Doug's R package installation list

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Learning how to get the right packages installed

You might find a needed package at the menu bar by clicking 'Packages' and then 'Load Packages.' If not then on the drop down menu click 'Install package(s)' - e.g.,

utils
help(utils)           #(see index of functions: one of them is update.packages)
update.packages 
help(ergm)
 Warning message:
 In print.help_files_with_topic("C:/PROGRA~1/R/R-26~1.2/library/ergm/chm/ergm") :
  No CHM help for 'ergm' in package 'ergm' is available: the CHM file for the package is missing
help(network)           #gives me help
help(igraph) #no help --> says "No documentation for 'igraph' in specified packages and libraries: you could try 'help.search("igraph")'
help.search("igraph")   #no help --> not installed ? tells me this might be foreign
install(igraph)  #says Error: could not find function "install" -- install from main menu "Packages"
#went to main menu 2008/02/21 abd installed igraph (not test with Peter McMahan
search()  # will show all installed packages - at this point I have
[1] ".GlobalEnv"        "package:ergm"      "package:network"   "package:stats"     "package:graphics"  "package:grDevices"
[7] "package:utils"     "package:datasets"  "package:methods"   "Autoloads"         "package:base" 
example(cohesive.blocks)  #From Peter McMahan doesn't work because I haven't installed "Digest"
help.search(digest) # no response
#so installed from Main menu packages - response
 package 'digest' successfully unpacked and MD5 sums checked
  The downloaded packages are in
    C:\Documents and Settings\User\Local Settings\Temp\RtmpcQ4U1C\downloaded_packages
    updating HTML package descriptions
> help(digest)  #No documentation for 'digest' in specified packages and libraries: you could try 'help.search("digest")'
>  help.search(digest) #Error in help.search(digest) : object "digest" not found
#The problem wasnt here tho but that I hadnt locally installed igraph:
library(igraph)   #NOW example(cohesive.blocks) works
example(cohesive.blocks)   #that all works
#installed statnet from Main Menu
#Says: also installing the dependencies ‘scatterplot3d’, ‘rgl’, ‘abind’, ‘shapes’, ‘latentnet’, ‘degreenet’, ‘sna’
search()   #results ok

My installation order

  1. Network
  2. iGraph Drawing graphs - see IGraph updates
Attaching package: 'igraph'
       The following object(s) are masked from package:network :
        %c%,
        add.edges,
        add.vertices,
        delete.edges,
        delete.vertices,
        get.edge.attribute,
        get.edges,
        get.vertex.attribute,
        is.directed,
        list.edge.attributes,
        list.vertex.attributes,
        set.edge.attribute,
        set.vertex.attribute 
  1. digest - needed to do cohesive.blocks Peter McMahan - Structural Cohesion instructions, needs iGraph - see Graph updates
  2. install.packages("ergm",contriburl="http://www.csde.washington.edu/~handcock") #for Running the simple model for complex networks with arbitrary degree distribution and clustering in R


help.search("install")

installFoundDepends(tools)                         A function to install unresolved dependencies
installed.packages(utils)                         Find Installed Packages
remove.packages(utils)                        Remove Installed Packages
update.packages(utils)                        Download Packages from CRAN-like repositories
INSTALL(utils)          Install Add-on Packages from Sources

Package commands

On Windows install.packages can also install a binary package from a local zip file by setting argument repos to NULL. Rgui.exe has a menu Packages with a GUI interface to install.packages, update.packages and library.

I need to update statnet and maybe latentnet -- hopefully will contain hetdata as well.

library() #---- tells you what packages are installed.

