculator to do basic operators. Make it a scientific calculator for added complexity. Unit Converter (temp, currency, volume, mass, and more) - Converts various units between one another. The user enters the type of unit being entered, the type of unit they want to convert to, and then the value. The program will then make the conversion. Alarm Clock - A simple clock where it plays a sound after X number of minutes/seconds or at a particular time. Distance Between Two Cities - Calculates the distance between two cities and allows the user to specify a unit of distance. This program may require finding coordinates for the cities like latitude and longitude. Credit Card Validator - Takes in a credit card number from a common credit card vendor (Visa, MasterCard, American Express, Discoverer) and validates it to make sure that it is a valid number (look into how credit cards use a checksum). Tax Calculator - Asks the user to enter a cost and either a country or state tax. It then returns the tax plus the total cost with tax. Factorial Finder - The Factorial of a positive integer, n, is defined as the product of the sequence n, n-1, n-2, ...1, and the factorial of zero, 0, is defined as being 1. Solve this using both loops and recursion. Complex Number Algebra - Show addition, multiplication, negation, and inversion of complex numbers in separate functions. (Subtraction and division operations can be made with pairs of these operations.) Print the results for each operation tested. Happy Numbers - A happy number is defined by the following process. Starting with any positive integer, replace the number by the sum of the squares of its digits, and repeat the process until the number equals 1 (where it will stay), or it loops endlessly in a cycle which does not include 1. Those numbers for which this process ends in 1 are happy numbers, while those that do not end in 1 are unhappy numbers. Display an example of your output here. Find the first 8 happy numbers. Number Names - Show how to spell out a number in English. You can use a preexisting implementation or roll your own, but you should support inputs up to at least one million (or the maximum value of your language's default bounded integer type if that's less). Optional: Support for inputs other than positive integers (like zero, negative integers, and floating-point numbers). Coin Flip Simulation - Write some code that simulates flipping a single coin however many times the user decides. The code should record the outcomes and count the number of tails and heads. Limit Calculator - Ask the user to enter f(x) and the limit value, then return the value of the limit statement Optional: Make the calculator capable of supporting infinite limits. Fast Exponentiation - Ask the user to enter 2 integers a and b and output a^b (i.e. pow(a,b)) in O(LG n) time complexity. Classic Algorithms Collatz Conjecture - Start with a number n > 1. Find the number of steps it takes to reach one using the following process: If n is even, divide it by 2. If n is odd, multiply it by 3 and add 1. Sorting - Implement two types of sorting algorithms: Merge sort and bubble sort. Closest pair problem - The closest pair of points problem or closest pair problem is a problem of computational geometry: given n points in metric space, find a pair of points with the smallest distance between them. Sieve of Eratosthenes - The sieve of Eratosthenes is one of the most efficient ways to find all of the smaller primes (below 10 million or so). Graph Graph from links - Create a program that will create a graph or network from a series of links. Eulerian Path - Create a program that will take as an input a graph and output either an Eulerian path or an Eulerian cycle, or state that it is not possible. An Eulerian path starts at one node and traverses every edge of a graph through every node and finishes at another node. An Eulerian cycle is an eulerian Path that starts and finishes at the same node. Connected Graph - Create a program that takes a graph as an input and outputs whether every node is connected or not. Dijkstra’s Algorithm - Create a program that finds the shortest path through a graph using its edges. Minimum Spanning Tree - Create a program that takes a connected, undirected graph with weights and outputs the minimum spanning tree of the graph i.e., a subgraph that is a tree, contains all the vertices, and the sum of its weights is the least possible. Data Structures Inverted index - An Inverted Index is a data structure used to create full-text search. Given a set of text files, implement a program to create an inverted index. Also, create a user interface to do a search using that inverted index which returns a list of files that contain the query term/terms. The search index can be in memory. Text Fizz Buzz - Write a program that prints the numbers from 1 to 100. But for multiples of three print “Fizz” instead of the number and for the multiples of five print “Buzz”. For numbers which are multiples of both three and five print “FizzBuzz”. Reverse a String - Enter a string and the program will reverse it and print it out. Pig Latin - Pig Latin is a game of alterations played in the English language game. To create the Pig Latin form of an English word the initial consonant sound is transposed to the end of the word and an ay is affixed (Ex.: "banana" would yield anana-bay). Read Wikipedia for more information on rules. Count Vowels - Enter a string and the program counts the number of vowels in the text. For added complexity have it report a sum of each vowel found. Check if Palindrome - Checks if the string entered by the user is a palindrome. That is that it reads the same forwards as backward like “racecar” Count Words in a String - Counts the number of individual words in a string. For added complexity read these strings in from a text file and generate a summary. Text Editor - Notepad-style application that can open, edit, and save text documents. Optional: Add syntax highlighting and other features. RSS Feed Creator - Given a link to RSS/Atom Feed, get all posts and display them. Quote Tracker (market symbols etc) - A program that can go out and check the current value of stocks for a list of symbols entered by the user. The user can set how often the stocks are checked. For CLI, show whether the stock has moved up or down. Optional: If GUI, the program can show green