[Rsiena-commits] r55 - in pkg/RSienaTest: . R doc man tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Feb 11 16:14:58 CET 2010
Author: ripleyrm
Date: 2010-02-11 16:14:57 +0100 (Thu, 11 Feb 2010)
New Revision: 55
Modified:
pkg/RSienaTest/DESCRIPTION
pkg/RSienaTest/R/globals.r
pkg/RSienaTest/R/siena07.r
pkg/RSienaTest/changeLog
pkg/RSienaTest/doc/s_man400.tex
pkg/RSienaTest/man/siena07.Rd
pkg/RSienaTest/tests/parallel.R
pkg/RSienaTest/tests/parallel.Rout.save
Log:
New silent option for siena07, test output altered
Modified: pkg/RSienaTest/DESCRIPTION
===================================================================
--- pkg/RSienaTest/DESCRIPTION 2010-02-11 14:31:32 UTC (rev 54)
+++ pkg/RSienaTest/DESCRIPTION 2010-02-11 15:14:57 UTC (rev 55)
@@ -4,7 +4,7 @@
Version: 1.0.10
Date: 2010-01-26
Author: Various
-Depends: R (>= 2.7.0), xtable
+Depends: R (>= 2.9.0), xtable
Imports: Matrix
Suggests: tcltk, rlecuyer, snow, network, codetools
SystemRequirements: GNU make, tcl/tk 8.5, Tktable
Modified: pkg/RSienaTest/R/globals.r
===================================================================
--- pkg/RSienaTest/R/globals.r 2010-02-11 14:31:32 UTC (rev 54)
+++ pkg/RSienaTest/R/globals.r 2010-02-11 15:14:57 UTC (rev 55)
@@ -18,18 +18,20 @@
cf <- NULL
##@Reportfun Reporting Part of global mechanism
-Reportfun<- function(x, verbose = FALSE)
+Reportfun<- function(x, verbose = FALSE, silent=FALSE)
{
x <- x
beverbose <- verbose
+ besilent <- silent
function(txt, dest, fill=FALSE, sep=" ", hdest,
open=FALSE, close=FALSE,
- type=c("a", "w"), projname="Siena" , verbose=FALSE)
+ type=c("a", "w"), projname="Siena" , verbose=FALSE, silent=FALSE)
{
if (open)
{
type <- match.arg(type)
beverbose <<- verbose
+ besilent <<- silent
if (type =='w')
{
x$outf <<- file(paste(projname, ".out", sep=""), open="w")
@@ -48,7 +50,10 @@
{
if (missing(dest) && missing(hdest))
{
- cat(txt, fill = fill, sep = sep)
+ if (!besilent)
+ {
+ cat(txt, fill = fill, sep = sep)
+ }
}
else
{
@@ -87,8 +92,9 @@
}
##@Report Globals
-Report <- local({verbose <- NULL;
- Reportfun(list(outf=outf, lf=lf, cf=cf, bof=bof), verbose)})
+Report <- local({verbose <- NULL; silent <- NULL;
+ Reportfun(list(outf=outf, lf=lf, cf=cf, bof=bof), verbose,
+ silent)})
##@UserInterrupt Siena07/GlobalFunctions Global (within siena07)
UserInterrupt <- local({A <- FALSE;function(x){if (!missing(x))A<<-x;A}})
##@EarlyEndPhase2 siena07/GlobalFunctions
Modified: pkg/RSienaTest/R/siena07.r
===================================================================
--- pkg/RSienaTest/R/siena07.r 2010-02-11 14:31:32 UTC (rev 54)
+++ pkg/RSienaTest/R/siena07.r 2010-02-11 15:14:57 UTC (rev 55)
@@ -11,8 +11,8 @@
## ****************************************************************************/
##@siena07 siena07
-siena07<- function(x, batch = FALSE, verbose = FALSE, useCluster = FALSE,
- nbrNodes = 2, initC=FALSE,
+siena07<- function(x, batch = FALSE, verbose = FALSE, silent=FALSE,
+ useCluster = FALSE, nbrNodes = 2, initC=FALSE,
clusterString=rep("localhost", nbrNodes), tt=NULL,
parallelTesting=FALSE, ...)
{
@@ -81,7 +81,7 @@
is.batch(batch)
## open the output file
- Report(open=TRUE, projname=x$projname, verbose=verbose)
+ Report(open=TRUE, projname=x$projname, verbose=verbose, silent=silent)
InitReports(seed, newseed)
## reset the globals for interrupts
Modified: pkg/RSienaTest/changeLog
===================================================================
--- pkg/RSienaTest/changeLog 2010-02-11 14:31:32 UTC (rev 54)
+++ pkg/RSienaTest/changeLog 2010-02-11 15:14:57 UTC (rev 55)
@@ -1,3 +1,10 @@
+2010-02-11 R-forge revision 55 (cf revision 52)
+
+ * R/globals.r, R/siena07.r, man/siena07.Rd:
+ new silent option with no output.
+ * tests/parallel.R, tests/parallel.Rout.save: suppress progress
+ message output and include prints of results.
+
2010-02-11 R-forge revision 54
* R/print07Report.r: source formatting
Modified: pkg/RSienaTest/doc/s_man400.tex
===================================================================
--- pkg/RSienaTest/doc/s_man400.tex 2010-02-11 14:31:32 UTC (rev 54)
+++ pkg/RSienaTest/doc/s_man400.tex 2010-02-11 15:14:57 UTC (rev 55)
@@ -6799,6 +6799,8 @@
(Programmers should consult the changeLog file on CRAN or in the R-forge
repository.)
\begin{itemize}
+\item 2010-02-11 R-forge revision 55 (RSienaTest only)
+New silent option for siena07.
