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Facto MIneR-PCA Datos Decathlon

- Principal Component Analysis (PCA) is performed on a decathlon dataset with 10 variables like 100m, long jump, etc. using the FactoMineR package in R. - The PCA identifies 32.7% and 17.4% of the variation in the data in the first and second principal components, respectively. - The biplot of the PCA shows clustering of individual decathletes and relationships between the variables. Additional variables like competition are then included in the PCA.

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142 views19 pages

Facto MIneR-PCA Datos Decathlon

- Principal Component Analysis (PCA) is performed on a decathlon dataset with 10 variables like 100m, long jump, etc. using the FactoMineR package in R. - The PCA identifies 32.7% and 17.4% of the variation in the data in the first and second principal components, respectively. - The biplot of the PCA shows clustering of individual decathletes and relationships between the variables. Additional variables like competition are then included in the PCA.

Uploaded by

Juan
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PDF, TXT or read online on Scribd
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Principal Component Analysis (PCA) with FactoMineR

(decathlon dataset)
François Husson & Magalie Houée-Bigot

Import data (data are imported from internet)

decathlon <- read.table("http://www.agrocampus-ouest.fr/math/RforStat/decathlon.csv",


header=TRUE, sep=";", row.names=1, check.names=FALSE)

header=TRUE : indicates that the file contains the names of the variables
sep=";" : indicates the fields separator (usually “;” or “,” for csv files)
row.names=1 : indicates the column of the table which contains the row names
check.names=FALSE : indicated that the names of the variables in the data frame are unchecked
It is important to check that the import is well done

summary(decathlon)

## 100m Long jump Shot put High jump


## Min. :10.44 Min. :6.61 Min. :12.68 Min. :1.850
## 1st Qu.:10.85 1st Qu.:7.03 1st Qu.:13.88 1st Qu.:1.920
## Median :10.98 Median :7.30 Median :14.57 Median :1.950
## Mean :11.00 Mean :7.26 Mean :14.48 Mean :1.977
## 3rd Qu.:11.14 3rd Qu.:7.48 3rd Qu.:14.97 3rd Qu.:2.040
## Max. :11.64 Max. :7.96 Max. :16.36 Max. :2.150
## 400m 110m H Discus Pole vault
## Min. :46.81 Min. :13.97 Min. :37.92 Min. :4.200
## 1st Qu.:48.93 1st Qu.:14.21 1st Qu.:41.90 1st Qu.:4.500
## Median :49.40 Median :14.48 Median :44.41 Median :4.800
## Mean :49.62 Mean :14.61 Mean :44.33 Mean :4.762
## 3rd Qu.:50.30 3rd Qu.:14.98 3rd Qu.:46.07 3rd Qu.:4.920
## Max. :53.20 Max. :15.67 Max. :51.65 Max. :5.400
## Javeline 1500m Rank Points
## Min. :50.31 Min. :262.1 Min. : 1.00 Min. :7313
## 1st Qu.:55.27 1st Qu.:271.0 1st Qu.: 6.00 1st Qu.:7802
## Median :58.36 Median :278.1 Median :11.00 Median :8021
## Mean :58.32 Mean :279.0 Mean :12.12 Mean :8005
## 3rd Qu.:60.89 3rd Qu.:285.1 3rd Qu.:18.00 3rd Qu.:8122
## Max. :70.52 Max. :317.0 Max. :28.00 Max. :8893
## Competition
## Decastar:13
## OlympicG:28
##
##
##
##

1
Loading FactoMineR

library(FactoMineR)

PCA with only active elements as active

res <- PCA(decathlon[,1:10])

Individuals factor map (PCA)


4

Casarsa

YURKOV
Parkhomenko Korkizoglou
2
Dim 2 (17.37%)

Smith Zsivoczky Sebrle


Pogorelov
MARTINEAU Terek SEBRLE Macey Clay
Barras
Uldal Turi HERNU CLAY KARPOV
BOURGUIGNON Qi McMULLEN Bernard Karpov
0

Karlivans BARRASSchoenbeck
BERNARD OjaniemiHernu
Smirnov ZSIVOCZKY
Schwarzl
GomezNool Averyanov
Lorenzo WARNERS
−2