up and red down arrows to show which direction the stock value has moved. Guestbook / Journal - A simple application that allows people to add comments or write journal entries. It can allow comments or not and timestamps for all entries. Could also be made into a shoutbox. Optional: Deploy it on Google App Engine or Heroku or any other PaaS (if possible, of course). Vigenere / Vernam / Ceasar Ciphers - Functions for encrypting and decrypting data messages. Then send them to a friend. Regex Query Tool - A tool that allows the user to enter a text string and then in a separate control enter a regex pattern. It will run the regular expression against the source text and return any matches or flag errors in the regular expression. Networking FTP Program - A file transfer program that can transfer files back and forth from a remote web sever. Bandwidth Monitor - A small utility program that tracks how much data you have uploaded and downloaded from the net during the course of your current online session. See if you can find out what periods of the day you use more and less and generate a report or graph that shows it. Port Scanner - Enter an IP address and a port range where the program will then attempt to find open ports on the given computer by connecting to each of them. On any successful connections mark the port as open. Mail Checker (POP3 / IMAP) - The user enters various account information include web server and IP, protocol type (POP3 or IMAP), and the application will check for email at a given interval. Country from IP Lookup - Enter an IP address and find the country that IP is registered in. Optional: Find the Ip automatically. Whois Search Tool - Enter an IP or host address and have it look it up through whois and return the results to you. Site Checker with Time Scheduling - An application that attempts to connect to a website or server every so many minute or a given time and check if it is up. If it is down, it will notify you by email or by posting a notice on the screen. Classes Product Inventory Project - Create an application that manages an inventory of products. Create a product class that has a price, id, and quantity on hand. Then create an inventory class that keeps track of various products and can sum up the inventory value. Airline / Hotel Reservation System - Create a reservation system that books airline seats or hotel rooms. It charges various rates for particular sections of the plane or hotel. For example, first class is going to cost more than a coach. Hotel rooms have penthouse suites which cost more. Keep track of when rooms will be available and can be scheduled. Company Manager - Create a hierarchy of classes - abstract class Employee and subclasses HourlyEmployee, SalariedEmployee, Manager, and Executive. Everyone's pay is calculated differently, research a bit about it. After you've established an employee hierarchy, create a Company class that allows you to manage the employees. You should be able to hire, fire, and raise employees. Bank Account Manager - Create a class called Account which will be an abstract class for three other classes called CheckingAccount, SavingsAccount, and BusinessAccount. Manage credits and debits from these accounts through an ATM-style program. Patient / Doctor Scheduler - Create a patient class and a doctor class. Have a doctor that can handle multiple patients and set up a scheduling program where a doctor can only handle 16 patients during an 8 hr workday. Recipe Creator and Manager - Create a recipe class with ingredients and put them in a recipe manager program that organizes them into categories like desserts, main courses, or by ingredients like chicken, beef, soups, pies, etc. Image Gallery - Create an image abstract class and then a class that inherits from it for each image type. Put them in a program that displays them in a gallery-style format for viewing. Shape Area and Perimeter Classes - Create an abstract class called Shape and then inherit from it other shapes like diamond, rectangle, circle, triangle, etc. Then have each class override the area and perimeter functionality to handle each shape type. Flower Shop Ordering To Go - Create a flower shop application that deals in flower objects and use those flower objects in a bouquet object which can then be sold. Keep track of the number of objects and when you may need to order more. Family Tree Creator - Create a class called Person which will have a name, when they were born, and when (and if) they died. Allow the user to create these Person classes and put them into a family tree structure. Print out the tree to the screen. Threading Create A Progress Bar for Downloads - Create a progress bar for applications that can keep track of a download in progress. The progress bar will be on a separate thread and will communicate with the main thread using delegates. Bulk Thumbnail Creator - Picture processing can take a bit of time for some transformations. Especially if the image is large. Create an image program that can take hundreds of images and converts them to a specified size in the background thread while you do other things. For added complexity, have one thread handling re-sizing, have another bulk renaming of thumbnails, etc. Web Page Scraper - Create an application that connects to a site and pulls out all links, or images, and saves them to a list. Optional: Organize the indexed content and don’t allow duplicates. Have it put the results into an easily searchable index file. Online White Board - Create an application that allows you to draw pictures, write notes and use various colors to flesh out ideas for projects. Optional: Add a feature to invite friends to collaborate on a whiteboard online. Get Atomic Time from Internet Clock - This program will get the true atomic time from an atomic time clock on the Internet. Use any one of the atomic clocks returned by a simple Google search. Fetch Current Weather - Get the current weather for a given zip/postal code. Optional: Try locating the user automatically. Scheduled Auto Login and Action - Make an application that logs into a given site on a schedule and invokes a certain action and then logs out. This can be useful for checking webmail, posting regular content, or getting info for other applications and saving it to your computer. E-Card Generator - Make a site that allows people to generate their