\item 2010-02-11 R-forge revision 54 (RSienaTest only)
Fix to covariate behavior effect bug.
\item 2010-02-11 R-forge revision 53
Modified: pkg/RSienaTest/man/siena07.Rd
===================================================================
--- pkg/RSienaTest/man/siena07.Rd 2010-02-11 14:31:32 UTC (rev 54)
+++ pkg/RSienaTest/man/siena07.Rd 2010-02-11 15:14:57 UTC (rev 55)
@@ -9,7 +9,7 @@
data for the model must be passed in using named arguments as the \code{...}.
(See examples)}
\usage{
-siena07(x, batch=FALSE, verbose=FALSE, useCluster=FALSE,
+siena07(x, batch=FALSE, verbose=FALSE, silent=FALSE, useCluster=FALSE,
nbrNodes=2, initC=FALSE, clusterString=rep("localhost", nbrNodes),
tt=NULL, parallelTesting=FALSE, ...)
}
@@ -18,6 +18,8 @@
\item{batch}{ Desired interface: 'batch' is a small amount of printout
to the console}
\item{verbose}{Produces various output to the console if TRUE}
+ \item{silent}{Produces no output to the console if TRUE, even if batch
+ mode}
\item{useCluster}{Boolean: whether to use a cluster of processes}
\item{nbrNodes}{Number of processes to use if useCluster is TRUE}
\item{initC}{Boolean: set to TRUE if the simulation will use C
Modified: pkg/RSienaTest/tests/parallel.R
===================================================================
--- pkg/RSienaTest/tests/parallel.R 2010-02-11 14:31:32 UTC (rev 54)
+++ pkg/RSienaTest/tests/parallel.R 2010-02-11 15:14:57 UTC (rev 55)
@@ -8,13 +8,17 @@
mymodel<- model.create(findiff=TRUE, fn = simstats0c, projname='test3',
cond=FALSE, nsub=2, n3=100)
print('test3')
-ans<- siena07(mymodel, data=mydata, effects=myeff, batch=TRUE, parallelTesting=TRUE, verbose=TRUE)#,dll='../siena/src/RSiena.dll')
+ans<- siena07(mymodel, data=mydata, effects=myeff, batch=TRUE, parallelTesting=TRUE, silent=TRUE)#,dll='../siena/src/RSiena.dll')
+ans
##test4
mymodel$projname <- 'test4'
mymodel$cconditional <- TRUE
mymodel$condvarno<- 1
print('test4')
-ans<- siena07(mymodel, data=mydata, effects=myeff, batch=TRUE, parallelTesting=TRUE, verbose=TRUE)#,dll='../siena/src/RSiena.dll')
+ans<- siena07(mymodel, data=mydata, effects=myeff, batch=TRUE,
+ parallelTesting=TRUE, silent=TRUE)
+##, verbose=TRUE)#,dll='../siena/src/RSiena.dll')
+ans
##test7
mynet1 <- sienaNet(array(c(tmp3,tmp4),dim=c(32,32,2)))
mydata <- sienaDataCreate(mynet1)
@@ -22,13 +26,19 @@
mymodel<- model.create(fn = simstats0c, projname='test7', nsub=2, n3=100,
cond=FALSE)
print('test7')
-ans<- siena07(mymodel, data=mydata, effects=myeff, batch=TRUE, parallelTesting=TRUE, verbose=TRUE)#,dll='../siena/src/RSiena.dll')
+ans<- siena07(mymodel, data=mydata, effects=myeff, batch=TRUE,
+ parallelTesting=TRUE, silent=TRUE)
+##, verbose=TRUE)#,dll='../siena/src/RSiena.dll')
+ans
##test8
mymodel$projname <- 'test8'
mymodel$cconditional <- TRUE
mymodel$condvarno<- 1
print('test8')
-ans<- siena07(mymodel, data=mydata, effects=myeff, batch=TRUE, parallelTesting=TRUE, verbose=TRUE)#,dll='../siena/src/RSiena.dll')
+ans <- siena07(mymodel, data=mydata, effects=myeff, batch=TRUE,
+ parallelTesting=TRUE, silent=TRUE)
+##, verbose=TRUE)#,dll='../siena/src/RSiena.dll')
+ans
##test9
mynet1 <- sienaNet(array(c(s501, s502, s503), dim=c(50, 50, 3)))
@@ -41,7 +51,10 @@
mymodel$projname <- 'test10'
mymodel$cconditional <- TRUE
mymodel$condvarno<- 1
-ans<- siena07(mymodel, data=mydata, effects=myeff, batch=TRUE, parallelTesting=TRUE, verbose=TRUE)
+ans <- siena07(mymodel, data=mydata, effects=myeff, batch=TRUE,
+ parallelTesting=TRUE, silent=TRUE)
+##, verbose=TRUE)
+ans
##test11
print('test11')
data501 <- sienaDataCreateFromSession("s50.csv", modelName="s50")
@@ -50,5 +63,7 @@
model501e <- model.create( projname="s50e", cond=FALSE, nsub=2, n3=100 )
ans501e <- siena07(model501e, data=data501e$mydata, effects=data501e$myeff,
- parallelTesting=TRUE, batch=TRUE, verbose=TRUE)
+ parallelTesting=TRUE, batch=TRUE, silent=TRUE)
+##, verbose=TRUE)
+ans501e
## compare with outputs in parallelchecked/
Modified: pkg/RSienaTest/tests/parallel.Rout.save
===================================================================
--- pkg/RSienaTest/tests/parallel.Rout.save 2010-02-11 14:31:32 UTC (rev 54)
+++ pkg/RSienaTest/tests/parallel.Rout.save 2010-02-11 15:14:57 UTC (rev 55)
@@ -17,340 +17,51 @@
> library(RSienaTest)
Loading required package: xtable
-> print(packageDescription("RSienaTest",fields="Repository/R-Forge/Revision"))
-[1] NA
->
-> ##test3
-> mynet1 <- sienaNet(array(c(tmp3, tmp4),dim=c(32, 32, 2)))
-> mydata <- sienaDataCreate(mynet1)
-> myeff<- getEffects(mydata)
-> mymodel<- model.create(findiff=TRUE, fn = simstats0c, projname='test3',
-+ cond=FALSE, nsub=2, n3=100)
-> print('test3')
-[1] "test3"
-> ans<- siena07(mymodel, data=mydata, effects=myeff, batch=TRUE, parallelTesting=TRUE, verbose=TRUE)#,dll='../siena/src/RSiena.dll')
-
-Stochastic approximation algorithm.