NOOL Warners

Drews
−4

−4 −2 0 2 4 6

Dim 1 (32.72%)

2
Variables factor map (PCA)
1.0

400m
400m Shot
Shot put
put
Discus
Discus
0.5

1500m
1500m
Javeline High
High jump
jump
Javeline
Dim 2 (17.37%)

110m H
100m 110m H
100m
0.0

Pole vault
Pole vault
Long
Long jump
jump
−0.5
−1.0

−1.0 −0.5 0.0 0.5 1.0

Dim 1 (32.72%)

Outputs can be summarized with the function summary.

summary(res)

Outputs are given for the first 2 dimensions (by default 3 dimensions are given).

summary(res, ncp=2)

##
## Call:
## PCA(X = decathlon[, 1:10])
##
##
## Eigenvalues
## Dim.1 Dim.2 Dim.3 Dim.4 Dim.5 Dim.6
## Variance 3.272 1.737 1.405 1.057 0.685 0.599

3
## % of var. 32.719 17.371 14.049 10.569 6.848 5.993
## Cumulative % of var. 32.719 50.090 64.140 74.708 81.556 87.548
## Dim.7 Dim.8 Dim.9 Dim.10
## Variance 0.451 0.397 0.215 0.182
## % of var. 4.512 3.969 2.148 1.822
## Cumulative % of var. 92.061 96.030 98.178 100.000
##
## Individuals (the 10 first)
## Dist Dim.1 ctr cos2 Dim.2 ctr cos2
## Sebrle | 4.843 | 4.038 12.158 0.695 | 1.366 2.619 0.080 |
## Clay | 4.647 | 3.919 11.451 0.711 | 0.837 0.984 0.032 |
## Karpov | 5.006 | 4.620 15.911 0.852 | 0.040 0.002 0.000 |
## Macey | 3.434 | 2.233 3.719 0.423 | 1.042 1.524 0.092 |
## Warners | 2.979 | 2.168 3.505 0.530 | -1.803 4.565 0.366 |
## Zsivoczky | 2.566 | 0.925 0.638 0.130 | 1.169 1.918 0.207 |
## Hernu | 1.824 | 0.889 0.589 0.238 | -0.618 0.537 0.115 |
## Nool | 3.098 | 0.295 0.065 0.009 | -1.546 3.354 0.249 |
## Bernard | 2.827 | 1.906 2.709 0.455 | -0.086 0.010 0.001 |
## Schwarzl | 1.971 | 0.081 0.005 0.002 | -1.353 2.572 0.472 |
##
## Variables
## Dim.1 ctr cos2 Dim.2 ctr cos2
## 100m | -0.775 18.344 0.600 | 0.187 2.016 0.035 |
## Long jump | 0.742 16.822 0.550 | -0.345 6.869 0.119 |
## Shot put | 0.623 11.844 0.388 | 0.598 20.607 0.358 |
## High jump | 0.572 9.998 0.327 | 0.350 7.064 0.123 |
## 400m | -0.680 14.116 0.462 | 0.569 18.666 0.324 |
## 110m H | -0.746 17.020 0.557 | 0.229 3.013 0.052 |
## Discus | 0.552 9.328 0.305 | 0.606 21.162 0.368 |
## Pole vault | 0.050 0.077 0.003 | -0.180 1.873 0.033 |
## Javeline | 0.277 2.347 0.077 | 0.317 5.784 0.100 |
## 1500m | -0.058 0.103 0.003 | 0.474 12.946 0.225 |

PCA with supplementary variables

res <- PCA(decathlon, quanti.sup=11:12, quali.sup=13)

4
Individuals factor map (PCA)
4

Casarsa

Parkhomenko
2

YURKOV
Korkizoglou
Dim 2 (17.37%)

Smith Zsivoczky Sebrle


Pogorelov SEBRLE Macey Clay
CLAY KARPOV
MARTINEAUHERNU
Turi Barras McMULLEN
Terek
Uldal Decastar OlympicG
BOURGUIGNON Bernard Karpov
0

Karlivans Qi Schoenbeck
BARRAS OjaniemiHernu
BERNARD Gomez
Smirnov Nool ZSIVOCZKY
Lorenzo AveryanovSchwarzl
WARNERS
Warners
−2

