Mapping spatial Distributions in R - r
My data set includes 17 stations and for each station there are 24 hourly temperature values.
I would like to map each stations value in each hour and doing so for all the hours.
What I want to do is something like the image.
The data is in the following format:
N2 N3 N4 N5 N7 N8 N10 N12 N13 N14 N17 N19 N25 N28 N29 N31 N32
1 1.300 -0.170 -0.344 2.138 0.684 0.656 0.882 0.684 1.822 1.214 2.046 2.432 0.208 0.312 0.530 0.358 0.264
2 0.888 -0.534 -0.684 1.442 -0.178 -0.060 0.430 -0.148 1.420 0.286 1.444 2.138 -0.264 -0.042 0.398 -0.196 -0.148
3 0.792 -0.564 -0.622 0.998 -0.320 1.858 -0.036 -0.118 1.476 0.110 0.964 2.048 -0.480 -0.434 0.040 -0.538 -0.322
4 0.324 -1.022 -1.128 1.380 -0.792 1.042 -0.054 -0.158 1.518 -0.102 1.354 2.386 -0.708 -0.510 0.258 -0.696 -0.566
5 0.650 -0.774 -0.982 1.124 -0.540 3.200 -0.052 -0.258 1.452 0.028 1.022 2.110 -0.714 -0.646 0.266 -0.768 -0.532
6 0.670 -0.660 -0.844 1.248 -0.550 2.868 -0.098 -0.240 1.380 -0.012 1.164 2.324 -0.498 -0.474 0.860 -0.588 -0.324
MeteoSwiss
1 -0.6
2 -1.2
3 -1.0
4 -0.8
5 -0.4
6 -0.2
where N2, N3, ...m MeteoSwiss are the stations and each row presents the station's temperature value for each hour.
id Longitude Latitude
2 7.1735 45.86880001
3 7.17254 45.86887001
4 7.171636 45.86923601
5 7.18018 45.87158001
7 7.177229 45.86923001
8 7.17524 45.86808001
10 7.179299 45.87020001
12 7.175189 45.86974001
13 7.179379 45.87081001
14 7.175509 45.86932001
17 7.18099 45.87262001
19 7.18122 45.87355001
25 7.15497 45.87058001
28 7.153399 45.86954001
29 7.152649 45.86992001
31 7.154419 45.87004001
32 7.156099 45.86983001
MeteoSwiss 7.184 45.896
I define a toy example more or less resembling your data:
vals <- matrix(rnorm(24*17), nrow=24)
cds <- data.frame(id=paste0('N', 1:17),
Longitude=rnorm(n=17, mean=7.1),
Latitude=rnorm(n=17, mean=45.8))
vals <- as.data.frame(t(vals))
names(vals) <- paste0('H', 1:24)
The sp package defines several classes and methods to store and
display spatial data. For your example you should use the
SpatialPointsDataFrame class:
library(sp)
mySP <- SpatialPointsDataFrame(coords=cds[,-1], data=data.frame(vals))
and the spplot method to display the information:
spplot(mySP, as.table=TRUE,
col.regions=bpy.colors(10),
alpha=0.8, edge.col='black')
Besides, you may find useful the spacetime package
(paper at JSS).
Related
How to remove the variable names from the diagonal and put them on axes in R function scatterplotMatrix?
I am trying to reproduce a matrix plot on a book. Here is the plot on the book:
Here are my codes:
y=read.table("T1-2.dat");
colnames(y) <- c("density","mach-dir","cross-dir");
library(car);
scatterplotMatrix(y,smooth=F, regLine=F, var.labels=colnames(y), diagonal=list(method="boxplot"));
And this is what it looks like right now:
.
How can I delete the names from the diagonal and put them on the side of the table just like the one on the book.
Thanks in advance.
Data:
> y
density mach-dir cross-dir
1 0.801 121.41 70.42
2 0.824 127.70 72.47
3 0.841 129.20 78.20
4 0.816 131.80 74.89
5 0.840 135.10 71.21
6 0.842 131.50 78.39
7 0.820 126.70 69.02
8 0.802 115.10 73.10
9 0.828 130.80 79.28
10 0.819 124.60 76.48
11 0.826 118.31 70.25
12 0.802 114.20 72.88
13 0.810 120.30 68.23
14 0.802 115.70 68.12
15 0.832 117.51 71.62
16 0.796 109.81 53.10
17 0.759 109.10 50.85
18 0.770 115.10 51.68
19 0.759 118.31 50.60
20 0.772 112.60 53.51
21 0.806 116.20 56.53
22 0.803 118.00 70.70
23 0.845 131.00 74.35
24 0.822 125.70 68.29
25 0.971 126.10 72.10
26 0.816 125.80 70.64
27 0.836 125.50 76.33
28 0.815 127.80 76.75
29 0.822 130.50 80.33
30 0.822 127.90 75.68
31 0.843 123.90 78.54
32 0.824 124.10 71.91
33 0.788 120.80 68.22
34 0.782 107.40 54.42
35 0.795 120.70 70.41
36 0.805 121.91 73.68
37 0.836 122.31 74.93
38 0.788 110.60 53.52
39 0.772 103.51 48.93
40 0.776 110.71 53.67
41 0.758 113.80 52.42
And by the way, can we also display "Max, Med, Min" and the corresponding values on the diagonal as well? Thanks.
Error trying to produce forecast errors in R
I am trying to modify some code that I have, which works, to instead work with a different function for estimating a model. The original code is the following, and it works with the ARIMA function:
S=round(0.75*length(ts_HHFCE_log))
h=1
error1.h <- c()
for (i in S:(length(ts_HHFCE_log)-h))
{
mymodel.sub <- arima(ts_HHFCE_log[1:i], order = c(0,1,3),seasonal=c(0,0,0))
predict.h <- predict(mymodel.sub,n.ahead=h)$pred[h]
error1.h <- c(error1.h,ts_HHFCE_log[i+h]-predict.h)
}
The intuition is the following: Your time series has length T. You start somewhere at the beginning of your sample, but to give enough observations to regress and obtain parameter coefficients for your alpha and betas. Let's call this t for simplicity. Then based on this, you produce a one-step ahead forecast, so for time period (t+1). Then your forecast error is the difference between the actual value for (t+1) and your forecast value based on regressing on data available until t. Then you iterate, and consider from the start to (t+1), regress, and forecast (t+2). Then you obtain a forecast error for (t+2). Then basically you keep on doing this iterative process until you reach (T-1) and produce a forecast for T. This provides with what is known as a dynamic out of sample forecast error series. You do this for different models and then ascertain using a statistical test which is the more appropriate model to use. It is a way to produce out of sample forecasting using only the data you already have.
