My Favorite Statistic and Mathematic Software

My Favorite Statistic and Mathematic Software

R (R and RStudio Portable) is a free software environment for statistical computing and graphics. This is one of my three musketeers (SAS with callable-SUDAAN, Stata, and R).

• Cheatsheets by RStudio
• Blog: R! related
• Blog: R Documentation and Learning Resources
• STHDA: Statistical tools for high-throughput data analysis. Data Visualization
• CRAN Task View organizes the packages into different groups such as Graphics, Survival Analysis, etc.
• Doug Hemken: Stata and R Markdown (Using Statamarkdown)
• How to run R from Stata and to run Stata from R
• Newson (2007): RSOURCE: Stata module to run R from inside Stata using an R source file
• Solt (2018): How to Switch Your Workflow from Stata to R, One Bit at a Time (RSOURCE)
• Reif (2020): RSCRIPT: call an R script from Stata. (similar to -resource-, but provide R output)
• Haghish (2016): Seamless R and Stata integration (Rcal;: seamless R in Stata) 
• John: Using R with Stata: Part I. Using R with Stata: Part II. How to Call R from Stata
• Yihui Xie: R Markddown Cookbook - Run Stata code
• Braglia: RStata: A Bit of Glue Between R and Stata. Command-line Stata
• Run Stata in R with R Markdown and Statamarkdown. 
• SSCC: Stata and R Markdown

Stata: 

• Cheatsheets by geocenter
• Blogs and Tips of Stata; Stata Documentation; Stata recorded webinars
• Blog: Stata Tips of the Stata Journal
• Blog: Useful and Interesting User-written ado Programs/packages
• StataBlog: Programming an estimation command in Stata: A map to posted entries
• Simons. Useful Stata Commands (pdf)
• Stata Cheat Sheets
• -ereturn display, eform(RR)-

Directed Acyclic Graphs (DAGs) and Structural Equation Models related

• DAGitty (R!) is a browser-based environment for creating, editing, and analyzing causal models. Textor(2016).Robust causal inference using directed acyclic graphs: the R package ‘dagitty’
• ggdag (R!) is bult on top of DAGitty for tidying and plot 'DAGitty' objects using 'ggplot2' and 'ggraph' (introduction to ggdag, common structures of bias, an introduction to DAGs)
• DAG program is a analysis tool, designed to select minimal sufficient adjustment sets within directed acyclic graphs.
• dagR is a R! package for directed acyclic graphics
• Belief and Decision Networks, a JAVA application, is for Bayesian Networks/Belief or Causal Networks.
• mediation: Causal Mediation Analysis. Mediation analysis in R and Stata
• sem is a R! package for fitting general linear structural equation models.
• lavaan is a R! package for latent variable modeling.
• semPlot is a R! package for unified visualizations of SEM models

Engauge Digitizer converts an image file showing a graph or map, into numbers.
Tabula helps you liberate data tables trapped inside PDF files.
Joinpoint is statistical software by the NCI for the analysis of trends using joinpoint models.

Meta Analysis 

• Abstrackr etc (Brown University)
• Machine learning functionality in EPPI-Reviewer

Microsoft Excel

• Daniel's XL Toolbox is a free, open-source add-in for Excel® that helps you to analyze and present data; it produces graphic files meeting the requirements of the majority of journals. Highly recommend it.
• Peltier: provides Excel examples for Making charts in Microsoft Excel
• Chart Chooser — the favorite tool for improved Excel and PowerPoint charts. there is R! version of Chart Chooser (not many charts on the site, but the idea is great)
• How to make a Scatter Plot with two groups (YouTube)
• Microsoft: How to transpose (rotate) data, transpose function

PQRS is a tool for calculating probabilities and quantiles associated with a large number of probability distributions.
SageMath is a free open-source mathematics software system licensed under the GPL.

Calculator:

• Blog: Doing Basic Calculus Using R! and online calculators
• Microsoft Mathematics
• RedCrab is a intuitive paper-kind scientific calculator with a full screen formula editor.
• Clinical Analyte Unit Conversion
• SpeedCrunch is a powerful desktop calculator.
• SpeQ is a small, extensive mathematics program.
• SMath Studio
• Eigenmath
• GeoGebra is free mathematics software for learning and teaching. You can run it online as well.

Converber is a unit converter. It is a powerful software utility that will help make easy conversions between 924 various units of measure in 31 categories. Converber converts everything from length and force to flow and temperature. Here is the PortableApps version.

OpenBUGS BUGS (Bayesian inference Using Gibbs Sampling) is for the Bayesian analysis of complex statistical models using Markov chain Monte Carlo (MCMC) methods, and is probably best known in its WinBugs incarnations.

PAST is a small, free, and easy-to-use data analysis package originally aimed at paleontology. It includes common statistical, plotting and modelling functions. It needs only one small program, amazing.

Epi Info -- You can use it to develop a questionnaire or form, customize the data entry process, and enter and analyze data, and to produces epidemiologic statistics, tables, graphs, and maps are produced with simple commands. I used this a lot before; it seems fading.

