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vignette examples system.time(s).txt
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vignette examples system.time(s).txt
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Example 1, part 1:
suppressPackageStartupMessages(library(Rmpfr));
suppressPackageStartupMessages(library(doParallel));
library(wmpvaer);
# prepare data
data(plastic);
Y<-as.matrix(plastic[,1:3]);
rate<-matrix(data=(plastic$rate),nrow(plastic),1);
additive<-matrix(data=(plastic$additive),nrow(plastic),1);
# run wmpvaer function
system.time(wmpvaerf(Y~ (rate*additive)));
user system elapsed
0.25 0.05 14.06
Example 2, part 1
suppressPackageStartupMessages(library(Rmpfr));
suppressPackageStartupMessages(library(doParallel));
library(wmpvaer);
# prepare data
data(wolf) ;
location<-matrix(data=(wolf$location),nrow(wolf),1);
sex<-matrix(data=(wolf$sex),nrow(wolf),1);
wolf$sex<-NULL;
wolf$location<-NULL;
wolfm1<-as.matrix(wolf[,1:9]);
# run wmpvaer function
system.time(wmpvaerf(wolfm1 ~ (sex * location)));
user system elapsed
0.25 0.04 65.31
Example 3, part 1
suppressPackageStartupMessages(library(Rmpfr));
suppressPackageStartupMessages(library(doParallel));
library(wmpvaer);
# prepare data
data(wolf) ;
location<-matrix(data=(wolf$location),nrow(wolf),1);
sex<-matrix(data=(wolf$sex),nrow(wolf),1);
w<-c(wolf$palatal_L, wolf$post_p_L,wolf$zygomatic_W);
wolfm1<-matrix(data=w,nrow(wolf),3);
# run wmpvaer function
system.time(wmpvaerf(wolfm1~sex*location));
user system elapsed
0.25 0.03 15.78
Example 4, part 1
suppressPackageStartupMessages(library(Rmpfr));
suppressPackageStartupMessages(library(doParallel));
library(wmpvaer);
# prepare data
data(soils) ;
soilsfactors<-soils[,1:3];
block<-as.factor(soilsfactors[,1]);
contour<-soilsfactors[,2];
depth<-soilsfactors[,3];
soilsm1<-as.matrix(soils[,4:12]);
# run wmpvaer function
system.time(wmpvaerf(soilsm1~ (block+contour*depth)));
user system elapsed
0.19 0.03 112.06
Example 5, part 1
suppressPackageStartupMessages(library(Rmpfr));
suppressPackageStartupMessages(library(doParallel));
library(wmpvaer);
# prepare data
data(soils) ;
soilsfactors<-soils[,1:3];
block<-as.factor(soilsfactors[,1]);
contour<-soilsfactors[,2];
depth<-soilsfactors[,3];
soilsm1<-as.matrix(soils[,4:10]);
# run wmpvaer function
system.time(wmpvaerf(soilsm1~ (block+contour*depth)));
user system elapsed
0.03 0.00 79.00
Example 1, part 1 mlandrf section
suppressPackageStartupMessages(library(Rmpfr));
suppressPackageStartupMessages(library(doParallel));
library(methods);
library(wmpvaer);
# prepare data
data(eigs_plastic);
eigsm<-as.matrix(eigs_plastic)
colnames(eigsm)<-c(" "," "," ");
rownames(eigsm)<-c("rate","additive","rate:additive");
e_dfm<-16;
m_dfm<-c(1,1,1);
# run S4 object "mlandr" wrapper function
system.time(mlandrf(e_dfm,m_dfm,eigsm));
user system elapsed
0.04 0.00 13.49
Example 2, part 1 mlandrf section
suppressPackageStartupMessages(library(Rmpfr));
suppressPackageStartupMessages(library(doParallel));
library(wmpvaer);
library(methods);