I have modified the code to be the following:
S=round(0.75*length(ts.GDP))
h=1
error1.h <- c()
for (i in S:(length(ts.GDP)-h))
{
mymodel.sub <- lm(ts.GDP[4:i] ~ ts.GDP[3:(i-1)] + ts.GDP[2:(i-2)] + ts.GDP[1:(i-3)])
predict.h <- predict(mymodel.sub,n.ahead=h)$pred[h]
error1.h <- c(error1.h,ts.GDP[i+h]-predict.h)
}
I'm trying to do an AR(3) model. The reason I am not using the ARIMA function is because I also then want to compare these forecast errors with an ARDL model, and to my knowledge there is no simple function for the ARDL model (I'd have to use lm(), hence why I want to do the AR(3) model using the lm() function).
The model I wish to compare the AR(3) model is the following:
model_ts.GDP_1 <- lm(ts.GDP[4:123] ~ ts.GDP[3:122] + ts.GDP[2:121] + ts.GDP[1:120] + ts.CCI_AGG[3:122] + ts.CCI_AGG[2:121] + ts.CCI_AGG[1:120])
I am unsure how further to modify the code to get what I am after. Hopefully the intuition bit I explained should be clear in what I am trying to do.
The data for GDP is basically the quarterly growth rate. It is stationary. The other variable in the second model is an index I've constructed using a dynamic PCA and taken first differences so it too is stationary. But in any case, in the second model, the forecast at t is based only on lagged data of each GDP and the index I constructed. Equally, given I am simulating out of sample forecast using data I have, there is no issue with actually properly forecasting. (In time series, this technique is seen as a more robust method to compare models than simply using things such as RMSE, etc.)
Thanks!
The data I am using:
Date GDP_qoq CCI_A_qoq
31/03/1988 2.956 0.540
30/06/1988 2.126 -0.743
30/09/1988 3.442 0.977
31/12/1988 3.375 -0.677
31/03/1989 2.101 0.535
30/06/1989 1.787 -0.667
30/09/1989 2.791 0.343
31/12/1989 2.233 -0.334
31/03/1990 1.961 0.520
30/06/1990 2.758 -0.763
30/09/1990 1.879 0.438
31/12/1990 0.287 -0.708
31/03/1991 1.796 -0.078
30/06/1991 1.193 -0.735
30/09/1991 0.908 0.896
31/12/1991 1.446 0.163
31/03/1992 0.870 0.361
30/06/1992 0.215 -0.587
30/09/1992 0.262 0.238
31/12/1992 1.646 -1.436
31/03/1993 2.375 0.646
30/06/1993 0.249 -0.218
30/09/1993 1.806 0.676
31/12/1993 1.218 -0.393
31/03/1994 1.501 0.346
30/06/1994 0.879 -0.501
30/09/1994 1.123 0.731
31/12/1994 2.089 0.062
31/03/1995 0.386 0.475
30/06/1995 1.238 -0.243
30/09/1995 1.836 0.263
31/12/1995 1.236 -0.125
31/03/1996 1.926 -0.228
30/06/1996 2.109 -0.013
30/09/1996 1.312 0.196
31/12/1996 0.972 -0.015
31/03/1997 1.028 -0.001
30/06/1997 1.086 -0.016
30/09/1997 2.822 0.156
31/12/1997 -0.818 -0.062
31/03/1998 1.418 0.408
30/06/1998 0.970 -0.548
30/09/1998 0.968 0.466
31/12/1998 2.826 -0.460
31/03/1999 0.599 0.228
30/06/1999 -0.651 -0.361
30/09/1999 1.289 0.579
31/12/1999 1.600 0.196
31/03/2000 2.324 0.535
30/06/2000 1.368 -0.499
30/09/2000 0.825 0.440
31/12/2000 0.378 -0.414
31/03/2001 0.868 0.478
30/06/2001 1.801 -0.521
30/09/2001 0.319 0.068
31/12/2001 0.877 0.045
31/03/2002 1.253 0.061
30/06/2002 1.247 -0.013
30/09/2002 1.513 0.625
31/12/2002 1.756 0.125
31/03/2003 1.443 -0.088
30/06/2003 0.874 -0.138
30/09/2003 1.524 0.122
31/12/2003 1.831 -0.075
31/03/2004 0.780 0.395
30/06/2004 1.665 -0.263
30/09/2004 0.390 0.543
31/12/2004 0.886 -0.348
31/03/2005 1.372 0.500
30/06/2005 2.574 -0.066
30/09/2005 0.961 0.058
31/12/2005 2.378 -0.061
31/03/2006 1.015 0.212
30/06/2006 1.008 -0.218
30/09/2006 1.105 0.593
31/12/2006 0.943 -0.144
31/03/2007 1.566 0.111
30/06/2007 1.003 -0.125
30/09/2007 1.810 0.268
31/12/2007 1.275 -0.592
31/03/2008 1.413 0.017
30/06/2008 -0.491 -0.891
30/09/2008 -0.617 -0.836
31/12/2008 -1.410 -1.092
31/03/2009 -1.593 0.182
30/06/2009 -0.106 -0.922
30/09/2009 0.788 0.351
31/12/2009 0.247 0.414
31/03/2010 1.221 -0.329
30/06/2010 1.561 -0.322
30/09/2010 0.163 0.376
31/12/2010 0.825 -0.104
31/03/2011 2.484 0.063
30/06/2011 -0.574 -0.107
30/09/2011 0.361 -0.006
31/12/2011 0.997 -0.304
31/03/2012 0.760 0.243
30/06/2012 0.143 -0.381
30/09/2012 2.547 0.315
31/12/2012 0.308 -0.046
31/03/2013 0.679 0.221
30/06/2013 0.766 -0.170
30/09/2013 1.843 0.352