NOOL

Drews
−4

−4 −2 0 2 4 6

Dim 1 (32.72%)

5
Variables factor map (PCA)
1.0

400m
400m Discus
Discus
Shot
Shot put
put
0.5

1500m
1500m
Javeline High
High jump
jump
Javeline
Dim 2 (17.37%)

100m
100m 110m
110m H
H
Rank
Rank
0.0

Points
Points

Pole vault
Pole vault
Long
Long jump
jump
−0.5
−1.0

−1.0 −0.5 0.0 0.5 1.0

Dim 1 (32.72%)

summary(res, ncp=2, nbelements=Inf)

##
## Call:
## PCA(X = decathlon, quanti.sup = 11:12, quali.sup = 13)
##
##
## Eigenvalues
## Dim.1 Dim.2 Dim.3 Dim.4 Dim.5 Dim.6
## Variance 3.272 1.737 1.405 1.057 0.685 0.599
## % of var. 32.719 17.371 14.049 10.569 6.848 5.993
## Cumulative % of var. 32.719 50.090 64.140 74.708 81.556 87.548
## Dim.7 Dim.8 Dim.9 Dim.10
## Variance 0.451 0.397 0.215 0.182
## % of var. 4.512 3.969 2.148 1.822
## Cumulative % of var. 92.061 96.030 98.178 100.000

6
##
## Individuals
## Dist Dim.1 ctr cos2 Dim.2 ctr cos2
## Sebrle | 4.843 | 4.038 12.158 0.695 | 1.366 2.619 0.080 |
## Clay | 4.647 | 3.919 11.451 0.711 | 0.837 0.984 0.032 |
## Karpov | 5.006 | 4.620 15.911 0.852 | 0.040 0.002 0.000 |
## Macey | 3.434 | 2.233 3.719 0.423 | 1.042 1.524 0.092 |
## Warners | 2.979 | 2.168 3.505 0.530 | -1.803 4.565 0.366 |
## Zsivoczky | 2.566 | 0.925 0.638 0.130 | 1.169 1.918 0.207 |
## Hernu | 1.824 | 0.889 0.589 0.238 | -0.618 0.537 0.115 |
## Nool | 3.098 | 0.295 0.065 0.009 | -1.546 3.354 0.249 |
## Bernard | 2.827 | 1.906 2.709 0.455 | -0.086 0.010 0.001 |
## Schwarzl | 1.971 | 0.081 0.005 0.002 | -1.353 2.572 0.472 |
## Pogorelov | 2.383 | 0.540 0.217 0.051 | 0.771 0.834 0.105 |
## Schoenbeck | 1.797 | 0.114 0.010 0.004 | -0.040 0.002 0.000 |
## Barras | 2.224 | 0.002 0.000 0.000 | 0.360 0.182 0.026 |
## Smith | 3.536 | 0.870 0.565 0.061 | 1.059 1.576 0.090 |
## Averyanov | 2.521 | 0.349 0.091 0.019 | -1.559 3.411 0.382 |
## Ojaniemi | 2.338 | 0.380 0.108 0.026 | -0.772 0.838 0.109 |
## Smirnov | 2.021 | -0.485 0.175 0.057 | -1.061 1.580 0.275 |
## Qi | 1.764 | -0.434 0.141 0.061 | -0.326 0.149 0.034 |
## Drews | 3.423 | -0.249 0.046 0.005 | -3.082 13.334 0.811 |
## Parkhomenko | 3.486 | -1.069 0.853 0.094 | 2.093 6.152 0.361 |
## Terek | 3.282 | -0.682 0.347 0.043 | 0.536 0.403 0.027 |
## Gomez | 2.613 | -0.290 0.063 0.012 | -1.197 2.011 0.210 |
## Turi | 3.069 | -1.542 1.772 0.252 | 0.427 0.256 0.019 |
## Lorenzo | 3.510 | -2.409 4.324 0.471 | -1.583 3.518 0.203 |
## Karlivans | 2.704 | -1.994 2.965 0.544 | -0.294 0.122 0.012 |
## Korkizoglou | 3.975 | -0.958 0.684 0.058 | 2.066 5.995 0.270 |
## Uldal | 2.946 | -2.562 4.894 0.757 | 0.245 0.085 0.007 |
## Casarsa | 4.921 | -2.857 6.085 0.337 | 3.798 20.252 0.596 |
## SEBRLE | 2.369 | 0.792 0.467 0.112 | 0.772 0.836 0.106 |
## CLAY | 3.507 | 1.235 1.137 0.124 | 0.575 0.464 0.027 |
## KARPOV | 3.396 | 1.358 1.375 0.160 | 0.484 0.329 0.020 |
## BERNARD | 2.763 | -0.610 0.277 0.049 | -0.875 1.074 0.100 |
## YURKOV | 3.018 | -0.586 0.256 0.038 | 2.131 6.376 0.499 |
## WARNERS | 2.428 | 0.357 0.095 0.022 | -1.685 3.986 0.482 |
## ZSIVOCZKY | 2.563 | 0.272 0.055 0.011 | -1.094 1.680 0.182 |
## McMULLEN | 2.561 | 0.588 0.257 0.053 | 0.231 0.075 0.008 |
## MARTINEAU | 3.742 | -1.995 2.968 0.284 | 0.561 0.442 0.022 |
## HERNU | 2.794 | -1.546 1.782 0.306 | 0.488 0.335 0.031 |
## BARRAS | 1.952 | -1.342 1.342 0.472 | -0.311 0.136 0.025 |
## NOOL | 3.734 | -2.345 4.099 0.394 | -1.966 5.429 0.277 |
## BOURGUIGNON | 4.299 | -3.979 11.802 0.857 | 0.200 0.056 0.002 |
##
## Variables
## Dim.1 ctr cos2 Dim.2 ctr cos2
## 100m | -0.775 18.344 0.600 | 0.187 2.016 0.035 |
## Long jump | 0.742 16.822 0.550 | -0.345 6.869 0.119 |
## Shot put | 0.623 11.844 0.388 | 0.598 20.607 0.358 |
## High jump | 0.572 9.998 0.327 | 0.350 7.064 0.123 |
## 400m | -0.680 14.116 0.462 | 0.569 18.666 0.324 |
## 110m H | -0.746 17.020 0.557 | 0.229 3.013 0.052 |
## Discus | 0.552 9.328 0.305 | 0.606 21.162 0.368 |

