Creating a "Mathis" R library?

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Creating a "Mathis" R library?

Post by Cr6 on Sun Nov 29, 2015 10:01 pm

Just wanted to throw this out there as a possible project down the road. It is technically beyond me at the moment.

This project would entail creating an "R" package for Mathis's calculations.

One package in R that is really interesting is the circular package and how it could be used to set-up a Mathis' style molecular bonding system.

https://cran.r-project.org/web/packages/circular/circular.pdf

Circular Statistics Definitions:
-------
http://www.ncss.com/wp-content/themes/ncss/pdf/Procedures/NCSS/Circular_Data_Analysis.pdf
http://webspace.ship.edu/pgmarr/Geo441/Lectures/Lec%2016%20-%20Directional%20Statistics.pdf
https://en.wikipedia.org/wiki/Directional_statistics

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Re: Creating a "Mathis" R library?

Post by LongtimeAirman on Fri Dec 04, 2015 10:44 pm

Cr6, I looked at the references. Is R a statistical application or a math based library? I don't know enough to give you change for a dollar.

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Re: Creating a "Mathis" R library?

Post by Cr6 on Sun Dec 06, 2015 10:16 pm

LongtimeAirman wrote:Cr6, I looked at the references. Is R a statistical application or a math based library? I don't know enough to give you change for a dollar.

Yes, it is Stats program like SAS/SPSS crossed with a Math program like MatLab. It is freeware and has a mix of stats libraries for running on various databases/mongo/unstructured data/json/etc. The cool thing is that it allows local development that can then be ported to bigger database/big data type systems. A lot of people do machine learning with it.

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Re: Creating a "Mathis" R library?

Post by Cr6 on Tue Dec 08, 2015 2:32 am

Also, R apps can be hosted on web servers like this:

http://opencpu.ocpu.io/stocks/www/

https://www.opencpu.org/demo.html


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Re: Creating a "Mathis" R library?

Post by Cr6 on Thu Dec 10, 2015 1:49 am

This is kind of where it can go. DeepLearning may provide a few tricks to hack Mathis and create "converter" tools to map to typical Chem notation.

http://www.slideshare.net/0xdata/h2-o-deeplearningarnocandel031115?next_slideshow=1

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Re: Creating a "Mathis" R library?

Post by LongtimeAirman on Sat Dec 12, 2015 1:34 pm

Cr6, Deep Learning. We're nowhere near it. Are we?

I can imagine nuclear charge flow in some aggregate form, crystalline streams that somehow maintain coherence, perhaps due to the presence of a wide range of energetic particles, including larger and slower ones like electrons, also recycling charge. Unconsciously, I think of atomic matter as charge field plumbing; I've often used plumbing analogies to describe electrical stuff to people. But that must be wrong. As Nevyn recently pointed out, it involves the power of non-linearity.

In the AC Current paper, Miles said we actually have two-way spun charge flow. Well, since he said it, there are algorithms waiting to be written to do that. That's one example.

Do you believe that we can assemble a library of MM algorithms?
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Re: Creating a "Mathis" R library?

Post by Cr6 on Sat Dec 12, 2015 11:40 pm

LongtimeAirman wrote:Cr6, Deep Learning. We're nowhere near it. Are we?

I can imagine nuclear charge flow in some aggregate form, crystalline streams that somehow maintain coherence, perhaps due to the presence of a wide range of energetic particles, including larger and slower ones like electrons, also recycling charge. Unconsciously, I think of atomic matter as charge field plumbing; I've often used plumbing analogies to describe electrical stuff to people. But that must be wrong. As Nevyn recently pointed out, it involves the power of non-linearity.

In the AC Current paper, Miles said we actually have two-way spun charge flow. Well, since he said it, there are algorithms waiting to be written to do that. That's one example.

Do you believe that we can assemble a library of MM algorithms?
.

