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This shows you the differences between two versions of the page.

--- sna_with_r [2016/08/24 11:25] – created hkimscil
+++ sna_with_r [2016/08/24 11:26] (current) – hkimscil
@@ Line 1: / Line 1: @@
-SNA with R
+Statistical tool R namespace
+====== SNA with R ======
+[[http://www.bojanorama.pl/snar:start|R labs]] at Stanford University \\
+[[http://www.r-bloggers.com/social-network-analysis-with-r/|Social Network Analysis with R]] \\
+[[http://www.r-bloggers.com/tag/social-network-analysis/|Tags > Social Network Analysis]] in Rbloggers.com \\
+[[http://www.bojanorama.pl/snar:start|Workshop session]] \\
+===== installing packages =====
+<code>install.packages("ergm", repos = "http://cran.cnr.berkeley.edu/", dependencies = TRUE)
+install.packages("reshape", repos = "http://cran.cnr.berkeley.edu/", dependencies = TRUE)
+install.packages("igraph", repos = "http://cran.cnr.berkeley.edu/", dependencies = TRUE)
+install.packages("sna", repos = "http://cran.cnr.berkeley.edu/", dependencies = TRUE)
+install.packages("numDeriv", repos = "http://cran.cnr.berkeley.edu/", dependencies = TRUE)
+install.packages("MatchIt", repos = "http://cran.cnr.berkeley.edu/", dependencies = TRUE)
+install.packages("coin", repos = "http://cran.cnr.berkeley.edu/", dependencies = TRUE)
+install.packages("boot", repos = "http://cran.cnr.berkeley.edu/", dependencies = TRUE)
+install.packages("Hmisc", repos = "http://cran.cnr.berkeley.edu/", dependencies = TRUE)
+install.packages("lattice", repos = "http://cran.cnr.berkeley.edu/", dependencies = TRUE)
+install.packages("triads", repos = "http://cran.cnr.berkeley.edu/", dependencies = TRUE)
+install.packages("psych", repos = "http://cran.cnr.berkeley.edu/", dependencies = TRUE)
+install.packages("nFactors", repos = "http://cran.cnr.berkeley.edu/", dependencies = TRUE)
+install.packages("animation", repos = "http://cran.cnr.berkeley.edu/", dependencies = TRUE)
+install.packages("NetData", repos = "http://cran.cnr.berkeley.edu/", dependencies = TRUE)
+install.packages("NetCluster", repos = "http://cran.cnr.berkeley.edu/", dependencies = TRUE)
+install.packages("igraphtosonia", repos = "http://cran.cnr.berkeley.edu/", dependencies = TRUE)
+</code>
+<code>install.packages("network", dependencies = TRUE)
+install.packages("statnet", dependencies = TRUE)
+install.packages("ggplot2", dependencies = TRUE)
+</code>
+====== Datasets available in R packages ======
+<code>Data sets in package ‘boot’:
+acme                   Monthly Excess Returns
+aids                   Delay in AIDS Reporting in England and Wales
+aircondit              Failures of Air-conditioning Equipment
+aircondit7             Failures of Air-conditioning Equipment
+amis                   Car Speeding and Warning Signs
+aml                    Remission Times for Acute Myelogenous
+                       Leukaemia
+beaver                 Beaver Body Temperature Data
+bigcity                Population of U.S. Cities
+brambles               Spatial Location of Bramble Canes
+breslow                Smoking Deaths Among Doctors
+calcium                Calcium Uptake Data
+cane                   Sugar-cane Disease Data
+capability             Simulated Manufacturing Process Data
+catsM                  Weight Data for Domestic Cats
+cav                    Position of Muscle Caveolae
+cd4                    CD4 Counts for HIV-Positive Patients
+cd4.nested             Nested Bootstrap of cd4 data
+channing               Channing House Data
+city                   Population of U.S. Cities
+claridge               Genetic Links to Left-handedness
+cloth                  Number of Flaws in Cloth
+co.transfer            Carbon Monoxide Transfer
+coal                   Dates of Coal Mining Disasters
+darwin                 Darwin's Plant Height Differences
+dogs                   Cardiac Data for Domestic Dogs
+downs.bc               Incidence of Down's Syndrome in British
+                       Columbia
+ducks                  Behavioral and Plumage Characteristics of
+                       Hybrid Ducks
+fir                    Counts of Balsam-fir Seedlings
+frets                  Head Dimensions in Brothers
+grav                   Acceleration Due to Gravity
+gravity                Acceleration Due to Gravity
+hirose                 Failure Time of PET Film
+islay                  Jura Quartzite Azimuths on Islay
+manaus                 Average Heights of the Rio Negro river at