# prepare data
data(plastic);
Y<-as.matrix(plastic[,1:3]);
rate<-matrix(data=(plastic$rate),nrow(plastic),1);
additive<-matrix(data=(plastic$additive),nrow(plastic),1);
# run lm( )
fit <-lm( Y ~ (rate*additive));
#compute m_df & e_df
mstats<-summary(manova(fit), test="Wilks")$stats;
fm<-as.matrix(mstats[,1]);
nrms<-nrow(fm);
m_df<-fm[1:(nrms-1),];
m_dfm<-as.matrix(fm[1:(nrms-1),]);
e_df<-fm[nrms,];
# get list of Sum of Squares matrices
ssv<-summary(manova(fit))$SS
m1<-length(ssv);
# first,derive E-Inv
em1<-ssv[[m1]]; #the last SS matrix in the ssv list is the residual matrix
e_inv<-solve(em1); # inverts the em1 matrix
# second, compute eigenvalues for an eigenvalue matrix
eigsm<-t(as.matrix(eigen((e_inv %*% ssv[[1]] ))$values))
if(m1>2){
for (i in (2:(m1-1))) {
eigenvs<-t(as.matrix(eigen((e_inv %*% ssv[[i]] ))$values))
eigsm<-rbind(eigsm,eigenvs);
}
}
colnames(eigsm)<-c(" "," "," ");
rownames(eigsm)<-rownames(m_dfm);
# run S4 object "mlandr" wrapper function
system.time(mlandrf(e_df,m_df,eigsm));
user system elapsed
0.07 0.03 13.81
Example 1: , part 2
suppressPackageStartupMessages(library(Rmpfr));
library(wmpvaer);
# prepare data
data(plastic);
plasticm<-as.matrix(plastic[,1:3]);
block_v<-c(2) # identify columns in block 1
system.time(statsBIf(plasticm,block_v));
user system elapsed
17.64 0.00 17.64
Example 2: , part 2
suppressPackageStartupMessages(library(Rmpfr));
library(wmpvaer);
# prepare data
data(wolf) ;
wolf$sex<-NULL;
wolf$location<-NULL;
wolfm1<-as.matrix(wolf[,1:9]);
block_v<-c(1,3,5,7) # identify columns in block 1
system.time(statsBIf(wolfm1,block_v));
user system elapsed
115.22 0.00 115.24
Example 3:, part 2
suppressPackageStartupMessages(library(Rmpfr));
suppressPackageStartupMessages(library(doParallel));
library(wmpvaer);
# prepare data
data(plastic);
plasticm<-as.matrix(plastic[,1:3]);
nc_at_time<-1;
system.time(statsBIncatf(plasticm,nc_at_time));
user system elapsed
0.00 0.03 21.36
Example 4: part 2
suppressPackageStartupMessages(library(Rmpfr));
suppressPackageStartupMessages(library(doParallel));
library(wmpvaer);
# prepare data
data(wolf) ;
wolf$sex<-NULL;
wolf$location<-NULL;
wolfm1<-as.matrix(wolf[,1:9]);
nc_at_time<-1;
system.time(statsBIncatf(wolfm1,nc_at_time));
user system elapsed
0.01 0.02 62.36
Example 1: part 3
suppressPackageStartupMessages(library(Rmpfr));
library(wmpvaer);
#prepare data
data(plastic)
# select obs w low additive
a1<-plastic[plastic$additive=="Low",];
# create matrix w dependent vars
low_additive<-as.matrix(a1[,1:3]);
# select obs w high additive
a2<-plastic[!(plastic$additive=="Low"),];
# create matrix w dependent vars
high_additive<-as.matrix(a2[,1:3]);
# run statsECMf with defined matrices
system.time(statsECMf(low_additive,high_additive));
user system elapsed
107.93 0.05 108.01
Example 1, part 4
suppressPackageStartupMessages(library(Rmpfr));
library(wmpvaer);
H2S_eigs<-c(1.317766, 1.004767, 0.4139226, 0.2641087, 0.1737016, 0.08137942, 0.01661141)
H2S_n_level<-11;
system.time(oneway_mss(H2S_n_level,H2S_eigs));
user system elapsed
37.62 0.00 37.62