That's a great question LTAM and your comment on the charge field is a good one IMHO. I do think that getting even a primitive "conversion" tool for MM that can take current Chem notation and transform it into a queryable-programmable-interactive type model in terms of MM is a good goal. It could get more people on board. In fact I bet a lot of people are curious but since there isn't a clearcut conversion for MM's work to traditional Physics/Chemistry, a lot of people may not take a risk to run with it or investigate it. Building this might also help discover what is complete and what isn't?
MM's algorithms and all the plumbing work to apply them could be useful if it was in a "library" of sorts that could be loaded for doing calcs with MM's numbers. We may need to start Meetups or "sessions" to spread the word to get other people to help do this kind of work....especially younger people.
I keep commenting on using JSON only because it could be flexible enough to allow changes and still allow them to be dropped into frameworks like Nevyn has created. Current database schemas are a bit primitive to represent Mathis' "world" and any revisions. As Mathis fleshes out "bonding" principles between atoms/molecules more and more... these interactions could be programmed in.

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Re: Creating a "Mathis" R library?

Post by Cr6 on Mon Mar 07, 2016 10:30 pm

Came across this. Would be kind of useful to create even a Mathematica Notebook demonstrating Mathis' theory.

---------
A Mathematica Notebook-CDF example:
http://demonstrations.wolfram.com/QuantumAngularMomentumMatrices/

Mathematica for Physics
Authors
Robert L. Zimmerman
Organization: University of Oregon
Department: Institute of Theoretical Science
Fredrick I. Olness
Organization: Southern Methodist University
Department: Department of Physics
http://library.wolfram.com/infocenter/Books/3588/

Description

Designed as a supplement for any of the core advanced undergraduate and graduate physics courses, Mathematica for Physics chooses the canonical problems from the physics curriculum, and solves these problems using Mathematica. This book takes the reader beyond the "textbook" solutions by challenging the student to cross check the results using the wide variety of Mathematica's analytical, numerical, and graphical tools. Throughout the book, the complexity of both the physics and Mathematica is systematically extended to broaden the tools the reader has at his or her disposal, and to broaden the range of problems that can be solved.

http://demonstrations.wolfram.com/QuantumAngularMomentumMatrices/
http://demonstrations.wolfram.com/topic.html?limit=20&topic=Physics

http://www.wolfram.com/cdf-player/

Book Files:
BookInfo.txt (6.8 KB) - General Information about the book
Download
ReadMe.txt (4.3 KB) - File list, installation instructions and general information
Download
ch1init.m (6.1 KB) - Chapter 1 Initialization
Download
ch1s6p16.nb (8.4 KB) - Section 6 Graphics: Examples 1-6
Download
ch2init.m (7.5 KB) - Chapter 2 Initialization
Download
ch2s2p1.nb (10.8 KB) - Coriolis and Centrifugal Forces
Download
ch2s3p2.nb (9.5 KB) - Uniformly Charged Sphere
Download
ch2s5p2.nb (7.2 KB) - Relativistic Collision
Download
ch3init.m (11.5 KB) - Chapter 3 Initialization
Download
ch3s2p4.nb (8.2 KB) - Motion of a Damped, Forced Nonlinear Pendulum
Download
ch3s3p1.nb (10.1 KB) - Two Coupled Harmonic Oscillators
Download
ch3s3p2a.nb (6.1 KB) - Three Coupled Harmonic Oscillators, Animation Only
Download
ch3s3p3a.nb (6.2 KB) - Double Pendulum, Animation Only
Download
ch4init.m (12.4 KB) - Chapter 4 Initialization
Download
ch4s1p3.nb (10.6 KB) - Bead on a Rotating Hoop
Download
ch4s2p4.nb (8.5 KB) - Numerical Solution for Orbits with Central Forces
Download
ch4s3p3.nb (8.9 KB) - Spherical Pendulum and Hamilton's Equations
Download
ch5init.m (11.5 KB) - Chapter 5 Initialization
Download
ch5s1p1.nb (7.8 KB) - Superposition of Point Charges
Download
ch5s2p5.nb (7.7 KB) - Conducting Cylinder with a Potential on the Surface
Download
ch6init.m (12.4 KB) - Chapter 6 Initialization
Download
ch6s1p2.nb (12.7 KB) - Particle bound in a Finite Potential Well
Download
ch6s1p3a.nb (8.3 KB) - Particle Hitting a Finite Step Potential, Animation Only
Download
ch6s1p4a.nb (7.1 KB) - Particle Propagating Towards a Rectangular Potential, Animation Only
Download
ch6s2p5.nb (8.9 KB) - The Hydrogen Atom in Spherical Coordinates
Download
ch7init.m (15.2 KB) - Chapter 7 Initialization
Download
ch7s1p3.nb (7.3 KB) - Compton Scattering
Download
ch7s2p5.nb (10 KB) - Time It Takes to Fall into a BlackHole

