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I am a university student working on a research project, because of our local lockdown I cannot go into the field to collect observation data, I am therefore looking for an R package that will allow me to model the effects of competition when testing for ideal free distribution (IFD).
To give you a better idea of what I am looking for I have described the project in more detail below.
In my original dataset (which I received i.e., I did not collect the data myself) I have two patches (A,B) which received random treatments of food input (1:1, 2:1, 5:1). Under the ideal free distribution hypothesis species should distribute into the patches in accordance with the treatment ratios. This is not the case.
Under normal circumstances I would go into the field and observe behaviour of individuals in the patches to see if dominance affects distribution. Since we are in a lockdown I am unable to do so. I am hoping that there is a package out there that would allow me to model this scenario and help me investigate how competition affects IFD.
I have already found two packages called coexist and EcoVirtual but they model coexistence and extinction dynamics, whereas I want to investigate how competition might alter distribution between profitable patches when there is variation in the level of competition.
I am fairly new to R and creating my own package is beyond my skillset at this point, so I would appreciate the help.
I hope this makes sense and thanks in advance.
Wow, that's an odd place to find another researcher of IFD. I do not believe there are packages on R specifically about IFD. Its too specific and most models are relatively simple to estimate using common tests. For example, the input-matching rule you mentioned can be tested using a simple run-of-the-mill t-test, already included in base R.
What you have is not a coding problem per say, or even an statistical one. It is a biological problem. What ratio would you expect when animals are ideal (full knowledge of the environment), free (no movement costs), but with the presence of competition? Is this ratio equal to the ratio in your dataset? Sutherland,1983 suggests animals would undermatch.
I would love to discuss this at depth, given my PhD was in IFD, but I fear you hit the wrong forum.
Currently, we are working on an eye-tracking study and we are not quite satisfied with the analysis option of SMI’s BeGaze. Hence, I would like to ask you know good way to extract data from BeGaze, which can be processed by a handy R-package, which is still working under R 3.6.1 – not like ETRAN.
It would be great to do add AOIs manually, do heat maps, analyze saccades, fixation times, and ratios between AOIs.
We came across eyetrackingR, but we are still struggling with extracting BeGaze's data in a processable way.
Any help, tutorial, hint, etc. is much appreciated.
David
I'm looking for advice on creating classification trees where each split is based on multiple variables. A bit of background: I'm helping design a vegetation classification system, and we're hoping to use a classification and regression tree algorithm to both classify new veg data and create (or at least help to create) visual keys which can be used in publications. The data I'm using is laid out as community data, with tree species as columns, and observations as rows, and the first column is a factor with classes. I'll also add that I'm very new to this type of analysis, and while I've tried to read about it as much as possible, it's quite likely that I've missed some simple but important aspects. My apologies.
Now the problem: R has excellent packages and great documentation for classification with univariate splits (e.g. rpart, partykit, C5.0). However, I would ideally like to be able to create classification trees where each split was based on multiple criteria - so instead of each split having one decision (e.g. "Percent cover of Species A > 6.67"), it would have multiple (Percent cover of Species A > 6.67 AND Percent cover of Species B < 4.2). I've had a lot of trouble finding packages that are capable of doing multivariate splits and creating trees. This answer: https://stats.stackexchange.com/questions/4356/does-rpart-use-multivariate-splits-by-default has been very useful, and I've tried all the packages suggested there for multivariate splitting. Prim does do multivariate splits, but doesn't seem to make trees; the partDSA package seems to be somewhat what I'm looking for, but it also only creates trees with one criteria per split; the optpart package also doesn't seem to be able to make classification trees. If anyone has advice on how I could go about making a classification tree based on a multivariate partitioning method, that would be super appreciated.
Also, this is my first question, and I am very open to suggestions about how to ask questions. I didn't feel that providing an example would be helpful in this case, but if necessary I easily can.
Many Thanks!
Instead of starting to code in Matlab, I recently started learning R, mainly because it is open-source. I am currently working in data mining and machine learning field. I found many machine learning algorithms implemented in R, and I am still exploring different packages implemented in R.
I have quick question: how do you compare R to Matlab for data mining application, its popularity, pros and cons, industry and academic acceptance etc.? Which one would you choose and why?
I went through various comparisons for Matlab vs R against various metrics but I am specifically interested to get answer for its applicability in Data Mining and ML.
Since both language are pretty new for me I was just wondering if R would be a good choice or not.