+                       Manaus
+melanoma               Survival from Malignant Melanoma
+motor                  Data from a Simulated Motorcycle Accident
+neuro                  Neurophysiological Point Process Data
+nitrofen               Toxicity of Nitrofen in Aquatic Systems
+nodal                  Nodal Involvement in Prostate Cancer
+nuclear                Nuclear Power Station Construction Data
+paulsen                Neurotransmission in Guinea Pig Brains
+poisons                Animal Survival Times
+polar                  Pole Positions of New Caledonian Laterites
+remission              Cancer Remission and Cell Activity
+salinity               Water Salinity and River Discharge
+survival               Survival of Rats after Radiation Doses
+tau                    Tau Particle Decay Modes
+tuna                   Tuna Sighting Data
+urine                  Urine Analysis Data
+wool                   Australian Relative Wool Prices
+Data sets in package ‘cluster’:
+agriculture            European Union Agricultural Workforces
+animals                Attributes of Animals
+chorSub                Subset of C-horizon of Kola Data
+flower                 Flower Characteristics
+plantTraits            Plant Species Traits Data
+pluton                 Isotopic Composition Plutonium Batches
+ruspini                Ruspini Data
+votes.repub            Votes for Republican Candidate in
+                       Presidential Elections
+xclara                 Bivariate Data Set with 3 Clusters
+Data sets in package ‘colorspace’:
+USSouthPolygon         Polygon for County Map of US South States:
+                       Alabama, Georgia, and South Carolina
+Data sets in package ‘datasets’:
+AirPassengers          Monthly Airline Passenger Numbers 1949-1960
+BJsales                Sales Data with Leading Indicator
+BJsales.lead (BJsales)
+                       Sales Data with Leading Indicator
+BOD                    Biochemical Oxygen Demand
+CO2                    Carbon Dioxide Uptake in Grass Plants
+ChickWeight            Weight versus age of chicks on different
+                       diets
+DNase                  Elisa assay of DNase
+EuStockMarkets         Daily Closing Prices of Major European Stock
+                       Indices, 1991-1998
+Formaldehyde           Determination of Formaldehyde
+HairEyeColor           Hair and Eye Color of Statistics Students
+Harman23.cor           Harman Example 2.3
+Harman74.cor           Harman Example 7.4
+Indometh               Pharmacokinetics of Indomethacin
+InsectSprays           Effectiveness of Insect Sprays
+JohnsonJohnson         Quarterly Earnings per Johnson & Johnson
+                       Share
+LakeHuron              Level of Lake Huron 1875-1972
+LifeCycleSavings       Intercountry Life-Cycle Savings Data
+Loblolly               Growth of Loblolly pine trees
+Nile                   Flow of the River Nile
+Orange                 Growth of Orange Trees
+OrchardSprays          Potency of Orchard Sprays
+PlantGrowth            Results from an Experiment on Plant Growth
+Puromycin              Reaction Velocity of an Enzymatic Reaction
+Seatbelts              Road Casualties in Great Britain 1969-84
+Theoph                 Pharmacokinetics of Theophylline
+Titanic                Survival of passengers on the Titanic
+ToothGrowth            The Effect of Vitamin C on Tooth Growth in
+                       Guinea Pigs
+UCBAdmissions          Student Admissions at UC Berkeley
+UKDriverDeaths         Road Casualties in Great Britain 1969-84
+UKgas                  UK Quarterly Gas Consumption
+USAccDeaths            Accidental Deaths in the US 1973-1978
+USArrests              Violent Crime Rates by US State
+USJudgeRatings         Lawyers' Ratings of State Judges in the US
+                       Superior Court
+USPersonalExpenditure
+                       Personal Expenditure Data
+UScitiesD              Distances Between European Cities and Between
+                       US Cities
+VADeaths               Death Rates in Virginia (1940)
+WWWusage               Internet Usage per Minute
+WorldPhones            The World's Telephones
+ability.cov            Ability and Intelligence Tests
+airmiles               Passenger Miles on Commercial US Airlines,
+-1960
+airquality             New York Air Quality Measurements
+anscombe               Anscombe's Quartet of 'Identical' Simple
+                       Linear Regressions
+attenu                 The Joyner-Boore Attenuation Data
