Accessing control chart results in R? - r

I have a short R script that loads a bunch of data and plots it in an XBar chart. Using the following code, I can plot the data and view the various statistical information.
library(qcc)
tir<-read.table("data.dat", header=T,,sep="\t")
names(tir)
attach(tir)
rand <- sample(tir)
xbarchart <- qcc(rand[1:100,],type="R")
summary(xbarchart)
I want to be able to do some process capability analysis (described here(PDF) on page 5) immediately after the XBar chart is created. In order to create the analysis chart, I need to store the LCL and UCL results from the XBar chart results created before as variables. Is there any way I can do this?

I shall answer your question using the example in the ?qcc help file.
x <- c(33.75, 33.05, 34, 33.81, 33.46, 34.02, 33.68, 33.27, 33.49, 33.20,
33.62, 33.00, 33.54, 33.12, 33.84)
xbarchart <- qcc(x, type="xbar.one", std.dev = "SD")
A useful function to inspect the structure of variables and function results is str(), short for structure.
str(xbarchart)
List of 11
$ call : language qcc(data = x, type = "xbar.one", std.dev = "SD")
$ type : chr "xbar.one"
$ data.name : chr "x"
$ data : num [1:15, 1] 33.8 33 34 33.8 33.5 ...
..- attr(*, "dimnames")=List of 2
.. ..$ Group : chr [1:15] "1" "2" "3" "4" ...
.. ..$ Samples: NULL
$ statistics: Named num [1:15] 33.8 33 34 33.8 33.5 ...
..- attr(*, "names")= chr [1:15] "1" "2" "3" "4" ...
$ sizes : int [1:15] 1 1 1 1 1 1 1 1 1 1 ...
$ center : num 33.5
$ std.dev : num 0.342
$ nsigmas : num 3
$ limits : num [1, 1:2] 32.5 34.5
..- attr(*, "dimnames")=List of 2
.. ..$ : chr ""
.. ..$ : chr [1:2] "LCL" "UCL"
$ violations:List of 2
..$ beyond.limits : int(0)
..$ violating.runs: num(0)
- attr(*, "class")= chr "qcc"
You will notice the second to last element in this list is called $limits and contains the two values for LCL and UCL.
It is simple to extract this element:
limits <- xbarchart$limits
limits
LCL UCL
32.49855 34.54811
Thus LCL <- limits[1] and UCL <- limits[2]