I appreciate any kind of suggestions.
For the past three years or so, i have used R daily, and the largest portion of that daily use is spent on Machine Learning/Data Mining problems.
I was an exclusive Matlab user while in University; at the time i thought it was
an excellent set of tools/platform. I am sure it is today as well.
The Neural Network Toolbox, the Optimization Toolbox, Statistics Toolbox,
and Curve Fitting Toolbox are each highly desirable (if not essential)
for someone using MATLAB for ML/Data Mining work, yet they are all separate from
the base MATLAB environment--in other words, they have to be purchased separately.
My Top 5 list for Learning ML/Data Mining in R:
Mining Association Rules in R
This refers to a couple things: First, a group of R Package that all begin arules (available from CRAN); you can find the complete list (arules, aruluesViz, etc.) on the Project Homepage. Second, all of these packages are based on a data-mining technique known as Market-Basked Analysis and alternatively as Association Rules. In many respects, this family of algorithms is the essence of data-mining--exhaustively traverse large transaction databases and find above-average associations or correlations among the fields (variables or features) in those databases. In practice, you connect them to a data source and let them run overnight. The central R Package in the set mentioned above is called arules; On the CRAN Package page for arules, you will find links to a couple of excellent secondary sources (vignettes in R's lexicon) on the arules package and on Association Rules technique in general.
The standard reference, The Elements of Statistical
Learning by Hastie et al.
The most current edition of this book is available in digital form for free. Likewise, at the book's website (linked to just above) are all data sets used in ESL, available for free download. (As an aside, i have the free digital version; i also purchased the hardback version from BN.com; all of the color plots in the digital version are reproduced in the hardbound version.) ESL contains thorough introductions to at least one exemplar from most of the major
ML rubrics--e.g., neural metworks, SVM, KNN; unsupervised
techniques (LDA, PCA, MDS, SOM, clustering), numerous flavors of regression, CART,
Bayesian techniques, as well as model aggregation techniques (Boosting, Bagging)
and model tuning (regularization). Finally, get the R Package that accompanies the book from CRAN (which will save the trouble of having to download the enter the datasets).
CRAN Task View: Machine Learning
The +3,500 Packages available
for R are divided up by domain into about 30 package families or 'Task Views'. Machine Learning
is one of these families. The Machine Learning Task View contains about 50 or so
Packages. Some of these Packages are part of the core distribution, including e1071
(a sprawling ML package that includes working code for quite a few of
the usual ML categories.)
Revolution Analytics Blog
With particular focus on the posts tagged with Predictive Analytics
ML in R tutorial comprised of slide deck and R code by Josh Reich
A thorough study of the code would, by itself, be an excellent introduction to ML in R.
And one final resource that i think is excellent, but didn't make in the top 5:
A Guide to Getting Stared in Machine Learning [in R]
posted at the blog A Beautiful WWW
Please look at the CRAN Task Views and in particular at the CRAN Task View on Machine Learning and Statistical Learning which summarises this nicely.
Both Matlab and R are good if you are doing matrix-heavy operations. Because they can use highly optimized low-level code (BLAS libraries and such) for this.
However, there is more to data-mining than just crunching matrixes. A lot of people totally neglect the whole data organization aspect of data mining (as opposed to say, plain machine learning).
And once you get to data organization, R and Matlab are a pain. Try implementing an R*-tree in R or matlab to take an O(n^2) algorithm down to O(n log n) runtime. First of all, it totally goes against the way R and Matlab are designed (use bulk math operations wherever possible), secondly it will kill your performance. Interpreted R code for example seems to run at around 50% of the speed of the C code (try R built-in k-means vs. flexclus k-means); and the BLAS libraries are optimized to an insane level, exploiting cache sizes, data alignment, advanced CPU features. If you are adventurous, try implementing a manual matrix multiplication in R or Matlab, and benchmark it against the native one.
Don't get me wrong. There is a lot of stuff where R and matlab are just elegant and excellent for prototyping. You can solve a lot of things in just 10 lines of code, and get a decent performance out of it. Writing the same thing by hand would be hundreds of lines, and probably 10x slower. But sometimes you can optimize by a level of complexity, which for large data sets does beat the optimized matrix operations of R and matlab.
If you want to scale up to "Hadoop size" on the long run, you will have to think about data layout and organization, too, unless all you need is a linear scan over the data. But then, you could just be sampling, too!