Files specific to Mathematica 2.2 version:
Download
ch1s6p16.ma (7.2 KB) - Section 6 Graphics: Examples 1-6
Download
ch2s2p1.ma (9.2 KB) - Coriolis and Centrifugal Forces
Download
ch2s3p2.ma (8.2 KB) - Uniformly Charged Sphere
Download
ch2s5p2.ma (6.6 KB) - Relativistic Collision
Download
ch3s2p4.ma (7.3 KB) - Motion of a Damped, Forced Nonlinear Pendulum
Download
ch3s3p1.ma (8.4 KB) - Two Coupled Harmonic Oscillators
Download
ch3s3p2a.ma (6.3 KB) - Three Coupled Harmonic Oscillators, Animation Only
Download
ch3s3p3a.ma (6.3 KB) - Double Pendulum, Animation Only
Download
ch4s1p3.ma (8.7 KB) - Bead on a Rotating Hoop
Download
ch4s2p4.ma (7.4 KB) - Numerical Solution for Orbits with Central Forces
Download
ch4s3p3.ma (7.8 KB) - Spherical Pendulum and Hamilton's Equations
Download
ch5s1p1.ma (7 KB) - Superposition of Point Charges
Download
ch5s2p5.ma (6.9 KB) - Conducting Cylinder with a Potential on the Surface
Download
ch6s1p2.ma (10.5 KB) - Particle bound in a Finite Potential Well
Download
ch6s1p3a.ma (7.8 KB) - Particle Hitting a Finite Step Potential, Animation Only
Download
ch6s1p4a.ma (7.1 KB) - Particle Propagating Towards a Rectangular Potential, Animation Only
Download
ch6s2p5.ma (7.9 KB) - The Hydrogen Atom in Spherical Coordinates
Download
ch7s1p3.ma (6.6 KB) - Compton Scattering
Download
ch7s2p5.ma (8.5 KB) - Time It Takes to Fall into a BlackHole

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Re: Creating a "Mathis" R library?

Post by Cr6 on Tue Mar 08, 2016 10:45 pm

Also came across this recent R "threejs" library. Could be a useful platform for building a Mathis style R object library.  It is static looking but is an interactive dynamic rendering of data points. Click the graphs to pivot them.  

https://bwlewis.github.io/1000_genomes_examples/PCA.html

https://bwlewis.github.io/rthreejs/doughnut/index.html

This could be data-driven from a Mathis style R data library:

https://bwlewis.github.io/rthreejs/pointcloud/index.html

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Re: Creating a "Mathis" R library?

Post by Cr6 on Sun Jul 03, 2016 3:49 pm

Don't mean to keep harping on this without anything to show for it yet. Looked at this "How to Build an R package" on Cran. 

If the data files contain Mathis' defaults and calcs from his various papers, it could be released and get attention from a pretty wide audience of people?

 It could also be useful in walking people through papers if the Mathis R package is used to help illustrate the detailed maths involved. Most of this would be a library of his functions.

https://cran.r-project.org/doc/contrib/Leisch-CreatingPackages.pdf
http://cran.r-project.org/doc/manuals/R-exts.pdf
http://www1.appstate.edu/~arnholta/Software/MakingPackagesUnderWindows.pdf

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Re: Creating a "Mathis" R library?

Post by Cr6 on Mon Aug 08, 2016 12:04 am

https://r-forge.r-project.org/

A place to submit and build an R program.

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Re: Creating a "Mathis" R library?

Post by LongtimeAirman on Mon Aug 08, 2016 1:26 pm

Cr6, To be perfectly clear, I'm drawing a blank. I am the least qualified among us to judge the relative merits of various applications packages designed for information presentation within contemporary Library Science.

I don't understand what you're asking for.

How may I help you? Tell me what to do.
.

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Getting started with R

Post by Cr6 on Mon Aug 08, 2016 8:16 pm

Sorry LTAM...