31/12/2013 0.756 0.080
31/03/2014 1.380 -0.080
30/06/2014 1.501 0.162
30/09/2014 0.876 0.017
31/12/2014 0.055 -0.251
31/03/2015 0.497 0.442
30/06/2015 1.698 -0.278
30/09/2015 0.066 0.397
31/12/2015 0.470 0.076
31/03/2016 1.581 0.247
30/06/2016 0.859 -0.342
30/09/2016 0.865 -0.011
31/12/2016 1.467 0.049
31/03/2017 1.006 0.087
30/06/2017 0.437 -0.215
30/09/2017 0.527 0.098
31/12/2017 0.900 0.218
The only thing you need to understand is how to get predictions using lm, it's not necessary to add other details (without reproducible data you're only making it more difficult). Create dummy data: set.seed(123) df<-data.frame(a=runif(10),b=runif(10),c=runif(10)) > print(df) a b c 1 0.2875775 0.95683335 0.8895393 2 0.7883051 0.45333416 0.6928034 3 0.4089769 0.67757064 0.6405068 4 0.8830174 0.57263340 0.9942698 5 0.9404673 0.10292468 0.6557058 6 0.0455565 0.89982497 0.7085305 7 0.5281055 0.24608773 0.5440660 8 0.8924190 0.04205953 0.5941420 9 0.5514350 0.32792072 0.2891597 10 0.4566147 0.95450365 0.1471136 Fit your model: model<-lm(c~a+b,data=df) Create new data: new_df<-data.frame(a=runif(1),b=runif(1)) > print(new_df) a b 1 0.9630242 0.902299 Get predictions from your new data: prediction<- predict(model,new_df) > print(prediction) 1 0.8270997 In your case, the new data new_df will be your lagged data, but you have to make the appropriate changes, OR provide reproducible data as above if you want us to go through the details of your problem. Hope this helps.
Averaging Duplicate Values in an R data frame
I have a df named ColorMap in which I am looking to average all numerical values corresponding to the same feature (further explanation below). Here is the df.
> ColorMap
KEGGnumber Colors
1 c("C00489" 0.162
2 "C06104" 0.162
3 "C02656") 0.162
4 C00163 -0.173
5 c("C02656" -0.140
6 "C00036" -0.140
7 "C00232" -0.140
8 "C01571" -0.140
9 "C00422") -0.140
10 c("C00402" 0.147
11 "C06664" 0.147
12 "C06687" 0.147
13 "C02059") 0.147
14 c("C00246" 0.069
15 "C00902") 0.069
**16 C00033 0.011
...
25 C00033 -0.073**
26 C00048 0.259
**27 c("C00803" 0.063
...
37 C00803 -0.200
38 C00803 -0.170**
39 c("C00164" -0.020
40 "C01712" -0.020
...
165 c("C00246" 0.076
166 "C00902") 0.076
**167 C00163 -0.063
...
169 C00163 0.046**
170 c("C00058" -0.208
171 "C00036") -0.208
172 C00121 -0.178
173 C00033 -0.193
174 C00163 -0.085
I would like the final to look something like this
> ColorMap
KEGGnumber Colors
1 C00489 0.162
2 C06104 0.162
3 C02656 0.162
4 C00163 -0.173
5 C02656 -0.140
6 C00036 -0.140
7 C00232 -0.140
8 C01571 -0.140
9 C00422 -0.140
10 C00402 0.147
11 C06664 0.147
12 C06687 0.147
13 C02059 0.147
14 C00246 0.069
15 C00902 0.069
**16 C00033 0.031**
26 C00048 0.259
**27 C00803 -0.100**
39 C00164 -0.020
40 C01712 -0.020
...
165 C00246 0.076
166 C00902 0.076
**167 C00163 0.0085**
170 C00058 -0.208
171 C00036 -0.208
172 C00121 -0.178
173 C00033 -0.193
174 C00163 -0.085
They do not need to be next to each other, I simply chose those for easy visualization. I would like the mean of all Colors to a single KEGGvalue. Thus, each KEGGvalue is unique, there are no duplicates.
You can clean that column using library(stringr) ColorMap$KEGGnumber <- str_extract(ColorMap$KEGGnumber, "[C][0-9]+") The argument pattern allows you to match with a regular expression, in this case, a simple one, telling you to match the capital letter C followed by any number of numbers. Afterwards, grouping using dplyr we have library(dplyr) ColorMap %>% group_by(KEGGnumber) %>% summarize(mean(Colors))
How to color the branches and tick labels in the heatmap.2?
I have done a Heat Map using the function heatmap.2 of gplots in R, but I don't have an idea of how to coloring the branches and tick labels per groups (Eg. if I cut the tree to have four gruops like in my second figure). I have checked that it is possible to color the dendrogram alone using dendextend package.
Also there is a heatmap here: selecting number of leaf nodes of dendrogram in heatmap.2 in R with a colored dendrogram, but I can't implement it in my example.
Somebody can help me with this issue?