Default

grid                    The Grid Graphics Package
KernSmooth              Functions for kernel smoothing for Wand & Jones
                       (1995)
lattice                 Lattice Graphics
MASS                    Main Package of Venables and Ripley's MASS
methods                 Formal Methods and Classes
mgcv                    GAMs with GCV smoothness estimation and GAMMs
                       by REML/PQL
network                 Classes for Relational Data
nlme                    Linear and Nonlinear Mixed Effects Models
nnet                    Feed-forward Neural Networks and Multinomial
                       Log-Linear Models
rcompgen                Completion generator for R
rpart                   Recursive Partitioning
spatial                 Functions for Kriging and Point Pattern
                       Analysis
splines                 Regression Spline Functions and Classes
stats                   The R Stats Package
stats4                  Statistical Functions using S4 Classes
survival                Survival analysis, including penalised
                       likelihood.
tcltk                   Tcl/Tk Interface
tools                   Tools for Package Development
utils                   The R Utils Package

R Library: Introduction to bootstrapping -- exists, doesnt open

Installed

installed.packages()

          Package      LibPath                          Version  
base       "base"       "C:/PROGRA~1/R/R-26~1.2/library" "2.6.2"  
boot       "boot"       "C:/PROGRA~1/R/R-26~1.2/library" "1.2-30" 
class      "class"      "C:/PROGRA~1/R/R-26~1.2/library" "7.2-40" 
cluster    "cluster"    "C:/PROGRA~1/R/R-26~1.2/library" "1.11.9" 
codetools  "codetools"  "C:/PROGRA~1/R/R-26~1.2/library" "0.1-3"  
datasets   "datasets"   "C:/PROGRA~1/R/R-26~1.2/library" "2.6.2"  
digest     "digest"     "C:/PROGRA~1/R/R-26~1.2/library" "0.3.1"  
ergm       "ergm"       "C:/PROGRA~1/R/R-26~1.2/library" "2.0-6"  
foreign    "foreign"    "C:/PROGRA~1/R/R-26~1.2/library" "0.8-23" 
graphics   "graphics"   "C:/PROGRA~1/R/R-26~1.2/library" "2.6.2"  
grDevices  "grDevices"  "C:/PROGRA~1/R/R-26~1.2/library" "2.6.2"  
grid       "grid"       "C:/PROGRA~1/R/R-26~1.2/library" "2.6.2"  
igraph     "igraph"     "C:/PROGRA~1/R/R-26~1.2/library" "0.5"    
KernSmooth "KernSmooth" "C:/PROGRA~1/R/R-26~1.2/library" "2.22-22"
lattice    "lattice"    "C:/PROGRA~1/R/R-26~1.2/library" "0.17-4" 
MASS       "MASS"       "C:/PROGRA~1/R/R-26~1.2/library" "7.2-40" 
methods    "methods"    "C:/PROGRA~1/R/R-26~1.2/library" "2.6.2"  
mgcv       "mgcv"       "C:/PROGRA~1/R/R-26~1.2/library" "1.3-29" 
network    "network"    "C:/PROGRA~1/R/R-26~1.2/library" "1.3"    
nlme       "nlme"       "C:/PROGRA~1/R/R-26~1.2/library" "3.1-86" 
nnet       "nnet"       "C:/PROGRA~1/R/R-26~1.2/library" "7.2-40" 
rcompgen   "rcompgen"   "C:/PROGRA~1/R/R-26~1.2/library" "0.1-17" 
rpart      "rpart"      "C:/PROGRA~1/R/R-26~1.2/library" "3.1-38" 
spatial    "spatial"    "C:/PROGRA~1/R/R-26~1.2/library" "7.2-40" 
splines    "splines"    "C:/PROGRA~1/R/R-26~1.2/library" "2.6.2"  
stats      "stats"      "C:/PROGRA~1/R/R-26~1.2/library" "2.6.2"  
stats4     "stats4"     "C:/PROGRA~1/R/R-26~1.2/library" "2.6.2"  
survival   "survival"   "C:/PROGRA~1/R/R-26~1.2/library" "2.34"   
tcltk      "tcltk"      "C:/PROGRA~1/R/R-26~1.2/library" "2.6.2"  
tools      "tools"      "C:/PROGRA~1/R/R-26~1.2/library" "2.6.2"  
utils      "utils"      "C:/PROGRA~1/R/R-26~1.2/library" "2.6.2"  
Priority Bundle Contains
base       "base"        NA     NA                       
boot       "recommended" NA     NA                       
class      "recommended" "VR"   "MASS class nnet spatial"
cluster    "recommended" NA     NA                       
codetools  "recommended" NA     NA                       
datasets   "base"        NA     NA                       
digest     NA            NA     NA                       
ergm       NA            NA     NA                       
foreign    "recommended" NA     NA                       
graphics   "base"        NA     NA                       
grDevices  "base"        NA     NA                       
grid       "base"        NA     NA                       
igraph     NA            NA     NA                       
KernSmooth "recommended" NA     NA                       
lattice    "recommended" NA     NA                       
MASS       "recommended" "VR"   "MASS class nnet spatial"
methods    "base"        NA     NA                       
mgcv       "recommended" NA     NA                       
network    NA            NA     NA                       
nlme       "recommended" NA     NA                       
nnet       "recommended" "VR"   "MASS class nnet spatial"
rcompgen   "recommended" NA     NA                       
rpart      "recommended" NA     NA                       
spatial    "recommended" "VR"   "MASS class nnet spatial"
splines    "base"        NA     NA                       
stats      "base"        NA     NA                       
stats4     "base"        NA     NA                       
survival   "recommended" NA     NA                       
tcltk      "base"        NA     NA                       
tools      "base"        NA     NA                        
utils      "base"        NA     NA                       
Depends