own little e-cards and send them to other people. Do not use Flash. Use a picture library and perhaps insightful mottos or quotes. Content Management System - Create a content management system (CMS) like Joomla, Drupal, PHP Nuke, etc. Start small. Optional: Allow for the addition of modules/addons. Web Board (Forum) - Create a forum for you and your buddies to post, administer and share thoughts and ideas. CAPTCHA Maker - Ever see those images with letters numbers when you signup for a service and then ask you to enter what you see? It keeps web bots from automatically signing up and spamming. Try creating one yourself for online forms. Files Quiz Maker - Make an application that takes various questions from a file, picked randomly, and puts together a quiz for students. Each quiz can be different and then reads a key to grade the quizzes. Sort Excel/CSV File Utility - Reads a file of records, sorts them, and then writes them back to the file. Allow the user to choose various sort style and sorting based on a particular field. Create Zip File Maker - The user enters various files from different directories and the program zips them up into a zip file. Optional: Apply actual compression to the files. Start with Huffman Algorithm. PDF Generator - An application that can read in a text file, HTML file, or some other file and generates a PDF file out of it. Great for a web-based service where the user uploads the file and the program returns a PDF of the file. Optional: Deploy on GAE or Heroku if possible. Mp3 Tagger - Modify and add ID3v1 tags to MP3 files. See if you can also add in the album art into the MP3 file’s header as well as other ID3v2 tags. Code Snippet Manager - Another utility program that allows coders to put in functions, classes, or other tidbits to save for use later. Organized by the type of snippet or language the coder can quickly lookup code. Optional: For extra practice try adding syntax highlighting based on the language. Databases SQL Query Analyzer - A utility application in which a user can enter a query and have it run against a local database and look for ways to make it more efficient. Remote SQL Tool - A utility that can execute queries on remote servers from your local computer across the Internet. It should take in a remote host, user name, and password, run the query and return the results. Report Generator - Create a utility that generates a report based on some tables in a database. Generates sales reports based on the order/order details tables or sums up the day's current database activity. Event Scheduler and Calendar - Make an application that allows the user to enter a date and time of an event, event notes, and then schedule those events on a calendar. The user can then browse the calendar or search the calendar for specific events. Optional: Allow the application to create re-occurrence events that reoccur every day, week, month, year, etc. Budget Tracker - Write an application that keeps track of a household’s budget. The user can add expenses, income, and recurring costs to find out how much they are saving or losing over a period of time. Optional: Allow the user to specify a date range and see the net flow of money in and out of the house budget for that time period. TV Show Tracker - Got a favorite show you don’t want to miss? Don’t have a PVR or want to be able to find the show to then PVR it later? Make an application that can search various online TV Guide sites, locate the shows/times/channels and add them to a database application. The database/website then can send you email reminders that a show is about to start and which channel it will be on. Travel Planner System - Make a system that allows users to put together their own little travel itinerary and keep track of the airline/hotel arrangements, points of interest, budget, and schedule. Graphics and Multimedia Slide Show - Make an application that shows various pictures in a slide show format. Optional: Try adding various effects like fade in/out, star wipe, and window blinds transitions. Stream Video from Online - Try to create your own online streaming video player. Mp3 Player - A simple program for playing your favorite music files. Add features you think are missing from your favorite music player. Watermarking Application - Have some pictures you want copyright protected? Add your own logo or text lightly across the background so that no one can simply steal your graphics off your site. Make a program that will add this watermark to the picture. Optional: Use threading to process multiple images simultaneously. Turtle Graphics - This is a common project where you create a floor of 20 x 20 squares. Using various commands you tell a turtle to draw a line on the floor. You have moved forward, left or right, lift or drop the pen, etc. Do a search online for "Turtle Graphics" for more information. Optional: Allow the program to read in the list of commands from a file. GIF Creator A program that puts together multiple images (PNGs, JPGs, TIFFs) to make a smooth GIF that can be exported. Optional: Make the program convert small video files to GIFs as well. Security Caesar cipher - Implement a Caesar cipher, both encoding, and decoding. The key is an integer from 1 to 25. This cipher rotates the letters of the alphabet (A to Z). The encoding replaces each letter with the 1st to 25th next letter in the alphabet (wrapping Z to A). So key 2 encrypts "HI" to "JK", but key 20 encrypts "HI" to "BC". This simple "monoalphabetic substitution cipher" provides almost no security, because an attacker who has the encoded message can either use frequency analysis to guess the key, or just try all 25 keys.
GitHub Repo
https://github.com/Tanitakidane/MyProfile-Assignment
Tanitakidane/MyProfile-Assignment
I am an executive pastry chef who worked at the Ritz in the Pennsylvania convention Center I've done everything from private dining to corporate functions feeling 10,000 people. As my industry became more incorporated into IT I decided that I wanted to work with food scientist and incorporate my background into this new endeavor. I'm really excited about this web development program I'believe thinking it' will give me the necessary background to work in securities protecting secret corporate recipe at mega corporations such as Unilever
GitHub Repo
https://github.com/AdekoyaOlatolokikiAyomide/CouseraDatasharing