Related

Interpreting the PCA axis Dim1 and Dim2 from CLARA plot results directly

I had a large dataset that contains more than 300,000 rows/observations and 22 variables. I used the CLARA method for the clustering and plotted the results using fviz_cluster. Using the silhouette method, I got 10 as my number of clusters and from there I applied it to my CLARA algorithm.
clara.res <- clara(df, 10, samples = 50,trace = 1,sampsize = 1000, pamLike = TRUE)
str(clara.res)
List of 10
$ sample : chr [1:1000] "100046" "100303" "10052" "100727" ...
$ medoids : num [1:10, 1:22] 0.925 0.125 0.701 0 0 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : chr [1:10] "193751" "137853" "229261" "257462" ...
.. ..$ : chr [1:22] "COD" "DMW" "HER" "SPR" ...
$ i.med : int [1:10] 104171 42062 143627 174961 300065 13836 192832 207079 185241 228575
$ clustering: Named int [1:302251] 1 1 1 2 3 4 5 3 3 3 ...
..- attr(*, "names")= chr [1:302251] "1" "10" "100" "1000" ...
$ objective : num 0.37
$ clusinfo : num [1:10, 1:4] 71811 40181 46271 10155 31309 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : NULL
.. ..$ : chr [1:4] "size" "max_diss" "av_diss" "isolation"
$ diss : 'dissimilarity' num [1:499500] 1.392 2.192 0.937 2.157 1.643 ...
..- attr(*, "Size")= int 1000
..- attr(*, "Metric")= chr "euclidean"
..- attr(*, "Labels")= chr [1:1000] "100046" "100303" "10052" "100727" ...
$ call : language clara(x = df, k = 10, samples = 50, sampsize = 1000, trace = 1, pamLike = TRUE)
$ silinfo :List of 3
..$ widths : num [1:1000, 1:3] 1 1 1 1 1 1 1 1 1 1 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : chr [1:1000] "83395" "181310" "34452" "42991" ...
.. .. ..$ : chr [1:3] "cluster" "neighbor" "sil_width"
..$ clus.avg.widths: num [1:10] 0.645 0.408 0.487 0.513 0.839 ...
..$ avg.width : num 0.612
$ data : num [1:302251, 1:22] 1 1 1 0.366 0.35 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : chr [1:302251] "1" "10" "100" "1000" ...
.. ..$ : chr [1:22] "COD" "DMW" "HER" "SPR" ...
- attr(*, "class")= chr [1:2] "clara" "partition"
For the plot:
fviz_cluster(clara.res,
palette = c(
"#004c6d",
"#00a1c1",
"#ffc334",
"#78ab63",
"#00ffff",
"#00cfe3",
"#6efa75",
"#cc0089",
"#ff9509",
"#ffb6de"
), # color palette
ellipse.type = "t",geom = "point",show.clust.cent = TRUE,repel = TRUE,pointsize = 0.5,
ggtheme = theme_classic()
)+ xlim(-7, 3) + ylim (-5, 4) + labs(title = "Plot of clusters")
The result:
I reckoned that this cluster plot is based on PCA and have been trying to figure out which variables in my original data were chosen as Dim1 and Dim2 or what these x and y-axis represent. Can somebody help me how to find out these Dim1 and Dim2 and eigenvalues/variance of the whole Dim that exist without running PCA separately?
I saw there are some other functions/packages for PCA such as get_eigenvalue in factoextra and FactomineR, but it seemed that will require me to use the PCA algorithm from the beginning? How can I integrate it directly with my CLARA results?
Also, my Dim1 only consists of 12.3% and Dim2 8.8%, does it mean that these variables are not representative enough or? considering that I would have 22 dimensions in total (from my 22 variables), I think it's alright, no? I am not sure how these percentages of Dim1 and Dim2 affect my cluster results. I was thinking to do the screeplot from my CLARA results but I also can't figure it out.
I'd appreciate any insights.

How do I extract summary of PCA as a dataframe in R using Prcomp?

res.pca = prcomp(y, scale = TRUE)
summ=summary(res.pca)
summ
Gives me the output Desired Output
I want to change this Summary in to a Data Frame,
I've Tried to use the do.call(cbind, lapply(res.pca, summary)) but it gives me the summary of Min/Max but not the one I desire.
Please See That I dont want to extract values from column names, I seek a general solution That I can use.
What you are looking for is in the "element" importance of summary(res.pca):
Example taken from Principal Components Analysis - how to get the contribution (%) of each parameter to a Prin.Comp.?:
a <- rnorm(10, 50, 20)
b <- seq(10, 100, 10)
c <- seq(88, 10, -8)
d <- rep(seq(3, 16, 3), 2)
e <- rnorm(10, 61, 27)
my_table <- data.frame(a, b, c, d, e)
res.pca <- prcomp(my_table, scale = TRUE)
summary(res.pca)$importance
# PC1 PC2 PC3 PC4 PC5
#Standard deviation 1.7882 0.9038 0.8417 0.52622 9.037e-17
#Proportion of Variance 0.6395 0.1634 0.1417 0.05538 0.000e+00
#Cumulative Proportion 0.6395 0.8029 0.9446 1.00000 1.000e+00
class(summary(res.pca)$importance)
#[1] "matrix"
N.B.:
When you want to "study" an object, it can be convenient to use str on it. Here, you can do str(summary(pca) to see where the information are and hence where you can get what you want:
str(summary(res.pca))
List of 6
$ sdev : num [1:5] 1.79 9.04e-01 8.42e-01 5.26e-01 9.04e-17
$ rotation : num [1:5, 1:5] 0.278 0.512 -0.512 0.414 -0.476 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : chr [1:5] "a" "b" "c" "d" ...
.. ..$ : chr [1:5] "PC1" "PC2" "PC3" "PC4" ...
$ center : Named num [1:5] 34.9 55 52 9 77.8
..- attr(*, "names")= chr [1:5] "a" "b" "c" "d" ...
$ scale : Named num [1:5] 22.4 30.28 24.22 4.47 26.11
..- attr(*, "names")= chr [1:5] "a" "b" "c" "d" ...
$ x : num [1:10, 1:5] -2.962 -1.403 -1.653 -0.537 1.186 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : NULL
.. ..$ : chr [1:5] "PC1" "PC2" "PC3" "PC4" ...
$ importance: num [1:3, 1:5] 1.788 0.64 0.64 0.904 0.163 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : chr [1:3] "Standard deviation" "Proportion of Variance" "Cumulative Proportion"
.. ..$ : chr [1:5] "PC1" "PC2" "PC3" "PC4" ...
- attr(*, "class")= chr "summary.prcomp"

R kohonen - Is the input data scaled and centred automatically?