Update
This is my Heat Map:
and I would like to have one like this with branches and tick labels in color according their four groups (this figure was edited with Illustrator to explain this question):
Here is the data and code that I have used:
Data
YEAR varA varB varC varD varE varF var1 var2 var3 var4 var5 var6 var7 var8 var9 var10 var11 var12 var13 var14 var15 var16 var17
2005 1.175290887 1.535846033 1.531113178 -1.10297075 0.0284 26 -25.5470 -24.2101 24.7900 3.3345 0.0468 0.5058 0.0087 1.7378 0.0703 2.7070 0.0183 0.0340 0.0177 0.0176 0.0240 0.0015 0.0292
2004 0.834733204 0.64917365 -0.403174087 0.116169692 0.033 50 -24.4170 -22.2574 27.3400 3.4106 0.1151 0.5822 0.0085 1.8133 0.0762 3.2604 0.0114 0.0178 0.0086 0.0086 0.0824 0.0018 0.0308
2003 1.297607635 1.224946337 0.4486378 0.227557968 0.0544 181 -24.5080 -23.2790 27.4200 3.5092 0.1052 0.5239 0.0038 0.9815 0.0681 2.7465 0.0074 0.0099 0.0025 0.0025 0.0142 0.0015 0.0298
2002 1.043780072 0.650695815 -0.337133061 0.016766696 0.0374 227 -22.6110 -21.7828 30.0200 3.6270 0.1119 0.5753 0.0106 0.7916 0.0805 3.0434 0.0069 0.0086 0.0109 0.0108 0.0313 0.0017 0.0288
2001 0.781864124 0.534881678 -0.740527443 0.171745261 0.0074 20 -23.9170 -23.2327 3.8007 0.1243 0.6216 0.0553 1.2333 0.3414 2.9606 0.0074 0.0384 0.0079 0.0082 0.0570 0.0018 0.0360
2000 0.742528229 0.667207042 -0.614740091 0.189253192 0.0257 88 -22.6420 -21.4066 30.8900 3.1693 0.0287 0.6244 0.0070 1.0256 0.1336 2.7033 0.0063 0.0102 0.0185 0.0186 0.0248 0.0015 0.0278
1999 0.701222612 1.059869033 0.772334853 0.290190993 0.0476 312 -22.4730 -21.8328 26.6600 3.0578 0.0719 0.6363 0.0032 0.7183 0.0649 2.5445 0.0066 0.0070 0.0063 0.0063 0.0095 0.0016 0.0252
1998 0.904634938 1.16455833 0.646654191 0.086214161 0.0546 332 -23.2070 -22.4399 26.1400 3.2344 0.0656 0.7096 0.0046 0.6709 0.0718 2.5656 0.0072 0.0166 0.0132 0.0131 0.0144 0.0016 0.0275
1997 0.965775183 1.362520795 0.653268963 0.007038426 0.0791 509 -23.4830 -22.4253 26.0400 3.0278 0.0438 0.7575 0.0081 0.5002 0.0657 2.5755 0.0077 0.0072 0.0083 0.0083 0.0108 0.0017 0.0252
1996 0.956113049 1.439534042 0.618648101 -0.334351083 0.0411 245 -23.4290 -23.0417 27.3000 2.9331 0.0363 0.9229 0.0050 0.4819 0.1306 2.7239 0.0072 0.0166 0.0027 0.0026 0.0174 0.0018 0.0240
1995 1.786742729 1.732091021 2.654237394 0.190377371 0.0842 646 -22.7600 -22.0212 24.2100 3.1562 0.0202 1.1728 0.0072 0.6133 0.0772 3.1313 0.0080 0.0051 0.0035 0.0035 0.0055 0.0022 0.0266
1994 0.811695681 0.670904284 0.76646691 2.163378723 0.0394 203 -22.4920 -21.3677 28.6500 3.2475 0.0132 1.7476 0.0084 0.9386 0.1880 3.8856 0.0082 0.0120 0.0129 0.0129 0.0151 0.0026 0.0280
1993 0.754876913 0.302624208 -0.927234708 -0.108263802 0.017 66 -22.3880 -21.2900 32.8400 3.5853 0.0008 1.6626 0.0221 1.2307 0.4173 3.8864 0.0079 0.0379 0.0199 0.0196 0.0225 0.0028 0.0319
1992 0.723058507 0.818965047 -0.52053294 0.384656566 0.0345 155 -21.4920 -20.8724 32.2000 3.3116 0.0068 1.5673 0.0104 0.9411 0.2245 4.0228 0.0075 0.0123 0.0308 0.0306 0.0112 0.0027 0.0287
1991 1.024225427 0.71537408 0.22672288 -0.029575009 0.0297 235 -23.4850 -22.7000 27.8400 4.4024 0.0097 1.6126 0.0698 0.6344 0.2832 4.4160 0.0108 0.0127 0.0184 0.0184 0.0122 0.0030 0.0356
1990 0.873807193 1.168599747 1.317306687 -0.335682786 0.0533 172 -23.7170 -23.5029 25.8100 4.0497 0.0170 1.5207 0.0065 0.5232 0.1734 4.6765 0.0104 0.0164 0.0131 0.0130 0.0093 0.0030 0.0332
1989 0.71498833 1.065965836 0.650281646 -0.048038841 0.0663 214 -23.5000 -23.1053 26.3500 4.1139 0.0159 1.6162 0.0096 0.5199 0.1426 4.7752 0.0106 0.0083 0.0098 0.0099 0.0076 0.0031 0.0341
1988 1.188282778 1.133076429 -0.167816244 0.448030288 0.007 64 -23.3750 -21.9900 29.3900 3.6893 0.0278 1.8392 0.0939 0.5658 1.2390 5.1103 0.0086 0.0775 0.0203 0.0202 0.0339 0.0034 0.0340
1987 0.788798159 0.276008942 -0.934596308 -0.039259431 0.012 65 -22.9540 -22.7758 28.3800 3.6375 0.0011 1.8331 0.0768 0.6187 0.6081 5.0475 0.0088 0.0554 0.0183 0.0180 0.0159 0.0038 0.0381
1986 0.757757883 1.395817348 0.455252572 -0.001274532 0.0125 47 -22.6120 -22.9011 29.7400 3.7060 0.0172 1.5279 0.0151 0.5897 0.6168 4.4917 0.0085 0.0160 0.0257 0.0256 0.0276 0.0033 0.0410