-Initial value for gain parameter = 0.2.
-Start of the algorithm.
-Target function values are
- 1. 51.0000 2. 129.0000 3. 58.0000
-
-Start phase 0
-theta: 4.81 -0.56 0.00
-Current parameter values:
- 4.8094118 -0.5603907 0.0000000
-
-Start phase 1
-Phase 1 Iteration 1 Progress: 0%
-Phase 1 Iteration 2 Progress: 1%
-Phase 1 Iteration 3 Progress: 1%
-Phase 1 Iteration 4 Progress: 2%
-Phase 1 Iteration 5 Progress: 2%
-Phase 1 Iteration 6 Progress: 3%
-Phase 1 Iteration 7 Progress: 3%
-Phase 1 Iteration 8 Progress: 3%
-Phase 1 Iteration 9 Progress: 4%
-Phase 1 Iteration 10 Progress: 4%
-Phase 1 Iteration 11 Progress: 5%
-Phase 1 Iteration 12 Progress: 5%
-Phase 1 Iteration 13 Progress: 5%
-Phase 1 Iteration 14 Progress: 6%
-Phase 1 Iteration 15 Progress: 6%
-Phase 1 Iteration 16 Progress: 7%
-Time per iteration in phase 1 = 0.02533
-Average deviations NR generated statistics and targets
-after phase 1:
- 32.437500
- 8.687500
- -25.875000
-
-Diagonal values of derivative matrix :
- 18.1935 90.6250 31.2500
-dfra :
-18.193493 4.375000 1.875000
- 4.938234 90.625000 34.375000
--3.638699 50.000000 31.250000
+> print(packageDescription("RSienaTest",fields="Repository/R-Forge/Revision"))
+[1] NA
+>
+> ##test3
+> mynet1 <- sienaNet(array(c(tmp3, tmp4),dim=c(32, 32, 2)))
+> mydata <- sienaDataCreate(mynet1)
+> myeff<- getEffects(mydata)
+> mymodel<- model.create(findiff=TRUE, fn = simstats0c, projname='test3',
++ cond=FALSE, nsub=2, n3=100)
+> print('test3')
+[1] "test3"
+> ans<- siena07(mymodel, data=mydata, effects=myeff, batch=TRUE, parallelTesting=TRUE, silent=TRUE)#,dll='../siena/src/RSiena.dll')
+> ans
+Estimates, standard errors and t-statistics for convergence
-inverse of dfra :
- 0.0553503550 -0.0021363295 -0.0009710589
--0.0138912725 0.0286063298 -0.0306334864
- 0.0286709404 -0.0460188784 0.0809005098
+ Estimate Standard t statistic
+ Error
+ 1. rate basic rate parameter mynet1 3.0264 ( 0.5202 ) -0.0780
+ 2. eval outdegree (density) -1.1343 ( 0.1653 ) 0.1078
+ 3. eval reciprocity 1.7921 ( 0.2370 ) -0.0392
-Full Quasi-Newton-Raphson step after phase 1:
-1. -1.801994
-2. -0.590561
-3. 1.563076
-This step is multiplied by the factor 0.10000.
-Phase 1 achieved after 16 iterations.
-theta: 4.629 -0.619 0.156
-Current parameter values:
- 4.6292124 -0.6194468 0.1563076
-
-Phase 2 has 2 subphases.
-Each subphase can be repeated up to 4 times
-
-Start phase 2.1
-Phase 2 Subphase 1 Iteration 1 Progress: 7%
-Phase 2 Subphase 1 Iteration 2 Progress: 7%
-theta 4.244 -0.648 0.310
-ac 1.46 1.30 1.00
-Phase 2 Subphase 1 Iteration 3 Progress: 7%
-Phase 2 Subphase 1 Iteration 4 Progress: 7%
-theta 3.772 -0.694 0.540
-ac 1.459 1.480 0.836
-Phase 2 Subphase 1 Iteration 5 Progress: 7%
-Phase 2 Subphase 1 Iteration 6 Progress: 7%
-theta 3.42 -0.76 0.72
-ac 1.25 1.94 0.65
-Phase 2 Subphase 1 Iteration 7 Progress: 7%
-Phase 2 Subphase 1 Iteration 8 Progress: 8%
-theta 3.244 -0.783 0.912
-ac 0.799 0.794 0.653
-Phase 2 Subphase 1 Iteration 9 Progress: 8%
-Phase 2 Subphase 1 Iteration 10 Progress: 8%
-theta 2.969 -0.838 1.040
-ac 0.792 0.780 0.653
-Warning: an autocorrelation is positive at the end of this subphase.