+attitude               The Chatterjee-Price Attitude Data
+austres                Quarterly Time Series of the Number of
+                       Australian Residents
+beaver1 (beavers)      Body Temperature Series of Two Beavers
+beaver2 (beavers)      Body Temperature Series of Two Beavers
+cars                   Speed and Stopping Distances of Cars
+chickwts               Chicken Weights by Feed Type
+co2                    Mauna Loa Atmospheric CO2 Concentration
+crimtab                Student's 3000 Criminals Data
+discoveries            Yearly Numbers of Important Discoveries
+esoph                  Smoking, Alcohol and (O)esophageal Cancer
+euro                   Conversion Rates of Euro Currencies
+euro.cross (euro)      Conversion Rates of Euro Currencies
+eurodist               Distances Between European Cities and Between
+                       US Cities
+faithful               Old Faithful Geyser Data
+fdeaths (UKLungDeaths)
+                       Monthly Deaths from Lung Diseases in the UK
+freeny                 Freeny's Revenue Data
+freeny.x (freeny)      Freeny's Revenue Data
+freeny.y (freeny)      Freeny's Revenue Data
+infert                 Infertility after Spontaneous and Induced
+                       Abortion
+iris                   Edgar Anderson's Iris Data
+iris3                  Edgar Anderson's Iris Data
+islands                Areas of the World's Major Landmasses
+ldeaths (UKLungDeaths)
+                       Monthly Deaths from Lung Diseases in the UK
+lh                     Luteinizing Hormone in Blood Samples
+longley                Longley's Economic Regression Data
+lynx                   Annual Canadian Lynx trappings 1821-1934
+mdeaths (UKLungDeaths)
+                       Monthly Deaths from Lung Diseases in the UK
+morley                 Michelson Speed of Light Data
+mtcars                 Motor Trend Car Road Tests
+nhtemp                 Average Yearly Temperatures in New Haven
+nottem                 Average Monthly Temperatures at Nottingham,
+-1939
+npk                    Classical N, P, K Factorial Experiment
+occupationalStatus     Occupational Status of Fathers and their Sons
+precip                 Annual Precipitation in US Cities
+presidents             Quarterly Approval Ratings of US Presidents
+pressure               Vapor Pressure of Mercury as a Function of
+                       Temperature
+quakes                 Locations of Earthquakes off Fiji
+randu                  Random Numbers from Congruential Generator
+                       RANDU
+rivers                 Lengths of Major North American Rivers
+rock                   Measurements on Petroleum Rock Samples
+sleep                  Student's Sleep Data
+stack.loss (stackloss)
+                       Brownlee's Stack Loss Plant Data
+stack.x (stackloss)    Brownlee's Stack Loss Plant Data
+stackloss              Brownlee's Stack Loss Plant Data
+state.abb (state)      US State Facts and Figures
+state.area (state)     US State Facts and Figures
+state.center (state)   US State Facts and Figures
+state.division (state)
+                       US State Facts and Figures
+state.name (state)     US State Facts and Figures
+state.region (state)   US State Facts and Figures
+state.x77 (state)      US State Facts and Figures
+sunspot.month          Monthly Sunspot Data, from 1749 to "Present"
+sunspot.year           Yearly Sunspot Data, 1700-1988
+sunspots               Monthly Sunspot Numbers, 1749-1983
+swiss                  Swiss Fertility and Socioeconomic Indicators
+                       (1888) Data
+treering               Yearly Treering Data, -6000-1979
+trees                  Girth, Height and Volume for Black Cherry
+                       Trees
+uspop                  Populations Recorded by the US Census
+volcano                Topographic Information on Auckland's Maunga
+                       Whau Volcano
+warpbreaks             The Number of Breaks in Yarn during Weaving
+women                  Average Heights and Weights for American
+                       Women
+Data sets in package ‘dichromat’:
+dalton                 Effects of Daltonism (Red-Green Color
+                       Blindness)
+dalton.colors (dalton)
+                       Effects of Daltonism (Red-Green Color
+                       Blindness)
+Data sets in package ‘ggplot2’:
+diamonds               Prices of 50,000 round cut diamonds
+economics              US economic time series.