1985 1.128413419 0.321849225 -0.904189697 -0.05362552 0.0705 291 -22.7200 -21.9357 28.4100 3.5887 0.0100 1.4955 0.0022 0.3538 0.1471 4.3125 0.0091 0.0157 0.0042 0.0042 0.0041 0.0029 0.0292
1984 1.015352865 1.014625668 0.39294569 -0.267936245 0.0419 121 -23.5170 -23.1678 25.6200 4.5018 0.0353 1.8985 0.0022 0.3420 0.2620 4.9867 0.0113 0.0069 0.0058 0.0058 0.0051 0.0033 0.0356
1983 0.393985784 0.474743555 -0.368393191 -0.222845745 0.0161 49 -24.5600 -23.9514 30.5300 3.0978 0.0270 0.9467 0.0421 0.3287 0.5616 3.1256 0.0075 0.0553 0.0154 0.0155 0.0084 0.0022 0.0323
1982 0.503744901 0.524683063 -0.946225504 0.016766696 0.0118 10 -23.5970 -24.0037 30.3100 2.7288 0.0011 1.2154 0.0097 0.3022 0.8415 4.3594 0.0083 0.0254 0.0075 0.0076 0.0134 0.0029 0.0304
1981 0.872025585 1.496555573 0.658923526 -0.175816424 0.0489 343 -23.8320 -23.4716 28.1100 4.6585 0.0128 1.9205 0.0031 0.2999 0.2278 5.6588 0.0134 0.0067 0.0072 0.0071 0.0087 0.0036 0.0437
1980 2.165460373 3.419095697 3.741300435 0.250364758 0.0644 626 -24.5010 -24.0323 28.7300 3.8474 0.0122 1.4827 0.0019 0.2164 0.1859 4.3602 0.0104 0.0056 0.0050 0.0050 0.0064 0.0028 0.0337
1979 1.00201444 0.453601121 0.109577407 0.73158507 0.0281 301 -23.6070 -22.9149 27.9100 4.5765 0.0467 1.6919 0.0344 0.1940 0.3453 5.1064 0.0132 0.0162 0.0078 0.0077 0.0554 0.0032 0.0389
1978 0.829984787 0.2021646 -0.724630653 -0.178430782 0.0000
1977 0.939170906 0.192142351 -1.029656979 0.50745842 0.0068 30 -24.3510 -22.5760 29.4900 6.1029 0.3417 2.4069 0.0938 0.2824 1.3937 6.6441 0.0136 0.0609 0.0395 0.0391 0.6074 0.0045 0.0591
1976 0.741090851 0.151474404 -0.439448642 0.359471579 0.056 396 -23.7450 -22.7680 28.3700 4.3464 0.0431 1.6901 0.0234 0.2937 0.2160 5.1366 0.0113 0.0147 0.0082 0.0081 0.0317 0.0034 0.0389
1975 1.061884929 0.396763153 -1.075320241 0.433356946 0.0299 322 -23.4320 -22.9732 25.7800 5.0301 0.1740 2.2028 0.0311 0.3131 0.4254 5.8683 0.0131 0.0160 0.0182 0.0182 0.2093 0.0038 0.0443
1974 1.052548763 0.491883924 0.28198823 -0.562241025 0.0215 267 -23.3350 -22.7075 26.4100 5.3407 0.1187 2.2436 0.0231 0.2984 0.5378 5.8795 0.0127 0.0208 0.0127 0.0128 0.0821 0.0038 0.0466
1973 0.519163031 1.120525721 0.960322396 -0.84893256 0.0129 49 -23.4350 -23.0556 31.3500 6.4341 0.1105 2.4298 0.0484 0.2783 0.9249 5.8779 0.0129 0.0428 0.0124 0.0123 0.1293 0.0038 0.0499
1972 0.703961551 1.359485416 -0.306513069 -1.150818704 0.0228 247 -23.7840 -23.3257 28.3000 6.3520 0.1096 2.6043 0.0439 0.4126 0.5335 6.3320 0.0154 0.0279 0.0061 0.0062 0.0874 0.0042 0.0593
1971 0.714252707 1.621333793 -1.065184704 0.003023451 0.0274 196 -23.2140 -22.2731 31.3800 5.1332 0.0873 1.9259 0.0872 0.3598 0.4714 4.9337 0.0112 0.0234 0.0073 0.0073 0.0688 0.0034 0.0426
1970 1.022643019 1.491401283 0.088239434 -0.973528472 0.025 206 -22.9870 -21.9506 30.6200 5.0770 0.0698 2.1145 0.1825 0.3537 0.4990 5.3274 0.0129 0.0873 0.0098 0.0098 0.0316 0.0040 0.0479
1969 2.157784838 1.796722133 0.731152565 -0.193891705 0.0547 505 -24.2820 -23.9048 26.2400 5.0183 0.0637 2.2673 0.0127 0.2893 0.2420 5.1038 0.0129 0.0244 0.0069 0.0069 0.0154 0.0037 0.0440
1968 0.913026742 1.271215847 0.196849717 -1.068149218 0.0132 112 -22.9850 -21.9397 32.2300 4.0568 0.0498 2.0576 0.0965 0.2188 0.9468 5.3597 0.0080 0.0513 0.0157 0.0154 0.0507 0.0039 0.0371
1967 0.749350643 0.439194622 -1.316546028 0.306149455 0.0209 196 -23.7020 -22.8580 30.5400 4.5873 0.0703 1.9639 0.4981 0.2136 0.6086 5.1528 0.0100 0.0934 0.0103 0.0102 0.0235 0.0042 0.0415
1966 0.732785384 0.74795644 -0.681581292 1.265096245 0.0189 204 -23.3746 -22.7452 30.0600 4.8598 0.0542 1.8172 0.0437 0.2605 0.6557 5.2782 0.0131 0.0118 0.0081 0.0080 0.0203 0.0036 0.0418
1965 0.613725701 0.507953446 -1.91048851 0.825418348 0.0073 75 -24.2131 -22.5251 30.1900 5.5445 0.0691 1.9367 0.9303 0.2240 1.6461 5.5971 0.0119 0.1519 0.0318 0.0322 0.0436 0.0053 0.0467
1964 0.761469549 0.591007527 -0.715988774 -0.038091331 0.0000
1963 0.863218851 0.888615198 -0.331691877 -0.251436807 0.0123 121 -25.0690 -24.5964 27.4600 6.3232 0.0777 2.0383 0.1999 0.2465 0.9724 5.8291 0.0133 0.0349 0.0130 0.0131 0.0240 0.0044 0.0519