Here's the step by step (for Windows):

1. Download RBase:
https://cran.r-project.org/bin/windows/base/

2. Download RStudio:
https://download1.rstudio.org/RStudio-0.99.903.exe

3. Open RStudio and click Help > Update
select a CRAN location and get the latest updates (R often requires package updating to get the latest features).

4. start with a simple intro site for simple math and assigning variables
https://cran.r-project.org/doc/contrib/Lemon-kickstart/index.html
http://tryr.codeschool.com/
http://trevorstephens.com/kaggle-titanic-tutorial/getting-started-with-r/
https://www.kaggle.com/c/titanic/details/new-getting-started-with-r
https://www.r-project.org/doc/bib/R-books.html


5. Install additional libraries as needed.
Fire up R and create an .r file.
Paste something like this in the window and run. (# is a comment).

 # Now we download, install and initialize the H2O package for R.
 install.packages("h2o", type="source", repos=(c("http://h2o-release.s3.amazonaws.com/h2o/rel-simons/4/R")))
 install.packages("deepnet")
 install.packages("rvest")
 install.packages("XML")
 install.packages("data.table")
 install.packages("clusterGeneration")

6. Work towards these scripts:
http://www.gcdataconcepts.com/coaster_script.html
http://www.gcdataconcepts.com/coaster_analysis.r
http://trevorstephens.com/competitions/armchair-particle-physicist/
https://github.com/tqchen/xgboost/tree/master/demo/kaggle-higgs
https://github.com/hetong007/higgsml
https://github.com/wehrley/wehrley.github.io/blob/master/SOUPTONUTS.md

7. Work towards building Mathis library with the Excel and Javascript files dumped to data files that can be loaded into R. Attempt to build functions that match Mathis' papers using his transforms-corrections, etc.
https://support.rstudio.com/hc/en-us/articles/200486488-Developing-Packages-with-RStudio
http://www.stt.msu.edu/~cui/Groupmeeting/R_package_tutorial.pdf


Last edited by Cr6 on Tue Aug 09, 2016 11:14 pm; edited 1 time in total

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Re: Creating a "Mathis" R library?

Post by LongtimeAirman on Mon Aug 08, 2016 9:44 pm

.
OK, I've got the RGui.



rsesssion.exe is giving me system errors because rgraphapp.dll and r.dll are missing.

It's mostly foreign looking, I'll read up on it.

I just may send personal correspondence for those embarassing moments.


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Re: Creating a "Mathis" R library?

Post by Nevyn on Tue Aug 09, 2016 1:13 am

We need a little test project to get a feel for what R can do for us. I don't know much about R but it seems to be a math visualisation package so we just need some math we want to visualise. You could take the math we discussed in the How to determine gravity thread, implement it in R and figure out how to show it.

Another potential project is to take Miles' angular velocity equation and plugin a doubling radius to show the angular velocity changes as new spin levels are added to a BPhoton. Then analyze the data from that to show the relationship between spin levels (take the ratio of each spin level to the level on top of it). That is how I found the spin level relationships that SpinSim is now based on.

Something I have been thinking about for a few years is to visualise the energy of photons as spins are added. Relate it back to the standard EM energy chart. It would be good to have a quick chart to see how stacked spins relate to photon frequency and wavelength, etc.
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Re: Creating a "Mathis" R library?

Post by Cr6 on Tue Aug 09, 2016 11:35 pm

LongtimeAirman wrote:.
OK, I've got the RGui.


rsesssion.exe is giving me system errors because rgraphapp.dll and r.dll are missing.

It's mostly foreign looking, I'll read up on it.

I just may send personal correspondence for those embarassing moments.


.

Just wanted to check that you are 64bit to 64bit across R.exe, RStudio and OS? Also you may need to set write permissions to the installation directory of R base.

You might want to look at starting with RStudio since it is easier to get started with than Rgui.  Just Open RStudio Menu > Tools > Options > set R install location (64 bit OS with 64 bit Rstudio and 64 bit R base install).
If this throws the .dll errors, then there should be more description of the issue from RStudio.

Two packages-libraries you should look at installing are the R Excel libraries to load Excel files.
install.packages("xlsx")
install.packages("XLConnect")
https://www.datacamp.com/community/tutorials/r-tutorial-read-excel-into-r

That's exactly the idea Nevyn.  Bring Mathis' and (yours) calcs-functions into an R library to support  findings.  Many R packages have a small file that is a sample data frame ( embedded .csv file) -- it would be cool to drop in a list of default values similar to the NIST values.