-Autocorrelations:
-0.1206780
-0.1117977
-0.1982289
-
-Time per iteration in phase 2.1 = 0.004089
-theta 3.10 -1.09 1.67
-ac 0.121 0.112 0.198
-Phase 2.1 ended after 225 iterations.
-Warning. Autocorrelation criterion not satisfied.
-theta: 3.10 -1.09 1.67
-Current parameter values:
- 3.102896 -1.092006 1.668237
-
-Start phase 2.2
-Phase 2 Subphase 2 Iteration 1 Progress: 30%
-Phase 2 Subphase 2 Iteration 2 Progress: 31%
-Phase 2 Subphase 2 Iteration 3 Progress: 31%
-Phase 2 Subphase 2 Iteration 4 Progress: 31%
-Phase 2 Subphase 2 Iteration 5 Progress: 31%
-Phase 2 Subphase 2 Iteration 6 Progress: 31%
-Phase 2 Subphase 2 Iteration 7 Progress: 31%
-Phase 2 Subphase 2 Iteration 8 Progress: 31%
-Phase 2 Subphase 2 Iteration 9 Progress: 31%
-Phase 2 Subphase 2 Iteration 10 Progress: 31%
-Time per iteration in phase 2.2 = 0.003992
-theta 3.03 -1.13 1.79
-ac 0.0471 -0.0488 0.0117
-Phase 2.2 ended after 263 iterations.
-theta: 3.03 -1.13 1.79
-Current parameter values:
- 3.026403 -1.134321 1.792116
-
-Start phase 3
-Simulated values, phase 3.
-Time per iteration in phase 3 = 0.0153
-dfrac :
-12.246820 11.600000 5.800000
- 3.555528 44.000000 10.800000
- 2.287182 16.200000 23.800000
-
-inverse of dfra :
- 0.089575512 -0.018702986 -0.013342257
--0.006153542 0.028570901 -0.011465344
--0.004419669 -0.017650062 0.051103141
-
-A full Quasi-Newton-Raphson step after phase 3
-would add the following numbers to the parameters, yielding the following results:
- change new value
- 1. 0.054275 3.080679
- 2. -0.027190 -1.161511
- 3. 0.022535 1.814651
-
-unconditional moment estimation.
-Information for convergence diagnosis.
-Averages, standard deviations, and t-ratios for deviations from targets:
- 1. -0.4800 6.1521 -0.0780
- 2. 0.7600 7.0526 0.1078
- 3. -0.2200 5.6131 -0.0392
-
Total of 604 iteration steps.
- at 3
-Estimates and standard errors
-
- 1. rate: basic rate parameter mynet1 3.0264 ( 0.5202)
- 2. eval: outdegree (density) -1.1343 ( 0.1653)
- 3. eval: reciprocity 1.7921 ( 0.2370)
-
-Derivative matrix of expected statistics X by parameters:
-
- 12.246820 11.600000 5.800000
- 3.555528 44.000000 10.800000
- 2.287182 16.200000 23.800000
-
-Covariance matrix of X (correlations below the diagonal):
- 37.848 14.469 7.914
- 0.333 49.740 22.735
- 0.229 0.574 31.507
-
-
> ##test4
> mymodel$projname <- 'test4'
> mymodel$cconditional <- TRUE
> mymodel$condvarno<- 1
> print('test4')
[1] "test4"
-> ans<- siena07(mymodel, data=mydata, effects=myeff, batch=TRUE, parallelTesting=TRUE, verbose=TRUE)#,dll='../siena/src/RSiena.dll')
+> ans<- siena07(mymodel, data=mydata, effects=myeff, batch=TRUE,
++ parallelTesting=TRUE, silent=TRUE)
+> ##, verbose=TRUE)#,dll='../siena/src/RSiena.dll')
+> ans
+Estimates, standard errors and t-statistics for convergence
-Stochastic approximation algorithm.
-Initial value for gain parameter = 0.2.
-Start of the algorithm.
-Target function values are
- 1. 129.0000 2. 58.0000
-
-Start phase 0
-theta: -0.56 0.00
-Current parameter values:
--0.5603907 0.0000000
-
-Start phase 1
-Phase 1 Iteration 1 Progress: 0%
-Phase 1 Iteration 2 Progress: 1%
-Phase 1 Iteration 3 Progress: 1%
-Phase 1 Iteration 4 Progress: 1%
-Phase 1 Iteration 5 Progress: 2%
-Phase 1 Iteration 6 Progress: 2%
-Phase 1 Iteration 7 Progress: 3%
-Phase 1 Iteration 8 Progress: 3%
-Phase 1 Iteration 9 Progress: 3%
-Phase 1 Iteration 10 Progress: 4%
-Phase 1 Iteration 11 Progress: 4%
-Phase 1 Iteration 12 Progress: 4%
-Phase 1 Iteration 13 Progress: 5%
-Time per iteration in phase 1 = 0.0100
-Average deviations NR generated statistics and targets
-after phase 1:
- 2.461538
- -16.923077
-
-Diagonal values of derivative matrix :
- 47.6923 23.0769
-dfra :
-47.692308 29.230769
- 3.076923 23.076923
-
-inverse of dfra :
- 0.022833724 -0.028922717
--0.003044496 0.047189696
-
-Full Quasi-Newton-Raphson step after phase 1:
-1. -0.545667
-2. 0.806089
-This step is multiplied by the factor 0.10000.