1962 1.194332086 1.123299319 1.400311402 -0.006545299 0.0296 250 -23.6850 -23.4588 29.3800 5.7280 0.0771 1.8900 0.0077 0.1952 0.4429 5.7635 0.0122 0.0047 0.0064 0.0063 0.0121 0.0041 0.0471
1961 0.685968021 0.396586649 -0.75076967 0.0168 201 -26.3352 -26.3457 5.5119 0.0726 1.9270 0.0180 0.1741 0.7887 5.7523 0.0121 0.0080 0.0119 0.0119 0.0208 0.0043 0.0496
1960 0.881343621 0.681729796 -0.466014418 0.0242 250 -25.5025 -25.2769 29.1200 6.5630 0.1133 2.2199 0.1176 0.2603 0.5894 6.4430 0.0159 0.0392 0.0062 0.0061 0.0308 0.0051 0.0647
1959 0.976463783 0.856497076 -0.769653776 0.0046 109 -24.9889 -25.0234 28.1000 7.4239 0.0760 3.3692 3.7315 0.4288 2.8041 7.8173 0.0178 0.6213 0.0559 0.0554 0.0902 0.0115 0.0722
1958 1.267054108 0.846073161 -0.698278256 0.0069 41 -24.5183 -25.8900 24.7200 8.4312 0.0602 3.1824 0.6086 0.4111 1.6313 7.3141 0.0165 0.0977 0.0280 0.0279 0.0575 0.0046 0.0709
1957 0.811849325 0.818326511 -1.087269506 0.0126 95 -23.4967 -23.5870 32.4900 5.6488 0.0761 2.6156 0.2207 0.4425 1.0305 7.3572 0.0159 0.0726 0.0380 0.0377 0.0437 0.0059 0.0573
1956 0.837065839 1.0007592 0.424525891 0.0115 76 -23.4403 -22.9419 32.1500 5.6087 0.0844 2.8347 0.3853 0.3125 1.1162 8.0455 0.0167 0.0696 0.0158 0.0157 0.0306 0.0058 0.0565
1955 2.044375189 1.828578166 0.0218 128 -24.9729 -24.2108 26.9000 7.4702 0.1659 4.0858 0.2619 0.3952 0.7023 9.7602 0.0222 0.0635 0.0111 0.0111 0.0338 0.0070 0.0731
1954 0.737033129 1.060103924 0.0029 8 -25.6604 -25.1068 28.9700 7.8034 0.0884 4.0907 1.8003 0.4834 5.0243 8.9409 0.0243 0.4037 0.0541 0.0529 0.2932 0.0091 0.0813
1953 0.619590578 0.647436408 0.0075 109 31.0400
1952 0.671851137 1.325676852 0.00562 41 33.1100
1951 0.894632264 1.397998867 0.00374 95 35.1800
1950 0.793048089 0.55195169 0.00186 76 -24.6750 -24.0405 37.2500 6.8214 0.1632 3.3876 1.0452 0.4622 1.7704 7.9556 0.0223 0.2316 0.0594 0.0592 0.3935 0.0066 0.0673
1949 0.70029018 1.053010492 0.0061 23 -25.2148 -26.0272 31.0900 5.8770 0.0532 3.0895 0.1231 0.4304 2.1365 7.9355 0.0165 0.1047 0.0204 0.0201 0.0735 0.0060 0.0578
1948 1.051413064 0.611568416 0.0105 86 -25.9116 -25.3761 29.6500 4.0905 0.0930 2.3578 0.7431 0.1757 1.3103 7.2889 0.0122 0.1378 0.0138 0.0136 0.0408 0.0056 0.0441
1947 0.706745895 0.323498221 0.0108 129 -26.5485 -25.8733 29.7700 5.7245 0.1294 3.2072 0.0524 0.2021 1.2550 9.1257 0.0150 0.1170 0.0155 0.0155 0.0393 0.0060 0.0588
1946 1.550656194 1.598435187 0.0164 381 -27.4603 -26.6368 28.0600 5.8659 0.1405 2.7682 0.0353 0.2424 0.3504 8.4089 0.0130 0.0437 0.0075 0.0075 0.0176 0.0057 0.0516
1945 0.877065687 0.539494611 0.0199 169 -26.7543 -26.0271 24.5700 6.2789 0.1407 2.9213 0.0309 0.3404 0.2888 7.9661 0.0131 0.0460 0.0079 0.0079 0.0185 0.0054 0.0507
1944 0.630508563 0.833959181 0.0116 20 -26.8748 -25.0203 29.4600 7.8427 0.0963 3.3664 0.8484 0.4187 0.4954 6.6868 0.0172 0.1799 0.0114 0.0114 0.0185 0.0066 0.0697
1943 0.948762137 0.552892235 0.0392 309 -24.8697 -26.9799 24.9700 7.2577 0.1020 3.2354 0.1611 0.3774 0.7706 8.0918 0.0196 0.0457 0.0060 0.0060 0.0120 0.0055 0.0699
1942 0.950673449 1.135547963 0.0148 18 -22.5094 -22.8155 28.5600 7.6926 0.1348 3.3979 0.6492 0.3347 1.3499 8.7744 0.0190 0.1142 0.0095 0.0095 0.0208 0.0072 0.0710
1941 1.185071356 1.263733805 0.0107 10 -24.3510 -22.5329 29.8200 6.2710 0.1459 3.3306 0.0560 0.3519 1.0068 9.4886 0.0179 0.0185 0.0196 0.0198 0.1190 0.0066 0.0613
1940 1.262322422 0.924262914 0.0168 133 -25.2962 -25.0828 26.2600 7.9568 0.1977 3.2329 0.0803 0.3561 3.2999 9.5743 0.0200 0.0232 0.0125 0.0125 0.0538 0.0065 0.0702
1939 1.114823086 1.548939022 0.0158 25 -25.5439 -24.3820 27.9800 4.2674 0.1624 2.3578 0.4553 0.3042 2.2656 7.3905 0.0087 0.0741 0.0100 0.0100 0.3075 0.0059 0.0413
1938 0.639727143 0.569847918 0.0115 5 -23.4696 -22.7480 5.0000 0.0751 2.6663 0.4021 0.2049 0.4997 7.9594 0.0121 0.0753 0.0093 0.0092 0.0819 0.0068 0.0485
1937 0.844930794 1.201811673 0.0269 13 -24.2616 -24.5915 25.9500 4.5623 0.0912 2.3393 0.0227 0.3172 0.2136 7.5512 0.0108 0.0093 0.0080 0.0079 0.1586 0.0049 0.0397
1936 0.603048989 0.528796963 0.0167 4 -23.4819 -23.1849 29.0200 7.1722 0.0600 2.7679 0.0126 0.2080 1.1025 7.5967 0.0175 0.0076 0.0094 0.0095 0.0608 0.0052 0.0569