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Re: Creating a "Mathis" R library?

Post by LongtimeAirman on Wed Aug 10, 2016 11:14 pm

.
OK, I've got RStudio. I was incorrectly trying to run RSession instead (D'Oh).

I've been through the RManual chap1 and Appendix A with follow along excersizes. That went well. Very nice plotting possibilities indeed.

More later.
.

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Re: Creating a "Mathis" R library?

Post by LongtimeAirman on Thu Aug 18, 2016 12:23 am

Cr6, Nevyn,

I’ve used excel often. Mainly to create various charts. Keeping a small set of required forms with embedded calcs and links current over many years was part of my last job. Aside from that, calculators, and dimly recalled card deck FORTRAN, computational s/w is new to me. I'll admit it, R does seem very interesting, but I still can’t imagine Data Analysis.

R Update:
I’ve been through the O’Reilly’s tutorial - http://tryr.codeschool.com/
I’ve believe I’ve downloaded the packages (copy/pasted from my .Rhistory):
install.packages("h2o", type="source", repos=(c("http://h2o release.s3.amazonaws.com/h2o/rel-simons/4/R")))
install.packages("deepnet")
install.packages("rvest")
install.packages("XML")
install.packages("data.table")
install.packages("clusterGeneration")
install.packages("xlsx")
install.packages("XLConnect")

Currently at: https://www.datacamp.com/ R Tutorial. Reading and Importing Excel Files into R. I ‘cleaned up’ (by simplifying as much as possible) an excel copy of http://nssdc.gsfc.nasa.gov/planetary/factsheet/index.html PlanetaryFactSheetMetric.txt (preliminary to How to determine gravity thread doc). No joy porting it into R yet.

Interesting text: Empirical Research in Economics, Growing up with R
http://csun.cfr.msstate.edu/docs/ererSamplePage211.pdf

I didn't get very far, it was a busy week. I’ll continue to follow both your directions.
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Re: Creating a "Mathis" R library?

Post by Cr6 on Sat Aug 20, 2016 1:07 am

LTAM and Nevyn,

Sounds like you guys are off to a good start.  There are developer tools for R that allows for the creation of custom libraries/functions. There are a lot of R libraries and it is easy to get swamped by them. I'll try and keep an eye on those that might be useful to help create a "Mathis" library. If I get something together that appears to work, I'll share it here.

If this becomes too burdensome... (or just time-wasting)... don't let it detract from other work/insights.  It takes awhile to get going with it. A lot of the imported text files have to "munged" with datatypes (e.g. numeric conversions) which is very time consuming.

I'll see what head-way I can make from Nevyn's suggested Gravity thread.

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Re: Creating a "Mathis" R library?

Post by LongtimeAirman on Sat Aug 27, 2016 12:58 am

R Update. So far so good. I continued with a nice BestFirstRTutorial.pdf. Turns out RStudio makes porting tables pretty easy with a walk-you-through step-by-step wizard.  

Trying to tailor a first project - How to determine Gravity?

What I currently imagine is starting with the following outline, then expanding it by loading all the appropriate equations.