-Phase 1 achieved after 13 iterations.
-theta: -0.6150 0.0806
-Current parameter values:
--0.6149574 0.0806089
-
-Phase 2 has 2 subphases.
-Each subphase can be repeated up to 4 times
-
-Start phase 2.1
-Phase 2 Subphase 1 Iteration 1 Progress: 5%
-Phase 2 Subphase 1 Iteration 2 Progress: 5%
-theta -0.581 0.289
-ac -2 1
-Phase 2 Subphase 1 Iteration 3 Progress: 5%
-Phase 2 Subphase 1 Iteration 4 Progress: 5%
-theta -0.665 0.514
-ac 3.333 0.882
-Phase 2 Subphase 1 Iteration 5 Progress: 5%
-Phase 2 Subphase 1 Iteration 6 Progress: 6%
-theta -0.732 0.705
-ac 2.500 0.812
-Phase 2 Subphase 1 Iteration 7 Progress: 6%
-Phase 2 Subphase 1 Iteration 8 Progress: 6%
-theta -0.732 0.982
-ac 2.526 0.825
-Phase 2 Subphase 1 Iteration 9 Progress: 6%
-Phase 2 Subphase 1 Iteration 10 Progress: 6%
-theta -0.732 1.121
-ac 2.350 0.802
-Warning: an autocorrelation is positive at the end of this subphase.
-Autocorrelations:
-0.02784048
-0.20161290
-
-Time per iteration in phase 2.1 = 0.004099
-theta -1.11 1.71
-ac 0.0278 0.2016
-Phase 2.1 ended after 222 iterations.
-Warning. Autocorrelation criterion not satisfied.
-theta: -1.11 1.71
-Current parameter values:
--1.108818 1.709165
-
-Start phase 2.2
-Phase 2 Subphase 2 Iteration 1 Progress: 32%
-Phase 2 Subphase 2 Iteration 2 Progress: 32%
-Phase 2 Subphase 2 Iteration 3 Progress: 32%
-Phase 2 Subphase 2 Iteration 4 Progress: 32%
-Phase 2 Subphase 2 Iteration 5 Progress: 33%
-Phase 2 Subphase 2 Iteration 6 Progress: 33%
-Phase 2 Subphase 2 Iteration 7 Progress: 33%
-Phase 2 Subphase 2 Iteration 8 Progress: 33%
-Phase 2 Subphase 2 Iteration 9 Progress: 33%
-Phase 2 Subphase 2 Iteration 10 Progress: 33%
-Time per iteration in phase 2.2 = 0.003818
-theta -1.10 1.70
-ac -0.072 -0.128
-Phase 2.2 ended after 55 iterations.
-theta: -1.10 1.70
-Current parameter values:
--1.095189 1.700653
-
-Start phase 3
-Simulated values, phase 3.
-Time per iteration in phase 3 = 0.0114
-dfrac :
-41.0 14.0
-22.2 22.8
-
-inverse of dfra :
- 0.03653846 -0.02243590
--0.03557692 0.06570513
-
-A full Quasi-Newton-Raphson step after phase 3
-would add the following numbers to the parameters, yielding the following results:
- change new value
- 1. -0.057269 -1.152458
- 2. 0.066288 1.766942
-
-conditional moment estimation.
-Information for convergence diagnosis.
-Averages, standard deviations, and t-ratios for deviations from targets:
- 1. 1.4200 6.4089 0.2216
- 2. -0.2400 5.7228 -0.0419
-
-Total of 390 iteration steps.
-
- at 3
-Estimates and standard errors
+ Estimate Standard t statistic
+ Error
Rate parameters:
- 0. Rate parameter 3.0428 ( 0.5235)
- 1. eval: outdegree (density) -1.0952 ( 0.1923)
- 2. eval: reciprocity 1.7007 ( 0.3089)
+ 0 Rate parameter 3.0428 ( 0.5235 )
+ 1. eval outdegree (density) -1.0952 ( 0.1923 ) 0.2216
+ 2. eval reciprocity 1.7007 ( 0.3089 ) -0.0419
-Derivative matrix of expected statistics X by parameters:
+Total of 390 iteration steps.
- 41.0 14.0
-22.2 22.8
-
-Covariance matrix of X (correlations below the diagonal):
- 41.074 20.950
- 0.571 32.750
-
-
> ##test7
> mynet1 <- sienaNet(array(c(tmp3,tmp4),dim=c(32,32,2)))
> mydata <- sienaDataCreate(mynet1)
@@ -359,307 +70,42 @@
+ cond=FALSE)
> print('test7')
[1] "test7"
-> ans<- siena07(mymodel, data=mydata, effects=myeff, batch=TRUE, parallelTesting=TRUE, verbose=TRUE)#,dll='../siena/src/RSiena.dll')
+> ans<- siena07(mymodel, data=mydata, effects=myeff, batch=TRUE,
++ parallelTesting=TRUE, silent=TRUE)
+> ##, verbose=TRUE)#,dll='../siena/src/RSiena.dll')
+> ans
+Estimates, standard errors and t-statistics for convergence
-Stochastic approximation algorithm.