1935 0.739921482 0.980951812 0.0369 402 -25.3542 -25.7692 30.5500 4.8218 0.0563 2.1489 0.0084 0.2337 1.3120 6.8994 0.0154 0.0044 0.0081 0.0081 0.0329 0.0047 0.0404
1934 0.936808475 1.350050919 0.0289 166 -26.1766 -24.8557 26.5700 4.2794 0.0626 2.1503 0.0112 0.3330 1.5501 6.8375 0.0072 0.0045 0.0248 0.0249 0.0818 0.0046 0.0362
1933 0.822006233 0.980858486 0.0187 215 -25.2825 -24.7483 27.0600 4.0682 0.0719 2.1376 0.0170 0.3042 3.6465 6.7130 0.0085 0.0074 0.0071 0.0071 0.0790 0.0047 0.0380
1932 1.128679304 1.122260931 0.0302 318 -26.5160 -24.7148 29.8100 3.4429 0.0475 2.1194 0.0111 0.2919 2.6147 7.5700 0.0093 0.0039 0.0069 0.0071 0.0472 0.0047 0.0336
1931 1.013960586 0.485124456 0.0189 13 -24.7074 -24.9517 30.7100 3.9828 0.0677 2.2806 0.0183 0.2268 3.7269 9.1548 0.0074 0.0089 0.0073 0.0073 0.0687 0.0057 0.0383
1930 1.148649752 1.029163891 0.0203 175 -26.8323 -26.0809 29.1800 3.0899 0.0697 3.5321 0.0158 0.3735 1.8765 13.0435 0.0121 0.0145 0.0103 0.0104 0.0397 0.0086 0.0506
1929 0.99387758 1.204846613 0.0376 104 -26.6411 -26.0890 28.1500 4.2733 0.0412 2.6675 0.0078 0.2893 0.1528 9.4824 0.0094 0.0112 0.0075 0.0075 0.0083 0.0064 0.0354
1928 0.905609551 0.772378969 0.0331 233 -25.8461 -26.2246 32.3600 5.8361 0.0440 2.8293 0.0095 0.2231 0.1736 8.7255 0.0186 0.0087 0.0074 0.0075 0.0091 0.0063 0.0476
1927 0.85672722 0.215215241 0.0171 152 -25.9555 -25.9299 28.1500 8.1915 0.1054 2.9585 0.0298 0.2692 0.3361 7.8459 0.0158 0.0135 0.0113 0.0112 0.2221 0.0057 0.0717
1926 0.932350398 0.425876672 0.0165 132 -27.7161 -26.9161 22.1900 7.5864 0.0875 3.2115 0.0256 0.2381 0.3483 8.4859 0.0152 0.0123 0.0127 0.0127 0.1256 0.0061 0.0618
1925 0.809324244 0.603492919 0.0174 48 -24.5765 -24.8562 28.9600 6.3520 0.0226 2.7524 0.0175 0.2355 0.3303 7.8838 0.0120 0.0130 0.0096 0.0096 0.0174 0.0058 0.0534
1924 1.735408827 1.991986688 0.027 253 -25.9985 -24.8571 31.4900 6.1000 0.1097 2.6762 0.0284 0.2676 2.2755 7.9132 0.0158 0.0089 0.0107 0.0106 0.2161 0.0054 0.0668
1923 0.787925712 1.573404755 0.0203 150 -24.6288 -25.1568 29.9300 5.6860 0.0967 2.5993 0.0231 0.2137 3.8395 9.0800 0.0128 0.0101 0.0098 0.0098 0.1010 0.0060 0.0536
1922 0.799163043 0.0208 334 -24.4215 -24.3729 28.8900 5.3341 0.0924 2.6394 0.0133 0.2462 3.8226 7.8138 0.0114 0.0069 0.0149 0.0150 0.0729 0.0054 0.0497
1921 0.77243578 0.0226 443 -23.4421 -23.8877 29.4300 6.1139 0.0805 3.2761 0.0156 0.2522 4.2754 10.1551 0.0128 0.0040 0.0195 0.0197 0.1065 0.0067 0.0623
1920 0.787155209 0.0385 278 -24.2587 -23.9798 29.2400 5.9896 0.0727 3.0804 0.0110 0.2266 3.7709 9.9680 0.0133 0.0038 0.0268 0.0269 0.0544 0.0067 0.0567
1919 0.836725864 0.0276 341 -24.7950 -24.8537 27.3900 6.5779 0.0798 3.1646 0.0126 0.2276 4.7733 10.8125 0.0149 0.0052 0.0154 0.0154 0.0604 0.0073 0.0629
1918 0.838156697 0.0058 392 -25.9260 -24.5236 30.6200 6.0259 0.0939 3.5283 0.0448 0.4603 6.5956 12.5834 0.0114 0.0238 0.0598 0.0605 0.2763 0.0095 0.0823
1917 0.966249549 0.0208 58 -25.5352 -24.7604 28.3400 5.8498 0.0925 2.8573 0.0143 0.2275 3.3143 9.2387 0.0118 0.0090 0.0238 0.0239 0.0445 0.0065 0.0535
1916 1.352618036 0.0152 567 -24.0530 -23.6626 27.6400 6.3964 0.0549 3.1876 0.0166 0.2559 6.1909 11.3232 0.0119 0.0088 0.0303 0.0302 0.0696 0.0078 0.0620
1915 0.56838431 0.0354 153 -23.6817 -23.9420 29.7600 5.9449 0.0494 3.1254 0.0118 0.2632 3.6600 10.8684 0.0125 0.0096 0.0234 0.0234 0.0455 0.0075 0.0580
1914 1.653698335 0.0096 355 -25.3230 -25.5543 30.4100 6.1042 0.0305 3.3067 0.0310 0.3592 11.7772 11.9468 0.0103 0.0189 0.0230 0.0230 0.0825 0.0083 0.0603
1913 0.673176646 0.018 479 -25.2734 -25.9128 31.0800 6.1167 0.1001 3.5575 0.0227 0.3392 8.3156 12.0722 0.0131 0.0069 0.0294 0.0291 0.0844 0.0083 0.0681
1912 1.168563731 0.0026 57 -25.4911 -25.0984 30.9900 8.2413 0.1793 5.4744 0.1320 0.7542 53.7132 17.0050 0.0120 0.1196 0.0562 0.0570 0.3436 0.0120 0.1118
1911 1.458277945 0.0119 43 -25.0742 -25.1744 29.2000 8.5525 0.0326 4.2884 0.0276 0.4920 13.5179 14.3376 0.0117 0.0126 0.0152 0.0153 0.0453 0.0096 0.0817
1910 1.653698335 0.0096 355 -25.3230 -25.5543 30.4100 6.1042 0.0305 3.3067 0.0310 0.3592 11.7772 11.9468 0.0103 0.0189 0.0230 0.0230 0.0825 0.0083 0.0603