Code:
##----------------------------------------------------
##
## What are the Planets' gravity and charge emission?
##
##----------------------------------------------------
## A Miles Mathis charge field R Script.
##    first project effort
##----------------------------------------------------
## Miles Mathis reference, The Moon Gives up a Secret
##      http://milesmathis.com/moon.html
##----------------------------------------------------
## The planetary source data is from NASA:
##    http://nssdc.gsfc.nasa.gov/planetary/factsheet/index.html
##    Modified as an excel doc and saved as
##    Planetary Fact Sheet Metric.txt
##----------------------------------------------------
## Some discussion. How to determine Gravity  
##    http://milesmathis.the-talk.net/t205-how-to-determine-gravity
##----------------------------------------------------
## Generally, everything here is in meters, seconds and
##    kilograms; density is kg/m^3, velocity is m/s,
##    acceleration is m/s^2, and mass is kg.
##----------------------------------------------------
## Let:
##    r = radius, (or r = diameter/2);
##    g = solo gravity;
##    d = density;
##    m = mass;
##    e = electromagnetic (E/M) emission;
##    v = apparent gravity.
##----------------------------------------------------
##  First example.
##    v_E = g_E + e_E = 9.80 (m/s^2)
##    v underscore E refers to earth's
##    apparent gravity. Apparent gravity is equal to solo
##    gravity plus E/M emission. The goal is to understand  
##    the given relationship. Is it possible to make this
##    equation interactive?
##----------------------------------------------------
##  In The Moon Gives up a Secret, Miles expresses
##    the Moon's: mass, radius and gravity; with
##    respect to Earth's.
##  Compared to Earth, the Moon's:
##    mass, m_M/m_E = 1/81;
##    radius, r_M/r_E = 1/3.67;
##    and gravity at the surface, v_M/v_E = 1/6.
##  Miles determines:
##    Earth's E/M emission, e_E = .009545 (m/s^2)
##    Moon's E/M emission, e_M = 1.051 (m/s^2)
##    Earth's solo gravity, g_E = 9.809545 (m/s^2)
##    Moon's solo gravity, g_M = 2.671 (m/s^2)
##----------------------------------------------------
##  Second example.
##    Work through the logic to obtain these results
##----------------------------------------------------
##  Third example.
##    What are the solo gravities and charge emissions
##    of the planets?

Does this sound realistic/reasonable? I don't know how interactive R can be, and I have no best practices to compare to yet.
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Re: Creating a "Mathis" R library?

Post by Cr6 on Mon Aug 29, 2016 10:14 pm

That sounds like a great plan LTAM. I've actually been working too much with this library lately:

https://cran.rstudio.com/web/packages/FFTrees/vignettes/FFTrees_overview.html


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Re: Creating a "Mathis" R library?

Post by Nevyn on Tue Aug 30, 2016 1:12 am

I've managed to find a way to get paid to look into R!

I'm about to take a month off work and this is my last week so my workload is a little light. A colleague was asking me about some system monitoring software we might be able to use and when he stated what he wanted to do, I suggested that I could look into R if he thought it would fit his requirements, which it did. So I get to play around with it during work hours and we get the knowledge for our projects here. That's the way life should work!

I think I will use Miles angular velocity equation as a test function and see what I can get out of it.

Just to be clear, R is not a system monitoring system but we will be using it to analyze the results as we do some load testing on some software we have built.
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Re: Creating a "Mathis" R library?

Post by Nevyn on Wed Aug 31, 2016 12:55 am

I haven't gotten very far into R yet, but from what I have seen, it is a very ugly language. Powerful, but ugly. Very Unix like with lots of abbreviated commands that you won't remember. I'm also struggling a bit because I don't understand a lot of the math they are using for examples. It will probably start making more sense when I begin writing my own equations and have some idea of what I want to do with them.
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Re: Creating a "Mathis" R library?

Post by Cr6 on Thu Sep 01, 2016 10:55 pm

Nevyn wrote:I haven't gotten very far into R yet, but from what I have seen, it is a very ugly language. Powerful, but ugly. Very Unix like with lots of abbreviated commands that you won't remember. I'm also struggling a bit because I don't understand a lot of the math they are using for examples. It will probably start making more sense when I begin writing my own equations and have some idea of what I want to do with them.

Yeah... it is like that. Like there are 6 different ways to do the same thing each a little cryptic and different from the other...kind of like PERL in a way. It mixes set and procedural concepts which can often be a problem.  There are a lot of  "artistic" or "Swedish Chef" ala "recipe" approaches over say an architectural approach or an approach with blue prints.  It is still one of the only languages where a lot of code has been converted from cpp and pascal for use.  

That's awesome that you have time to really look into the R language.  It can be rewarding and it does work with "Big Data" on the cheap unlike a lot of other languages.  It does have past and a pretty bright future. That's why I'm kind of leaning towards creating a lot of Mathis' equations/theorems with it in a published package. It can get attention from a lot of people.
It is becoming the "Truth Bench" for a lot people.  Cool

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Re: Creating a "Mathis" R library?

Post by LongtimeAirman on Sat Sep 10, 2016 4:18 pm

.
An update, proof that I'm still at it.  


y <- (0.3 * sin(25*x)) + (sin(x))
.

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