I have been following an online example for R Kohonen self-organising maps (SOM) which suggested that the data should be centred and scaled before computing the SOM.
However, I've noticed the object created seems to have attributes for centre and scale, in which case am I really applying a redundant step by centring and scaling first? Example script below
# Load package
require(kohonen)
# Set data
data(iris)
# Scale and centre
dt <- scale(iris[, 1:4],center=TRUE)
# Prepare SOM
set.seed(590507)
som1 <- som(dt,
somgrid(6,6, "hexagonal"),
rlen=500,
keep.data=TRUE)
str(som1)
The output from the last line of the script is:
List of 13
$ data :List of 1
..$ : num [1:150, 1:4] -0.898 -1.139 -1.381 -1.501 -1.018 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : NULL
.. .. ..$ : chr [1:4] "Sepal.Length" "Sepal.Width" "Petal.Length"
"Petal.Width"
.. ..- attr(*, "scaled:center")= Named num [1:4] 5.84 3.06 3.76 1.2
.. .. ..- attr(*, "names")= chr [1:4] "Sepal.Length" "Sepal.Width"
"Petal.Length" "Petal.Width"
.. ..- attr(*, "scaled:scale")= Named num [1:4] 0.828 0.436 1.765 0.762
.. .. ..- attr(*, "names")= chr [1:4] "Sepal.Length" "Sepal.Width"
"Petal.Length" "Petal.Width"
$ unit.classif : num [1:150] 3 5 5 5 4 2 4 4 6 5 ...
$ distances : num [1:150] 0.0426 0.0663 0.0768 0.0744 0.1346 ...
$ grid :List of 6
..$ pts : num [1:36, 1:2] 1.5 2.5 3.5 4.5 5.5 6.5 1 2 3 4 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : NULL
.. .. ..$ : chr [1:2] "x" "y"
..$ xdim : num 6
..$ ydim : num 6
..$ topo : chr "hexagonal"
..$ neighbourhood.fct: Factor w/ 2 levels "bubble","gaussian": 1
..$ toroidal : logi FALSE
..- attr(*, "class")= chr "somgrid"
$ codes :List of 1
..$ : num [1:36, 1:4] -0.376 -0.683 -0.734 -1.158 -1.231 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : chr [1:36] "V1" "V2" "V3" "V4" ...
.. .. ..$ : chr [1:4] "Sepal.Length" "Sepal.Width" "Petal.Length"
"Petal.Width"
$ changes : num [1:500, 1] 0.0445 0.0413 0.0347 0.0373 0.0337 ...
$ alpha : num [1:2] 0.05 0.01
$ radius : Named num [1:2] 3.61 0
..- attr(*, "names")= chr [1:2] "66.66667%" ""
$ user.weights : num 1
$ distance.weights: num 1
$ whatmap : int 1
$ maxNA.fraction : int 0
$ dist.fcts : chr "sumofsquares"
- attr(*, "class")= chr "kohonen"
Note notice that in lines 7 and 10 of the output there are references to centre and scale. I would appreciate an explanation as to the process here.
Your step with scaling is not redundant because in source code there are no scaling, and attributes, that you see in 7 and 10 are attributes from train dataset.
To check this, just run and compare results of this chunk of code:
# Load package
require(kohonen)
# Set data
data(iris)
# Scale and centre
dt <- scale(iris[, 1:4],center=TRUE)
#compare train datasets
str(dt)
str(as.matrix(iris[, 1:4]))
# Prepare SOM
set.seed(590507)
som1 <- kohonen::som(dt,
kohonen::somgrid(6,6, "hexagonal"),
rlen=500,
keep.data=TRUE)
#without scaling
som2 <- kohonen::som(as.matrix(iris[, 1:4]),
kohonen::somgrid(6,6, "hexagonal"),
rlen=500,
keep.data=TRUE)
#compare results of som function
str(som1)
str(som2)