+economics_long         US economic time series.
+faithfuld              2d density estimate of Old Faithful data
+luv_colours            'colors()' in Luv space.
+midwest                Midwest demographics.
+mpg                    Fuel economy data from 1999 and 2008 for 38
+                       popular models of car
+msleep                 An updated and expanded version of the
+                       mammals sleep dataset.
+presidential           Terms of 11 presidents from Eisenhower to
+                       Obama.
+seals                  Vector field of seal movements.
+txhousing              Housing sales in TX.
+Data sets in package ‘lattice’:
+barley                 Yield data from a Minnesota barley trial
+environmental          Atmospheric environmental conditions in New
+                       York City
+ethanol                Engine exhaust fumes from burning ethanol
+melanoma               Melanoma skin cancer incidence
+singer                 Heights of New York Choral Society singers
+Data sets in package ‘MASS’:
+Aids2                  Australian AIDS Survival Data
+Animals                Brain and Body Weights for 28 Species
+Boston                 Housing Values in Suburbs of Boston
+Cars93                 Data from 93 Cars on Sale in the USA in 1993
+Cushings               Diagnostic Tests on Patients with Cushing's
+                       Syndrome
+DDT                    DDT in Kale
+GAGurine               Level of GAG in Urine of Children
+Insurance              Numbers of Car Insurance claims
+Melanoma               Survival from Malignant Melanoma
+OME                    Tests of Auditory Perception in Children with
+                       OME
+Pima.te                Diabetes in Pima Indian Women
+Pima.tr                Diabetes in Pima Indian Women
+Pima.tr2               Diabetes in Pima Indian Women
+Rabbit                 Blood Pressure in Rabbits
+Rubber                 Accelerated Testing of Tyre Rubber
+SP500                  Returns of the Standard and Poors 500
+Sitka                  Growth Curves for Sitka Spruce Trees in 1988
+Sitka89                Growth Curves for Sitka Spruce Trees in 1989
+Skye                   AFM Compositions of Aphyric Skye Lavas
+Traffic                Effect of Swedish Speed Limits on Accidents
+UScereal               Nutritional and Marketing Information on US
+                       Cereals
+UScrime                The Effect of Punishment Regimes on Crime
+                       Rates
+VA                     Veteran's Administration Lung Cancer Trial
+abbey                  Determinations of Nickel Content
+accdeaths              Accidental Deaths in the US 1973-1978
+anorexia               Anorexia Data on Weight Change
+bacteria               Presence of Bacteria after Drug Treatments
+beav1                  Body Temperature Series of Beaver 1
+beav2                  Body Temperature Series of Beaver 2
+biopsy                 Biopsy Data on Breast Cancer Patients
+birthwt                Risk Factors Associated with Low Infant Birth
+                       Weight
+cabbages               Data from a cabbage field trial
+caith                  Colours of Eyes and Hair of People in
+                       Caithness
+cats                   Anatomical Data from Domestic Cats
+cement                 Heat Evolved by Setting Cements
+chem                   Copper in Wholemeal Flour
+coop                   Co-operative Trial in Analytical Chemistry
+cpus                   Performance of Computer CPUs
+crabs                  Morphological Measurements on Leptograpsus
+                       Crabs
+deaths                 Monthly Deaths from Lung Diseases in the UK
+drivers                Deaths of Car Drivers in Great Britain
+-84
+eagles                 Foraging Ecology of Bald Eagles
+epil                   Seizure Counts for Epileptics
+farms                  Ecological Factors in Farm Management
+fgl                    Measurements of Forensic Glass Fragments
+forbes                 Forbes' Data on Boiling Points in the Alps
+galaxies               Velocities for 82 Galaxies
+gehan                  Remission Times of Leukaemia Patients
+genotype               Rat Genotype Data
+geyser                 Old Faithful Geyser Data
+gilgais                Line Transect of Soil in Gilgai Territory
+hills                  Record Times in Scottish Hill Races
+housing                Frequency Table from a Copenhagen Housing
+                       Conditions Survey
+immer                  Yields from a Barley Field Trial
+leuk                   Survival Times and White Blood Counts for
+                       Leukaemia Patients
+mammals                Brain and Body Weights for 62 Species of Land
+                       Mammals
+mcycle                 Data from a Simulated Motorcycle Accident