7
## Pole vault | 0.050 0.077 0.003 | -0.180 1.873 0.033 |
## Javeline | 0.277 2.347 0.077 | 0.317 5.784 0.100 |
## 1500m | -0.058 0.103 0.003 | 0.474 12.946 0.225 |
##
## Supplementary continuous variables
## Dim.1 cos2 Dim.2 cos2
## Rank | -0.671 0.450 | 0.051 0.003 |
## Points | 0.956 0.914 | -0.017 0.000 |
##
## Supplementary categories
## Dist Dim.1 cos2 v.test Dim.2 cos2 v.test
## Decastar | 0.946 | -0.600 0.403 -1.430 | -0.038 0.002 -0.123 |
## OlympicG | 0.439 | 0.279 0.403 1.430 | 0.017 0.002 0.123 |

In order to print the results in a file:

summary(res, nbelements=Inf, file="summaryResult.txt")

Description of the dimensions

dimdesc(res)

## $Dim.1
## $Dim.1$quanti
## correlation p.value
## Points 0.9561543 2.099191e-22
## Long jump 0.7418997 2.849886e-08
## Shot put 0.6225026 1.388321e-05
## High jump 0.5719453 9.362285e-05
## Discus 0.5524665 1.802220e-04
## Rank -0.6705104 1.616348e-06
## 400m -0.6796099 1.028175e-06
## 110m H -0.7462453 2.136962e-08
## 100m -0.7747198 2.778467e-09
##
##
## $Dim.2
## $Dim.2$quanti
## correlation p.value
## Discus 0.6063134 2.650745e-05
## Shot put 0.5983033 3.603567e-05
## 400m 0.5694378 1.020941e-04
## 1500m 0.4742238 1.734405e-03
## High jump 0.3502936 2.475025e-02
## Javeline 0.3169891 4.344974e-02
## Long jump -0.3454213 2.696969e-02
##
##
## $Dim.3
## $Dim.3$quanti