base       NA                                               
boot       "R (>= 2.4.0), graphics, stats"                  
class      "R (>= 2.4.0), grDevices, graphics, stats, utils"
cluster    "R (>= 2.2.1), stats, graphics, utils"           
codetools  "R (>= 2.1)"                                     
datasets   NA                                               
digest     "R (>= 2.4.1)"                                   
ergm       "network"                                        
foreign    "R (>= 2.6.0), stats"                            
graphics   NA                                               
grDevices  NA                                               
grid       NA                                               
igraph     "stats"                                          
KernSmooth "R (>= 2.5.0), stats"                            
lattice    "R (>= 2.5.0)"                                   
MASS       "R (>= 2.4.0), grDevices, graphics, stats, utils"
methods    NA                                               
mgcv       "R (>= 2.3.0)"                                   
network    "R (>= 2.0.0), utils"                            
nlme       "graphics, stats, R (>= 2.4.0)"                  
nnet       "R (>= 2.4.0), grDevices, graphics, stats, utils"
rcompgen   "R (>= 2.5.0)"                                   
rpart      "R (>= 2.4.0), graphics, stats, grDevices"       
spatial    "R (>= 2.4.0), grDevices, graphics, stats, utils"
splines    NA                                               
stats      NA                                               
stats4     "methods, graphics, stats"                       
survival   "stats, utils, graphics, splines, R (>= 2.0.0)"  
tcltk      NA                                               
tools      NA                                               
utils      NA                                               
Imports
base       NA                                       
boot       NA                                       
class      NA                                       
cluster    NA                                       
codetools  NA                                       
datasets   NA                                       
digest     NA                                       
ergm       NA                                       
foreign    "methods, utils"                         
graphics   "grDevices"                              
grDevices  NA                                       
grid       "grDevices"                              
igraph     NA                                       
KernSmooth NA                                       
lattice    "grid, grDevices, graphics, stats, utils"
MASS       NA                                       
methods    "utils"                                  
mgcv       "graphics, stats"                        
network    NA                                       
nlme       "lattice"                                
nnet       NA                                       
rcompgen   "utils, methods"                         
rpart      NA                                       
spatial    NA                                       
splines    "graphics, stats"                        
stats      NA                                       
stats4     NA                                       
survival   NA                                       
tcltk      NA                                       
tools      NA                                       
utils      NA                                       
Suggests Built
base       NA                                    "2.6.2"
boot       "survival"                            "2.6.2"
class      "lattice, nlme, survival"             "2.6.2"
cluster    NA                                    "2.6.2"
codetools  NA                                    "2.6.2"
datasets   NA                                    "2.6.2"
digest     NA                                    "2.6.0"
ergm       "coda, KernSmooth, sna"               "2.6.2"
foreign    NA                                    "2.6.2"
graphics   NA                                    "2.6.2"
grDevices  NA                                    "2.6.2"
grid       "lattice"                             "2.6.2"
igraph     "stats4, rgl, tcltk, RSQLite, digest" "2.6.2"
KernSmooth "MASS"                                "2.6.2"
lattice    "grid"                                "2.6.2"
MASS       "lattice, nlme, survival"             "2.6.2"
methods    NA                                    "2.6.2"
mgcv       "nlme (>= 3.1-64), MASS (>= 7.2-2)"   "2.6.2"
network    "sna, statnet"                        "2.6.2"
nlme       NA                                    "2.6.2"
nnet       "lattice, nlme, survival"             "2.6.2"
rcompgen   NA                                    "2.6.2"
rpart      "survival"                            "2.6.2"
spatial    "lattice, nlme, survival"             "2.6.2"
splines    NA                                    "2.6.2"
stats      NA                                    "2.6.2"
stats4     NA                                    "2.6.2"
survival   NA                                    "2.6.2"
tcltk      NA                                    "2.6.2"
tools      NA                                    "2.6.2"
utils      NA                                    "2.6.2"