-Initial value for gain parameter = 0.2.
-Start of the algorithm.
-Target function values are
- 1. 51.0000 2. 129.0000 3. 58.0000
+ Estimate Standard t statistic
+ Error
+ 1. rate basic rate parameter mynet1 3.1122 ( 0.4077 ) 0.1685
+ 2. eval outdegree (density) -1.1288 ( 0.2181 ) 0.1968
+ 3. eval reciprocity 1.7487 ( 0.4069 ) 0.1410
-Start phase 0
-theta: 4.81 -0.56 0.00
-Current parameter values:
- 4.8094118 -0.5603907 0.0000000
-
-Start phase 1
-Phase 1 Iteration 1 Progress: 0%
-Phase 1 Iteration 2 Progress: 0%
-Phase 1 Iteration 3 Progress: 0%
-Phase 1 Iteration 4 Progress: 1%
-Phase 1 Iteration 5 Progress: 1%
-Phase 1 Iteration 10 Progress: 2%
-Phase 1 Iteration 15 Progress: 2%
-Time per iteration in phase 1 = 0.005333
-Average deviations NR generated statistics and targets
-after phase 1:
- 32.437500
- 8.687500
- -25.875000
-
-Diagonal values of derivative matrix :
- 13.8076 64.3695 10.7603
-dfra :
-13.807562 25.392227 8.668270
- 3.619206 64.369544 4.601454
--3.209852 -2.343346 10.760317
-
-inverse of dfra :
- 0.069880120 -0.029161393 -0.043823515
--0.005336113 0.017523947 -0.003195145
- 0.019683480 -0.004882671 0.079165481
-
-Full Quasi-Newton-Raphson step after phase 1:
-1. -3.1473302
-2. -0.0618235
-3. 1.4523421
-This step is multiplied by the factor 0.10000.
-Phase 1 achieved after 16 iterations.
-theta: 4.495 -0.567 0.145
-Current parameter values:
- 4.4946787 -0.5665730 0.1452342
-
-Phase 2 has 2 subphases.
-Each subphase can be repeated up to 4 times
-
-Start phase 2.1
-Phase 2 Subphase 1 Iteration 1 Progress: 10%
-Phase 2 Subphase 1 Iteration 2 Progress: 10%
-theta 3.988 -0.601 0.591
-ac 1.75 1.38 1.20
-Phase 2 Subphase 1 Iteration 3 Progress: 10%
-Phase 2 Subphase 1 Iteration 4 Progress: 10%
-theta 3.466 -0.669 1.186
-ac 1.79 1.03 1.20
-Phase 2 Subphase 1 Iteration 5 Progress: 11%
-Phase 2 Subphase 1 Iteration 6 Progress: 11%
-theta 3.278 -0.753 1.112
-ac 1.431 1.069 0.634
-Phase 2 Subphase 1 Iteration 7 Progress: 11%
-Phase 2 Subphase 1 Iteration 8 Progress: 11%
-theta 2.988 -0.859 1.186
-ac 1.18 1.64 0.69
-Phase 2 Subphase 1 Iteration 9 Progress: 11%
-Phase 2 Subphase 1 Iteration 10 Progress: 11%
-theta 2.90 -0.92 1.19
-ac 1.182 1.643 0.689
-Warning: an autocorrelation is positive at the end of this subphase.
-Autocorrelations:
- 0.14682200
- 0.03195180
--0.00410509
-
-Time per iteration in phase 2.1 = 0.004089
-theta 3.12 -1.11 1.73
-ac 0.14682 0.03195 -0.00411
-Phase 2.1 ended after 225 iterations.
-Warning. Autocorrelation criterion not satisfied.
-theta: 3.12 -1.11 1.73
-Current parameter values:
- 3.118108 -1.109539 1.728403
-
-Start phase 2.2
-Phase 2 Subphase 2 Iteration 1 Progress: 44%
-Phase 2 Subphase 2 Iteration 2 Progress: 45%
-Phase 2 Subphase 2 Iteration 3 Progress: 45%
-Phase 2 Subphase 2 Iteration 4 Progress: 45%
-Phase 2 Subphase 2 Iteration 5 Progress: 45%
-Phase 2 Subphase 2 Iteration 6 Progress: 45%
-Phase 2 Subphase 2 Iteration 7 Progress: 45%
-Phase 2 Subphase 2 Iteration 8 Progress: 46%
-Phase 2 Subphase 2 Iteration 9 Progress: 46%
-Phase 2 Subphase 2 Iteration 10 Progress: 46%
-Time per iteration in phase 2.2 = 0.004286
-theta 3.11 -1.13 1.75
-ac -0.112 -0.219 -0.157
-Phase 2.2 ended after 63 iterations.
-theta: 3.11 -1.13 1.75
-Current parameter values:
- 3.112224 -1.128763 1.748732
-
-Start phase 3
-Simulated values, phase 3.
-Time per iteration in phase 3 = 0.0052
-dfrac :
-18.4056484 3.7142613 -0.3794248
- 2.1526407 49.1035790 18.8351756
- 0.8324594 30.4016978 22.7488175
-
-inverse of dfra :
- 0.055061810 -0.009712224 0.008959730
--0.003366908 0.042378759 -0.035144194
- 0.002484657 -0.056279901 0.090597437
-
-A full Quasi-Newton-Raphson step after phase 3
-would add the following numbers to the parameters, yielding the following results:
- change new value
- 1. -0.063242 3.048982
- 2. -0.023482 -1.152245
- 3. -0.003230 1.745503
-
-unconditional moment estimation.