+menarche               Age of Menarche in Warsaw
+michelson              Michelson's Speed of Light Data
+minn38                 Minnesota High School Graduates of 1938
+motors                 Accelerated Life Testing of Motorettes
+muscle                 Effect of Calcium Chloride on Muscle
+                       Contraction in Rat Hearts
+newcomb                Newcomb's Measurements of the Passage Time of
+                       Light
+nlschools              Eighth-Grade Pupils in the Netherlands
+npk                    Classical N, P, K Factorial Experiment
+npr1                   US Naval Petroleum Reserve No. 1 data
+oats                   Data from an Oats Field Trial
+painters               The Painter's Data of de Piles
+petrol                 N. L. Prater's Petrol Refinery Data
+phones                 Belgium Phone Calls 1950-1973
+quine                  Absenteeism from School in Rural New South
+                       Wales
+road                   Road Accident Deaths in US States
+rotifer                Numbers of Rotifers by Fluid Density
+ships                  Ships Damage Data
+shoes                  Shoe wear data of Box, Hunter and Hunter
+shrimp                 Percentage of Shrimp in Shrimp Cocktail
+shuttle                Space Shuttle Autolander Problem
+snails                 Snail Mortality Data
+steam                  The Saturated Steam Pressure Data
+stormer                The Stormer Viscometer Data
+survey                 Student Survey Data
+synth.te               Synthetic Classification Problem
+synth.tr               Synthetic Classification Problem
+topo                   Spatial Topographic Data
+waders                 Counts of Waders at 15 Sites in South Africa
+whiteside              House Insulation: Whiteside's Data
+wtloss                 Weight Loss Data from an Obese Patient
+Data sets in package ‘Matrix’:
+CAex                   Albers' example Matrix with "Difficult" Eigen
+                       Factorization
+KNex                   Koenker-Ng Example Sparse Model Matrix and
+                       Response Vector
+USCounties             USCounties Contiguity Matrix
+Data sets in package ‘mgcv’:
+columb                 Reduced version of Columbus OH crime data
+columb.polys           Reduced version of Columbus OH crime data
+Data sets in package ‘nlme’:
+Alfalfa                Split-Plot Experiment on Varieties of Alfalfa
+Assay                  Bioassay on Cell Culture Plate
+BodyWeight             Rat weight over time for different diets
+Cefamandole            Pharmacokinetics of Cefamandole
+Dialyzer               High-Flux Hemodialyzer
+Earthquake             Earthquake Intensity
+Fatigue                Cracks caused by metal fatigue
+Gasoline               Refinery yield of gasoline
+Glucose                Glucose levels over time
+Glucose2               Glucose Levels Following Alcohol Ingestion
+Gun                    Methods for firing naval guns
+IGF                    Radioimmunoassay of IGF-I Protein
+Machines               Productivity Scores for Machines and Workers
+MathAchSchool          School demographic data for MathAchieve
+MathAchieve            Mathematics achievement scores
+Meat                   Tenderness of meat
+Milk                   Protein content of cows' milk
+Muscle                 Contraction of heart muscle sections
+Nitrendipene           Assay of nitrendipene
+Oats                   Split-plot Experiment on Varieties of Oats
+Orthodont              Growth curve data on an orthdontic
+                       measurement
+Ovary                  Counts of Ovarian Follicles
+Oxboys                 Heights of Boys in Oxford
+Oxide                  Variability in Semiconductor Manufacturing
+PBG                    Effect of Phenylbiguanide on Blood Pressure
+Phenobarb              Phenobarbitol Kinetics
+Pixel                  X-ray pixel intensities over time
+Quinidine              Quinidine Kinetics
+Rail                   Evaluation of Stress in Railway Rails
+RatPupWeight           The weight of rat pups
+Relaxin                Assay for Relaxin
+Remifentanil           Pharmacokinetics of remifentanil
+Soybean                Growth of soybean plants
+Spruce                 Growth of Spruce Trees
+Tetracycline1          Pharmacokinetics of tetracycline
+Tetracycline2          Pharmacokinetics of tetracycline
+Wafer                  Modeling of Analog MOS Circuits
+Wheat                  Yields by growing conditions
+Wheat2                 Wheat Yield Trials
+bdf                    Language scores
+ergoStool              Ergometrics experiment with stool types
+Data sets in package ‘plyr’:
+baseball               Yearly batting records for all major league
+                       baseball players
+ozone                  Monthly ozone measurements over Central
+                       America.