Old ergm package

library(ergm)

Loading required package: network Classes for Relational Data Version 1.3 created on January 31, 2008. copyright (c) 2005, Carter T. Butts, University of California-Irvine

                   Mark S. Handcock, University of Washington
                   David R. Hunter, Penn State University
                   Martina Morris, University of Washington

For citation information, type citation("network"). Type help(package="network-package") to get started.

ergm: Fit, Simulate and Diagnose Exponential-Family Models for Networks Version 2.0-6 created on February 17, 2008 copyright (c) 2003, Mark S. Handcock, University of Washington

                   David R. Hunter, Penn State University
                   Carter T. Butts, University of California-Irvine
                   Steven M. Goodreau, University of Washington
                   Martina Morris, University of Washington

Type help(package="ergm") to get started.

Based on "statnet" project software (http://statnetproject.org).

For license and citation information see http://statnetproject.org/attribution
or type citation("ergm").

New ergm and example

Running the simple model for complex networks with arbitrary degree distribution and clustering in R

From Mark S. Handcock: You need:

install.packages("ergm",contriburl="http://www.csde.washington.edu/~handcock")

examplesimmeltie.r

source("C:\\Program Files\\R\\R-2.6.2\\Handcock_Simmel\\examplesimmeltie.r") Error in library(netdata) : there is no package called 'netdata'

ERRORS:

> install.packages("ergm",contriburl="http://www.csde.washington.edu/~handcock")
Warning: package 'ergm' is in use and will not be installed
> update.packages("ergm",contriburl="http://www.csde.washington.edu/~handcock")
Warning message:
In list.files(lib) : list.files: 'ergm' is not a readable directory
> update("ergm",contriburl="http://www.csde.washington.edu/~handcock")
Error in update.default("ergm", contriburl = "http://www.csde.washington.edu/~handcock") : 
 need an object with call component
In addition: Warning message:
In object$call : $ operator is invalid for atomic vectors, returning NULL
#careful: egrm already installed:
help(ergm)        #gives me output

update.packages("ergm",contriburl="http://www.csde.washington.edu/~handcock")

install.packages("ergm",contriburl="http://www.csde.washington.edu/~handcock")

Supplem. Ref: Inference in curved exponential family models for networks. David R. Hunter. Mark S. Handcock. November 3, 2005. Abstract ...