-Information for convergence diagnosis.
-Averages, standard deviations, and t-ratios for deviations from targets:
- 1. 1.2500 7.4201 0.1685
- 2. 1.3500 6.8584 0.1968
- 3. 0.8400 5.9573 0.1410
-
Total of 404 iteration steps.
- at 3
-Estimates and standard errors
-
- 1. rate: basic rate parameter mynet1 3.1122 ( 0.4077)
- 2. eval: outdegree (density) -1.1288 ( 0.2181)
- 3. eval: reciprocity 1.7487 ( 0.4069)
-
-Derivative matrix of expected statistics X by parameters:
-
- 18.4056484 3.7142613 -0.3794248
- 2.1526407 49.1035790 18.8351756
- 0.8324594 30.4016978 22.7488175
-
-Covariance matrix of X (correlations below the diagonal):
- 55.058 7.194 4.475
- 0.141 47.038 26.976
- 0.101 0.660 35.489
-
-
> ##test8
> mymodel$projname <- 'test8'
> mymodel$cconditional <- TRUE
> mymodel$condvarno<- 1
> print('test8')
[1] "test8"
-> ans<- siena07(mymodel, data=mydata, effects=myeff, batch=TRUE, parallelTesting=TRUE, verbose=TRUE)#,dll='../siena/src/RSiena.dll')
+> ans <- siena07(mymodel, data=mydata, effects=myeff, batch=TRUE,
++ parallelTesting=TRUE, silent=TRUE)
+> ##, verbose=TRUE)#,dll='../siena/src/RSiena.dll')
+> ans
+Estimates, standard errors and t-statistics for convergence
-Stochastic approximation algorithm.
-Initial value for gain parameter = 0.2.
-Start of the algorithm.
-Target function values are
- 1. 129.0000 2. 58.0000
-
-Start phase 0
-theta: -0.56 0.00
-Current parameter values:
--0.5603907 0.0000000
-
-Start phase 1
-Phase 1 Iteration 1 Progress: 0%
-Phase 1 Iteration 2 Progress: 0%
-Phase 1 Iteration 3 Progress: 0%
-Phase 1 Iteration 4 Progress: 1%
-Phase 1 Iteration 5 Progress: 1%
-Phase 1 Iteration 10 Progress: 2%
-Time per iteration in phase 1 = 0.004167
-Average deviations NR generated statistics and targets
-after phase 1:
- 2.461538
- -18.461538
-
-Diagonal values of derivative matrix :
- 37.9097 17.1918
-dfra :
-37.90974 14.52753
-28.35958 17.19178
-
-inverse of dfra :
- 0.07170969 -0.06059666
--0.11829240 0.15812767
-
-Full Quasi-Newton-Raphson step after phase 1:
-1. -1.295224
-2. 3.210461
-This step is multiplied by the factor 0.10000.
-Phase 1 achieved after 13 iterations.
-theta: -0.690 0.321
-Current parameter values:
--0.6899131 0.3210461
-
-Phase 2 has 2 subphases.
-Each subphase can be repeated up to 4 times
-
-Start phase 2.1
-Phase 2 Subphase 1 Iteration 1 Progress: 6%
-Phase 2 Subphase 1 Iteration 2 Progress: 7%
-theta -0.679 0.577
-ac -0.25 1.38
-Phase 2 Subphase 1 Iteration 3 Progress: 7%
-Phase 2 Subphase 1 Iteration 4 Progress: 7%
-theta -0.785 0.763
-ac -0.800 0.607
-Phase 2 Subphase 1 Iteration 5 Progress: 7%
-Phase 2 Subphase 1 Iteration 6 Progress: 7%
-theta -0.817 1.135
-ac 0.111 0.718
-Phase 2 Subphase 1 Iteration 7 Progress: 7%
-Phase 2 Subphase 1 Iteration 8 Progress: 8%
-theta -0.87 1.25
-ac 0.156 0.571
-Phase 2 Subphase 1 Iteration 9 Progress: 8%
-Phase 2 Subphase 1 Iteration 10 Progress: 8%
-theta -0.922 1.368
-ac 0.109 0.535
-Time per iteration in phase 2.1 = 0.003936
-theta -1.11 1.66
-ac -0.0414 0.0000
-Phase 2.1 ended after 94 iterations.
-theta: -1.11 1.66
-Current parameter values:
--1.109191 1.657303
-
-Start phase 2.2
-Phase 2 Subphase 2 Iteration 1 Progress: 43%
-Phase 2 Subphase 2 Iteration 2 Progress: 43%
-Phase 2 Subphase 2 Iteration 3 Progress: 43%
-Phase 2 Subphase 2 Iteration 4 Progress: 43%
-Phase 2 Subphase 2 Iteration 5 Progress: 43%
-Phase 2 Subphase 2 Iteration 6 Progress: 43%
-Phase 2 Subphase 2 Iteration 7 Progress: 44%
-Phase 2 Subphase 2 Iteration 8 Progress: 44%
-Phase 2 Subphase 2 Iteration 9 Progress: 44%
-Phase 2 Subphase 2 Iteration 10 Progress: 44%
-Time per iteration in phase 2.2 = 0.004032
-theta -1.12 1.74
-ac -0.0299 -0.3052
-Phase 2.2 ended after 62 iterations.