+Data sets in package ‘reshape2’:
+french_fries           Sensory data from a french fries experiment.
+smiths                 Demo data describing the Smiths.
+tips                   Tipping data
+Data sets in package ‘rpart’:
+car.test.frame         Automobile Data from 'Consumer Reports' 1990
+car90                  Automobile Data from 'Consumer Reports' 1990
+cu.summary             Automobile Data from 'Consumer Reports' 1990
+kyphosis               Data on Children who have had Corrective
+                       Spinal Surgery
+solder                 Soldering of Components on Printed-Circuit
+                       Boards
+stagec                 Stage C Prostate Cancer
+Data sets in package ‘sna’:
+coleman                Coleman's High School Friendship Data
+Data sets in package ‘survival’:
+aml (leukemia)         Acute Myelogenous Leukemia survival data
+bladder                Bladder Cancer Recurrences
+bladder1 (bladder)     Bladder Cancer Recurrences
+bladder2 (bladder)     Bladder Cancer Recurrences
+cancer                 NCCTG Lung Cancer Data
+cgd                    Chronic Granulotomous Disease data
+cgd0 (cgd)             Chronic Granulotomous Disease data
+colon                  Chemotherapy for Stage B/C colon cancer
+flchain                Assay of serum free light chain for 7874
+                       subjects.
+heart                  Stanford Heart Transplant data
+jasa (heart)           Stanford Heart Transplant data
+jasa1 (heart)          Stanford Heart Transplant data
+kidney                 Kidney catheter data
+leukemia               Acute Myelogenous Leukemia survival data
+logan                  Data from the 1972-78 GSS data used by Logan
+lung                   NCCTG Lung Cancer Data
+mgus                   Monoclonal gammapothy data
+mgus1 (mgus)           Monoclonal gammapothy data
+mgus2                  Monoclonal gammapothy data
+nwtco                  Data from the National Wilm's Tumor Study
+ovarian                Ovarian Cancer Survival Data
+pbc                    Mayo Clinic Primary Biliary Cirrhosis Data
+pbcseq (pbc)           Mayo Clinic Primary Biliary Cirrhosis,
+                       sequential data
+rats                   Rat treatment data from Mantel et al
+rats2 (rats)           Rat data from Gail et al.
+stanford2              More Stanford Heart Transplant data
+survexp.mn (survexp)   Census Data Sets for the Expected Survival
+                       and Person Years Functions
+survexp.us (survexp)   Census Data Sets for the Expected Survival
+                       and Person Years Functions
+survexp.usr (survexp)
+                       Census Data Sets for the Expected Survival
+                       and Person Years Functions
+tobin                  Tobin's Tobit data
+transplant             Liver transplant waiting list
+uspop2                 Projected US Population
+veteran                Veterans' Administration Lung Cancer study
+Data sets in package ‘tm’:
+acq                    50 Exemplary News Articles from the
+                       Reuters-21578 Data Set of Topic acq
+crude                  20 Exemplary News Articles from the
+                       Reuters-21578 Data Set of Topic crude
+</code>