Extract statistics from Anderson-Darling test (list)

I would like to extract the p-values from the Anderson-Darling test (ad.test from package kSamples). The test result is a list of 12 containing a 2x3 matrix. The p value is part of the 2x3 matrix and is present in element 7.
When using the following code:
lapply(AD_result, "[[", 7)
I get the following subset of AD test results (first 2 of a total of 50 shown)
[[1]]
AD T.AD asympt. P-value
version 1: 1.72 0.94536 0.13169
version 2: 1.51 0.66740 0.17461
[[2]]
AD T.AD asympt. P-value
version 1: 12.299 14.624 6.9248e-07
version 2: 11.900 14.144 1.1146e-06
My question is how to extract only the p-value (e.g. from version 1) and put these 50 results into a vector
The output from str(AD_result) is:
List of 55
$ :List of 12
..$ test.name : chr "Anderson-Darling"
..$ k : int 2
..$ ns : int [1:2] 103 2905
..$ N : int 3008
..$ n.ties : int 2873
..$ sig : num 0.762
..$ ad : num [1:2, 1:3] 1.72 1.51 0.945 0.667 0.132 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : chr [1:2] "version 1:" "version 2:"
.. .. ..$ : chr [1:3] "AD" "T.AD" " asympt. P-value"
..$ warning : logi FALSE
..$ null.dist1: NULL
..$ null.dist2: NULL
..$ method : chr "asymptotic"
..$ Nsim : num 1
..- attr(*, "class")= chr "kSamples"
You could try:
unlist(lapply(AD_result, function(x) x$ad[,3]))

extract lmg from calc.relimp in R

I'm trying to extract the lmg information from the results i'm getting from calc.relimp found in the relaimpo package.
when i view my results i see
Response variable: DS[, 2]
Total response variance: 107.5848
Analysis based on 21985 observations
3 Regressors:
DS[, 33] DS[, 18] DS[, 23]
Proportion of variance explained by model: 1.39%
Metrics are not normalized (rela=FALSE).
Relative importance metrics:
lmg
DS[, 33] 0.007041436
DS[, 18] 0.001038892
DS[, 23] 0.005823708
Average coefficients for different model sizes:
1X 2Xs 3Xs
DS[, 33] -1.9229313 -2.3138967 -2.4784731
DS[, 18] -0.9155606 -0.8011497 -0.6107294
DS[, 23] 1.3592192 2.0488534 2.3525688
i would ideally like to extract 33 0.00704, 18 0.00103, 23 0.00582 so i can run more analysis on the lmg values.
Thank you for your help!
relaimpo also caters for users who are used to lists and the $ extractor, i.e. the following would also work:
library(relaimpo)
ll <- calc.relimp(swiss)
ll$lmg ## instead of ll#lmg
You can see the structure of your object calculated with calc.relimp() function using function list().
lmg values are stored in list element with the same name and can selected as object#lmg.
Here is example using data from this package
library(relaimpo)
data(swiss)
ll<-calc.relimp(swiss)
str(ll)
Formal class 'relimplm' [package "relaimpo"] with 36 slots
..# var.y : num 156
..# R2 : num 0.707
..# R2.decomp : num 0.707
..# lmg : Named num [1:5] 0.0571 0.1712 0.2601 0.1056 0.1128
.. ..- attr(*, "names")= chr [1:5] "Agriculture" "Examination" "Education" "Catholic" ...
.....
..# car.diff : num(0)
..# namen : chr [1:6] "Fertility" "Agriculture" "Examination" "Education" ...
..# nobs : int 47
..# ave.coeffs : num [1:5, 1:5] 0.194 -1.011 -0.862 0.139 1.786 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : chr [1:5] "Agriculture" "Examination" "Education" "Catholic" ...
.. .. ..$ : chr [1:5] "1X" "2Xs" "3Xs" "4Xs" ...
....
ll#lmg
Agriculture Examination Education Catholic Infant.Mortality
0.05709122 0.17117303 0.26013468 0.10557015 0.11276592

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