D3.js is a JavaScript library for manipulating documents bzsed on data. D3 helps you bring data to life using HTML, SVG and CSS.

Datawrapper is an open scource tool helping anyone to ceate simple, correct and embeddable charts in minutes.

Venn Diagram: eulerAPE (PLOS ONE), VennMaster, Venn Diagram Plotter

PS is an interactive program for performing power and sample size calculations.
Mondrian is a general purpose statistical data-visualization system.
Scilab -- a scientific software package for numerical computations in a user-friendly environment. This is a sophisticated programming language with a MatLab-like syntax.

MathCast is an equation editor, an application that allows you to input mathematical equations. These equations can be used in documents, emails, and webpages.

PSPP is a program for statistical analysis of sampled data. It is a free replacement for the proprietary program SPSS. PSPP has both text-based and graphical user interfaces. It sounds good but I have not used it yet.
SaTScan is a free software that analyzes spatial, temporal and space-time data using the spatial, temporal, or space-time scan statistics.
Zelig is a general purpose statistics program fro estimating, interpreting, and presenting results from any statistical method


You can find more free statistical software here.

Jokes

Bayesian

A Bayesian is one who, vaguely expecting a horse, and catching a glimpse of a donkey, strongly believes he has seen a mule.
from http://www.ilstu.edu/~gcramsey/Pearson.html

Five statisticians and five epidemiologists

There is a group of five statisticians on a train. At the next stop, five epidemiologists get on. They all seem to know each other and start chatting. It transpires that all the epidemiologists have bought a ticket, but the statisticians have only bought one between the five of them. "Why did you do that?" asks one of the epidemiologists. "Surely you're going to get caught and thrown off the train?" "Just wait and see!", smiles one of the statisticians.
As the ticket inspector is approaching to check everyone's tickets, the statisticians all go off to the nearest toilet - the inspector passes the epidemiologists and inspects all their tickets then moves on and notices that the toilet is locked. "Tickets please!", shouts the inspector. One of the statisticians pushes their ticket under the toilet door, which the inspector checks and returns under the door. Once the inspector has gone, all the statisticians return to their seats to the awe and amazement of the epidemiologists. "That's incredibly clever!" says one of the epidemiologists.
A few weeks later they all find themselves on the same train again. They sit together and start chatting once more. "We've done what you suggested", says one of the epidemiologists. "And just bought one ticket between the five of us!" "Oh really", says one of the statisticians. "we haven't bought ANY tickets this time!" The epidemiologists look at each other in amazement. "OK, one ticket between you is fine but not buying any at all is ludicrous!"
As the ticket inspector approaches the epidemiologists hurry off to the toilet. Once they're inside, the statisticians follow them. "Tickets please!" shouts one of the statisticians. The ticket appears under the door and they take it away and all bundle into a different toilet. The inspector gets to the toilet with the epidemiologists in it. "Tickets please!" he shouts. No reply. "Tickets please!" The epidemiologists admit defeat and come out of the toilet only to be thrown off the train at the next station.
THE MORAL OF THIS STORY: Epidemiologists should not attempt to use statistical methods without fully understanding the theory behind them!
*Kudos to Dave Ewart from the Imperial Cancer Research Fund, Oxford UK for this clever story.
from http://www.ilstu.edu/~gcramsey/Pearson.html

What is epidemiology?

ep·i·de·mi·ol·o·gy

Pronunciation: ĕp'ĭ-dē'mē-ŏl'ə-jē, -dĕm'ē-

Function: noun

Etymology: Late Latin epidemia + International Scientific Vocabulary -logy

1. The Greek physician Hippocrates (~400 BC) was the first physician systmatically examined the relation of envirnomental factors and risk of a disease; he coined two terms ‘endemic’ and ‘epidemic’.
2. a branch of medical science that deals with the incidence, distribution, and control of disease in a population.
3. the sum of the factors controlling the presence or absence of a disease or pathogen.
4. Hirsch (1883): science of the distribution of diseases of mankind.
5. Frost (1927): the science of the mass-phenomena of infectious disease, or as the natural history of infectious disease; - conscerned not merely with describing the distribution of disease, but equally or more fitting into a consistent philosophy.
6. Greenwood (1934): the study of disease as a mass phenomenon.
7. Frost (1936): epidemiology at any given time is something more than the total of its established factors. It includes their orderly arrangement into chains of inference which extend more or less beyond the bounds of direct observation.
8. Maxcy (1951): ...relationships of the various factors and conditions which determine the frequencies and distribution of an infectious process, a disease or a physiologic state in a human community.
9. Leavell & Clark (1958): factors influencing distribution of health, disease, disorder, death.
10. MacMahon B (1960): the study of the distribution and determinants of disease prevalence in man.
11. Lilienfeld AM (1985): the study of the distribution of a disease or condition in a population and of those factors which influence their distribution.

Epidemiology from Wikipedia, the free encyclopedia: http://en.wikipedia.org/wiki/Epidemiology