-theta: -1.12 1.74
-Current parameter values:
--1.122423 1.739476
-
-Start phase 3
-Simulated values, phase 3.
-Time per iteration in phase 3 = 0.0041
-dfrac :
-33.189028 8.787036
-15.949957 19.294151
-
-inverse of dfra :
- 0.03857277 -0.01756700
--0.03188708 0.06635135
-
-A full Quasi-Newton-Raphson step after phase 3
-would add the following numbers to the parameters, yielding the following results:
- change new value
- 1. -0.013756 -1.136179
- 2. 0.026921 1.766396
-
-conditional moment estimation.
-Information for convergence diagnosis.
-Averages, standard deviations, and t-ratios for deviations from targets:
- 1. 0.2200 6.3494 0.0346
- 2. -0.3000 5.4781 -0.0548
-
-Total of 269 iteration steps.
-
- at 3
-Estimates and standard errors
+ Estimate Standard t statistic
+ Error
Rate parameters:
- 0. Rate parameter 3.1368 ( 0.4867)
- 1. eval: outdegree (density) -1.1224 ( 0.2040)
- 2. eval: reciprocity 1.7395 ( 0.2947)
+ 0 Rate parameter 3.1368 ( 0.4867 )
+ 1. eval outdegree (density) -1.1224 ( 0.2040 ) 0.0346
+ 2. eval reciprocity 1.7395 ( 0.2947 ) -0.0548
-Derivative matrix of expected statistics X by parameters:
+Total of 269 iteration steps.
- 33.189028 8.787036
-15.949957 19.294151
-
-Covariance matrix of X (correlations below the diagonal):
- 40.315 20.390
- 0.586 30.010
-
-
> ##test9
>
> mynet1 <- sienaNet(array(c(s501, s502, s503), dim=c(50, 50, 3)))
@@ -673,197 +119,32 @@
> mymodel$projname <- 'test10'
> mymodel$cconditional <- TRUE
> mymodel$condvarno<- 1
-> ans<- siena07(mymodel, data=mydata, effects=myeff, batch=TRUE, parallelTesting=TRUE, verbose=TRUE)
+> ans <- siena07(mymodel, data=mydata, effects=myeff, batch=TRUE,
++ parallelTesting=TRUE, silent=TRUE)
+> ##, verbose=TRUE)
+> ans
+Estimates, standard errors and t-statistics for convergence
-Stochastic approximation algorithm.
-Initial value for gain parameter = 0.2.
-Start of the algorithm.
-Target function values are
- 1. 238.00000 2. 160.00000 3. 27.00000 4. 33.00000 5. 11.66667
- 6. 121.07111
-
-Start phase 0
-theta: -1.468 0.000 0.150 0.196 0.347 0.000
-Current parameter values:
--1.4677046 0.0000000 0.1502785 0.1962158 0.3469993 0.0000000
-
-Start phase 1
-Phase 1 Iteration 1 Progress: 0%
-Phase 1 Iteration 2 Progress: 0%
-Phase 1 Iteration 3 Progress: 0%
-Phase 1 Iteration 4 Progress: 1%
-Phase 1 Iteration 5 Progress: 1%
-Phase 1 Iteration 10 Progress: 1%
-Phase 1 Iteration 15 Progress: 2%
-Phase 1 Iteration 20 Progress: 3%
-Phase 1 Iteration 25 Progress: 3%
-Time per iteration in phase 1 = 0.01125
-Average deviations NR generated statistics and targets
-after phase 1:
- 11.760000
- -109.520000
- -14.240000
- -18.040000
- -15.400000
- 19.210667
-
-Diagonal values of derivative matrix :
-184.1470 41.2023 130.8936 56.9510 17.8468 65.4993
-dfra :
-184.1469860 33.7901540 -55.2718152 -87.6656728 -8.6492102 -0.8484742
- 71.5353970 41.2023497 -85.3876923 -15.8453356 -5.3931674 0.4452829
--10.4182899 -1.8666885 130.8936185 0.0000000 -1.2121271 -11.7894165
--17.1952963 -1.7312880 0.0000000 56.9510154 -0.9785957 -8.3938226
--20.3796807 -11.0092783 37.5315279 19.3423699 17.8467508 -7.0803547
--15.8582504 1.8407313 -23.1128153 -29.1206022 1.7265029 65.4993016
-
-inverse of dfra :
- 0.0097471595 -0.0067280929 -0.0008168317 0.0131062002 0.0031559329 0.0020457072
--0.0138770754 0.0371631474 0.0172862934 -0.0118096551 0.0048679310 0.0016917950
- 0.0009758352 -0.0001930769 0.0079895533 0.0020720409 0.0008953170 0.0018143342
- 0.0031700032 -0.0011771922 0.0005407109 0.0230843148 0.0021601393 0.0033381839
--0.0011193332 0.0154670271 -0.0066450197 -0.0157777957 0.0585582149 0.0029923843
- 0.0045331185 -0.0036725600 0.0025512730 0.0149152745 0.0003600641 0.0177605731
-
-Full Quasi-Newton-Raphson step after phase 1:
-1. -0.6173812
-2. 4.3088786
-3. 0.0974626
-4. 0.2270728
-5. 2.1721665
-6. -0.4857740
-This step is multiplied by the factor 0.10000.
-Phase 1 achieved after 25 iterations.
-theta: -1.5294 0.4309 0.1600 0.2189 0.5642 -0.0486
-Current parameter values:
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/rsiena -r 55
More information about the Rsiena-commits
mailing list