Yesterday I found two new books about Data mining. These series of books entitled by ‘Data Mining’ address the need by presenting in-depth description of novel mining algorithms and many useful applications. In addition to understanding each section deeply, the two books present useful hints and strategies to solving problems in the following chapters.The progress of data mining technology and large public popularity establish a need for a comprehensive text on the subject. Books are: “New Fundamental Technologies in Data Mining” here http://www.intechopen.com/books/show/title/new-fundamental-technologies-in-data-mining & “Knowledge-Oriented Applications in Data Mining” here http://www.intechopen.com/books/show/title/knowledge-oriented-applications-in-data-mining These are open access books so you can download it for free or just read on online reading platform like I do. Cheers!
We should not forget the origin sources for these two software: scientific computation and also signal processing leads to Matlab but statistics leads to R.
I used matlab a lot in University since we have one installed on Unix and open to all students. However, the price for Matlab is too high especially compared to free R. If your major focus is not on matrix computation and signal processing, R should work well for your needs.
I think it also depends in which field of study you are. I know of people in coastal research that use a lot of Matlab. Using R in this group would make your life more difficult. If a colleague has solved a problem, you can't use it because he fixed it using Matlab.
I would also look at the capabilities of each when you are dealing with large amounts of data. I know that R can have problems with this, and might be restrictive if you are used to an iterative data mining process. For example looking at multiple models concurrently. I don't know if MATLAB has a data limitation.
I admit to favoring MATLAB for data mining problems, and I give some of my reasoning here:
Why MATLAB for Data Mining?
I will admit to only a passing familiarity with R/S-Plus, but I'll make the following observations:
R definitely has more of a statistical focus than MATLAB. I prefer building my own tools in MATLAB, so that I know exactly what they're doing, and I can customize them, but this is more of a necessity in MATLAB than it would be in R.
Code for new statistical techniques (spatial statistics, robust statistics, etc.) often appears early in S-Plus (I assume that this carries over to R, at least some).
Some years ago, I found the commercial version of R, S-Plus to have an extremely limited capacity for data. I cannot say what the state of R/S-Plus is today, but you may want to check if your data will fit into such tools comfortably.
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What datasets exist out on the internet that I can run statistical analysis on?
The datasets package is included with base R. Run this command to see a full list:
library(help="datasets")
Beyond that, there are many packages that can pull data, and many others that contain important data. Of these, you may want to start by looking at the HistData package, which "provides a collection of small data sets that are interesting and important in the history of statistics and data visualization".
For financial data, the quantmod package provides a common interface for pulling time series data from google, yahoo, FRED, and others:
library(quantmod)
getSymbols("YHOO",src="google") # from google finance
getSymbols("GOOG",src="yahoo") # from yahoo finance
getSymbols("DEXUSJP",src="FRED") # FX rates from FRED
FRED (the Federal Reserve of St. Louis) is really a landmine of free economic data.
Many R packages come bundled with data that is specific to their goal. So if you're interested in genetics, multilevel models, etc., the relevant packages will frequently have the canonical example for that analysis. Also, the book packages typically ship with the data needed to reproduce all the examples.
Here are some examples of relevant packages:
alr3: includes data to accompany Applied Linear Regression (http://www.stat.umn.edu/alr)
arm: includes some of the data from Gelman's "Data Analysis Using Regression and Multilevel/Hierarchical Models" (the rest of the data and code is on the book's website)
BaM: includes data from "Bayesian Methods: A Social and Behavioral Sciences Approach"
BayesDA: includes data from Gelman's "Bayesian Data Analysis"
cat: includes data for analysis of categorical-variable datasets
cimis: from retrieving data from CIMIS, the California Irrigation Management Information System
cshapes: includes GIS data boundaries and data
ecdat: data sets for econometrics
ElemStatLearn: includes data from "The Elements of Statistical Learning, Data Mining, Inference, and Prediction"
emdbook: data from "Ecological Models and Data"
Fahrmeir: data from the book "Multivariate Statistical Modelling Based on Generalized Linear Models"
fEcoFin: "Economic and Financial Data Sets" for Rmetrics
fds: functional data sets
fma: data sets from "Forecasting: methods and applications"
gamair: data for "Generalized Additive Models: An Introduction with R"
geomapdata: data for topographic and Geologic Mapping
nutshell: contains all the data from the "R in a Nutshell" book
nytR: provides access to congressional vote data through the NY Times API
openintro: data from the book
primer: includes data for "A Primer of Ecology with R"
qtlbook: includes data for the R/qtl book
RGraphics: includes data from the "R Graphics" book
Read.isi: access to old World Fertility Survey data
A broad selection on the Web. For instance, here's a massive directory of sports databases (all providing the data free of charge, at least that's my experience). In that directory is databaseBaseball.com, which contains among other things, complete datasets for every player who has ever played professional baseball since about 1915.