8
## correlation p.value
## 1500m 0.7821428 1.554450e-09
## Pole vault 0.6917567 5.480172e-07
## Javeline -0.3896554 1.179331e-02

dimdesc(res, proba=0.2) # change the significance threshold to characterize the dimension

## $Dim.1
## $Dim.1$quanti
## correlation p.value
## Points 0.9561543 2.099191e-22
## Long jump 0.7418997 2.849886e-08
## Shot put 0.6225026 1.388321e-05
## High jump 0.5719453 9.362285e-05
## Discus 0.5524665 1.802220e-04
## Javeline 0.2771108 7.942460e-02
## Rank -0.6705104 1.616348e-06
## 400m -0.6796099 1.028175e-06
## 110m H -0.7462453 2.136962e-08
## 100m -0.7747198 2.778467e-09
##
## $Dim.1$quali
## R2 p.value
## Competition 0.05110487 0.1552515
##
## $Dim.1$category
## Estimate p.value
## OlympicG 0.4393744 0.1552515
## Decastar -0.4393744 0.1552515
##
##
## $Dim.2
## $Dim.2$quanti
## correlation p.value
## Discus 0.6063134 2.650745e-05
## Shot put 0.5983033 3.603567e-05
## 400m 0.5694378 1.020941e-04
## 1500m 0.4742238 1.734405e-03
## High jump 0.3502936 2.475025e-02
## Javeline 0.3169891 4.344974e-02
## 110m H 0.2287933 1.501925e-01
## Long jump -0.3454213 2.696969e-02
##
##
## $Dim.3
## $Dim.3$quanti
## correlation p.value
## 1500m 0.7821428 1.554450e-09
## Pole vault 0.6917567 5.480172e-07
## High jump -0.2595119 1.013160e-01
## Javeline -0.3896554 1.179331e-02

9
Graph of the individuals with a title and a smaller size for the labels

plot(res, cex=0.8, invisible="quali", title="Graph of the individuals")

Graph of the individuals


4

Casarsa

Korkizoglou
2

Parkhomenko YURKOV
Dim 2 (17.37%)

Zsivoczky Sebrle
Macey
SEBRLE Smith Clay
MARTINEAU Turi Pogorelov CLAY
UldalHERNU Terek Barras KARPOV
BOURGUIGNON McMULLEN Karpov
0

Karlivans BARRAS Schoenbeck Bernard


Qi Hernu
BERNARD Ojaniemi
Gomez ZSIVOCZKY
Smirnov
Schwarzl Nool
Lorenzo Averyanov
WARNERS
−2

Warners
NOOL

Drews
−4

−4 −2 0 2 4 6

Dim 1 (32.72%)

With many individuals and if the labels are not useful, one can suppress the labels with the argument
label=“none”.

plot(res, cex=0.8, invisible="quali", label="none", title="Graph of the individuals")

Drawing individuals according to the competition

plot(res, cex=0.8, habillage="Competition")

10
Individuals factor map (PCA)

Decastar
OlympicG
4

Casarsa

Parkhomenko
2

Korkizoglou YURKOV
Dim 2 (17.37%)

Zsivoczky Smith Sebrle


Macey
SEBRLEPogorelov Clay
MARTINEAUHERNU Terek CLAY KARPOV
McMULLEN
Uldal Turi Barras Schoenbeck
BOURGUIGNON Karpov
0

Decastar Qi OlympicG Bernard


Karlivans
BARRAS Hernu
BERNARD Ojaniemi
Smirnov
Gomez ZSIVOCZKY
Schwarzl Averyanov
Lorenzo WARNERS Nool
−2

Warners
NOOL

Drews
−4

−4 −2 0 2 4 6

Dim 1 (32.72%)

We could have written:

plot(res, cex=0.8, habillage=13)

11
Confidence ellipses around the categories

plotellipses(res)

Confidence ellipses around the categories of Competition

Decastar
OlympicG
4

Casarsa

YURKOV
2

Parkhomenko Korkizoglou
Dim 2 (17.37%)

Smith Zsivoczky Sebrle


Pogorelov SEBRLE Macey Clay
MARTINEAUHERNU CLAY KARPOV
BOURGUIGNON Barras McMULLEN
Terek
Turi Schoenbeck
Uldal OlympicG Bernard Karpov
0

KarlivansDecastar
BARRAS Qi OjaniemiHernu
BERNARDSmirnov ZSIVOCZKY
GomezNoolSchwarzl
Lorenzo WARNERS Averyanov Warners
−2

NOOL

Drews
−4

−4 −2 0 2 4 6

Dim 1 (32.72%)

If several qualitative variables are available, there will be as many graphs as qualitative variables. And on
each graph the confidence ellipses around the categories of a categorical variable.

