README.md

In mephas/mephas.tools: Implements for Medical and Pharmaceutical Statistics

mephas

• Web server MEPHAS
• R package mephas, installations
  • Installation from GitHub in RStudio console
  • Installation from ".tar.gz" file
  • Find a statistical methods using the flowchart
  • Commands to open mephas windows

MEPHAS is a shiny-based statistical software that was developed to support statistical data analyses for medical and pharmaceutical students, researchers, and doctors.

Two platforms are available: (1) web server and (2) R package.

Web server MEPHAS

Homepage and source code at GitHub

R package mephas, installations

R package needs to be installed in R console, if you have not installed R, download R firstly:

• R (latest version, >=3.5.0), download here

You can use RStudio console, R console, and even command line interface to open the R environment

• RStudio is an integrated development environment (IDE) for R. Download RStudio here

The followings show how to install in RStudio, which is the same in R console and R in command line interface

Installation from GitHub in RStudio console

Before installing, check the existence of R package "devtools", see details about "devtools"

> packageVersion("devtools")

If R package "devtools" has been installed, then install "mephas" package from GitHub

> devtools::install_github(“mephas/mephas”,upgrade="never")

If error message said "there is no package called ‘devtools'", then install "devtools" package firstly

> install.packages("devtools")
> devtools::install_github(“mephas/mephas”,upgrade="never")

Note: upgrade="never": suppress the updates of the R packages, see details here; package "remotes" and "devtools" shared the same install_github function, thus package "devtools" can be replaced by package "remotes", see details about "remotes"

Videos of the installation process on windows

Installation from ".tar.gz" file

File: mephas_1.1.tar.gz (updated 2020-1)

Check whether you have installed the following packages

> mephas.need.packages <- c("DescTools",
                        "DT",
                        "exactRankTests",
                        "dunn.test",
                        "ROCR",
                        "ggplot2",
                        "magrittr",
                        "psych",
                        "pls",
                        "plotly",
                        "reshape",
                        "shiny",
                        "shinythemes",
                        "shinyWidgets",
                        "survival",
                        "survminer",
                        "survAUC",
                        "spls")
> not.installed.packages <- mephas.need.packages[!(mephas.need.packages %in% installed.packages()[,"Package"])]
> not.installed.packages

If some packages have not been installed, install them first

> if(length(not.installed.packages)) install.packages(not.installed.packages)

Videos of the installation process on windows

Find a statistical methods using the flowchart

Flowchart.pdf

Commands to open mephas windows

Load the package

Before open the applications, please load the package mephas

> library(mephas)

Then, you can open the applications as follows.

All-in-one function

> mephasOpen()

Videos of the opening process on windows

Alternatively, open each interfaces using the method names

1. Probability distributions

Continuous probability distribution, web server

> MFScondist()

Discrete probability distribution, web server

> MFSdisdist()

2. Parametric T test for means, web server

> MFSttest()

3. Non-parametric tests for median, web server

> MFSnptest()

4. Test for binomial proportions, web server

> MFSproptest()

5. Test for contingency tables, web server

> MFSrctabtest()

6. Analysis of variance, web server

> MFSanova()

7. Statistical model,

Linear regression, web server

> MFSlr()

Logistic regression, web server

> MFSlogit()

Survival analysis, web server

> MFSsurv()

8. Dimensional analysis

Dimensional analysis 1, web server

> MFSpca()

Dimensional analysis 2, web server

> MFSpls()

More functions are under construction...

mephas/mephas.tools documentation built on Feb. 20, 2020, 10:11 p.m.