StatLib is an other excellent resource--beautifully convenient. This single web page lists 4-5 line summaries of over a hundred databases, all of which are available in flat-file form just by clicking the 'Table' link at the beginning of each data set summary.
The base distribution of R comes pre-packaged with a large and varied collection of datasts (122 in R 2.10). To get a list of them (as well as a one-line description):
data(package="datasets")
Likewise, most packages come with several data sets (sometimes a lot more). You can see those the same way:
data(package="latticeExtra")
data(package="vcd")
These data sets are the ones mentioned in the package manuals and vignettes for a given package, and used to illustrate the package features.
A few R packages with a lot of datasets (which again are easy to scan so you can choose what's interesting to you): AER, DAAG, and vcd.
Another thing i find so impressive about R is its I/O. Suppose you want to get some very specific financial data via the yahoo finance API. Let's say closing open and closing price of S&P 500 for every month from 2001 to 2009, just do this:
tick_data = read.csv(paste("http://ichart.finance.yahoo.com/table.csv?",
"s=%5EGSPC&a=03&b=1&c=2001&d=03&e=1&f=2009&g=m&ignore=.csv"))
In this one line of code, R has fetched the tick data, shaped it to a dataframe and bound it to 'tick_data' all . (Here's a handy cheat sheet w/ the Yahoo Finance API symbols used to build the URLs as above)
http://www.data.gov.uk/data
Recently setup by Tim Berners-Lee
Obviously UK based data, but that shouldn't matter. Covers everything from abandoned cars to school absenteeism to agricultural price indexes
Have you considered Stack Overflow Data Dumps?
You are already familiar with what the data represents i.e. the business logic it tracks
A good start to look for economic data are always the following three addresses:
World Bank - Research Datasets
IMF - Data and Statistics
National Bureau of Economic Research
A nice summary of dataset links for development economists can be found at:
Devecondata
Edit:
The World Bank decided last week to open up a lot of its previously non-free datasets and published them online on its revised homepage. The new internet appearance looks pretty nice as well.
The World Bank - Open Data
Another good site is UN Data.
The United Nations Statistics Division
(UNSD) of the Department of Economic
and Social Affairs (DESA) launched a
new internet based data service for
the global user community. It brings
UN statistical databases within easy
reach of users through a single entry
point (http://data.un.org/). Users can
now search and download a variety of
statistical resources of the UN
system.
http://www.data.gov/ probably has something you can use.
In their catalog of raw data you can set your criteria for the data and find what you're looking for http://www.data.gov/catalog/raw
A bundle of 268 small text files (the worked examples of "The R Book") can be found in The R Book's companion website.
You could look on this post on FlowingData
Collection of over 800 datasets in ARFF format understood by Weka and other data analysis packages, gathered in TunedIT.org Repository.
See the data competition set up by Hadley Wickham for the Data Expo of the ASA Statistical Computing and Statistical Graphics section. The competition is over, the data is still there.
UC Irvine Machine Learning Repository has currently 190 data sets.
The UCI Machine Learning Repository is
a collection of databases, domain
theories, and data generators that are
used by the machine learning community
for the empirical analysis of machine
learning algorithms.
I've seen on your other questions that you are apparently interested in data visualization. Have then a look at many eyes project (form IBM) and the sample data sets.
Similar to data.gov, but european centered is eurostat
http://epp.eurostat.ec.europa.eu/portal/page/portal/statistics/search_database
and there is a chinese statistics departement, too, as mentioned by Wildebeests
http://www.stats.gov.cn/english/statisticaldata/monthlydata/index.htm
Then there are some "social data services" which offer the download of datasets, such as
swivel, manyeyes, timetric, ckan, infochimps..
The FAO offers the aquastat database with data with various water related indicators differentiated by country.
The Naval Oceanography Portal offers, for instance, Fraction of the Moon Illuminated.
The blog "curving normality" has a list of interesting data sources.
Another collection of datasets.
Here's an R package with several agricultural datasets from books and papers. Example analyses included: agridat