12
Graph for dimensions 3 and 4

plot(res, choix="ind", cex=0.8, habillage=13, title="Graph of the individuals", axes=3:4)

Graph of the individuals

Decastar
OlympicG
BERNARD Nool
Sebrle
2

Parkhomenko Clay
SEBRLE
Schoenbeck
1

YURKOV
Dim 4 (10.57%)

Zsivoczky Ojaniemi
Barras Smirnov Schwarzl BOURGUIGNON
Lorenzo NOOL
OlympicG HERNU Terek
Gomez
0

Uldal Averyanov
Hernu
Qi Decastar Turi Warners
CLAY
BARRAS WARNERS
MARTINEAU Pogorelov
Macey Casarsa Drews
−1

Smith Karlivans Karpov Korkizoglou


Bernard
McMULLEN
ZSIVOCZKY
−2

KARPOV

−2 −1 0 1 2 3

Dim 3 (14.05%)

plot(res, choix="var", title="Graph of the variables", axes=3:4)

13
Graph of the variables
1.0

Javeline
Pole vault
0.5

110m H Points
Dim 4 (10.57%)

Shot put
Long jump
0.0

400m
100m Rank
High jump 1500m
Discus
−0.5
−1.0

−1.0 −0.5 0.0 0.5 1.0

Dim 3 (14.05%)

14
Selecting individuals
select="cos2 0.7" : select the individuals that have a quality of representation on the map greater than 0.7
select="cos2 5" : select the 5 individuals that have the best quality of representation on the map
select="contrib 5" : select the 5 individuals that contribute the most to the construction of the map
select=c("nom1","nom2") : select the individuals by their name

plot(res, cex=0.8, habillage=13, select="cos2 0.7")

Individuals factor map (PCA)

Decastar
OlympicG
4

Casarsa
2
Dim 2 (17.37%)

Sebrle
Clay

BOURGUIGNON Uldal Decastar Karpov


0

OlympicG
−2

Warners

Drews
−4

−4 −2 0 2 4 6

Dim 1 (32.72%)

plot(res, cex=0.8, habillage=13, select="contrib 5")

15
Individuals factor map (PCA)

Decastar
OlympicG
4

Casarsa
2
Dim 2 (17.37%)

Sebrle

Clay

BOURGUIGNON
0

Decastar OlympicG Karpov


−2
−4

−4 −2 0 2 4 6

Dim 1 (32.72%)

plot(res, cex=0.8, habillage=13, select=c("Clay","Karpov"))

16
Individuals factor map (PCA)

Decastar
OlympicG
4
2
Dim 2 (17.37%)

Clay

OlympicG
0

Decastar Karpov
−2
−4

−4 −2 0 2 4 6

Dim 1 (32.72%)

Selecting variables

plot(res, choix="var", select="contrib 5")

17
Variables factor map (PCA)
1.0

400m Discus Shot put


0.5
Dim 2 (17.37%)

100m
0.0

Long jump
−0.5
−1.0

−1.0 −0.5 0.0 0.5 1.0

Dim 1 (32.72%)

18
Graph with different options

plot(res, cex=0.8, habillage=13, select="cos2 0.7", title="Decathlon",


cex.main=1.1, cex.axis=0.9, shadow=TRUE, auto="y")

Decathlon

Decastar
OlympicG
4

Casarsa
Casarsa
2
Dim 2 (17.37%)

Sebrle
Sebrle
Clay
Clay

Uldal
Uldal OlympicG
OlympicG
BOURGUIGNON
BOURGUIGNON Karpov
Karpov
0

Decastar
Decastar
−2

Warners
Warners

Drews
Drews
−4

−4 −2 0 2 4 6

Dim 1 (32.72%)

19

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