Code
# reading data
test <- read.delim("clipboard", sep="")
rnames <- test[,1]
test <- data.matrix(test[,2:ncol(test)]) # to matrix
rownames(test) <- rnames
test <- scale(test, center=T, scale=T) # data standarization
test <- t(test) # transpose
## Creating a color palette & color breaks
my_palette <- colorRampPalette(c("forestgreen", "yellow", "red"))(n = 299)
col_breaks = c(seq(-1,-0.5,length=100), # forestgreen
seq(-0.5,0.5,length=100), # yellow
seq(0.5,1,length=100)) # red
# distance & hierarchical clustering
distance= dist(test, method ="euclidean")
hcluster = hclust(distance, method ="ward.D")
# Creating Heat Map
heatmap.2(test,
main = paste( "test"),
trace="none",
margins =c(5,7),
col=my_palette,
breaks=col_breaks,
dendrogram="row",
Rowv = as.dendrogram(hcluster),
Colv = "NA",
key.xlab = "Concentration (index)",
cexRow =0.6,
cexCol = 0.8,
na.rm = TRUE )
Solution: use the color_branches function from the dendextend package (or the set function, with the "branches_k_color", "k", and "value" parameters ).
First we need to get the data into R and create the relevant objects ready (this part is the same as the code in the question):
test <- read.delim("clipboard", sep="")
rnames <- test[,1]
test <- data.matrix(test[,2:ncol(test)]) # to matrix
rownames(test) <- rnames
test <- scale(test, center=T, scale=T) # data standarization
test <- t(test) # transpose
## Creating a color palette & color breaks
my_palette <- colorRampPalette(c("forestgreen", "yellow", "red"))(n = 299)
col_breaks = c(seq(-1,-0.5,length=100), # forestgreen
seq(-0.5,0.5,length=100), # yellow
seq(0.5,1,length=100)) # red
# distance & hierarchical clustering
distance= dist(test, method ="euclidean")
hcluster = hclust(distance, method ="ward.D")
Next, we get the dendrogram and the heatmap ready:
dend1 <- as.dendrogram(hcluster)
# Get the dendextend package
if(!require(dendextend)) install.packages("dendextend")
library(dendextend)
# get some colors
cols_branches <- c("darkred", "forestgreen", "orange", "blue")
# Set the colors of 4 branches
dend1 <- color_branches(dend1, k = 4, col = cols_branches)
# or with:
# dend1 <- set(dend1, "branches_k_color", k = 4, value = cols_branches)
# get the colors of the tips of the dendrogram:
# col_labels <- cols_branches[cutree(dend1, k = 4)] # this may need tweaking in various cases - the following is a more general solution.
# The following code will work on its own once I uplode dendextend 0.18.6 to CRAN - but that can
# take several good weeks until that happens. In the meantime
# Either use devtools::install_github('talgalili/dendextend')
# Or just the following:
source("https://raw.githubusercontent.com/talgalili/dendextend/master/R/attr_access.R")
col_labels <- get_leaves_branches_col(dend1)
# But due to the way heatmap.2 works - we need to fix it to be in the
# order of the data!
col_labels <- col_labels[order(order.dendrogram(dend1))]
# Creating Heat Map
if(!require(gplots)) install.packages("gplots")
library(gplots)
heatmap.2(test,
main = paste( "test"),
trace="none",
margins =c(5,7),
col=my_palette,
breaks=col_breaks,
dendrogram="row",
Rowv = dend1,
Colv = "NA",
key.xlab = "Concentration (index)",
cexRow =0.6,
cexCol = 0.8,
na.rm = TRUE,
RowSideColors = col_labels, # to add nice colored strips
colRow = col_labels # to add nice colored labels - only for qplots 2.17.0 and higher
)
Which produces this plot:
For more details on the package, you can have a look at its vignette.
p.s.: to get the labels colored depends on parameters of heatmap.2, and this should be asked from the maintainer of gplots (i.e.: from greg at warnes.net)
update: this answer now includes the new "colRow" parameter in qplots 2.17.0.
this is the maintainer of the gplots package. I've added two new arguments to the gplots::heatmap.2 function, 'colRow' and 'colCol' to control the colors of the row and column labels. This will be part of gplots 2.17.0 which should be submitted to CRAN in the next day or so.
pca in R with princomp() and using svd() [duplicate]
This question already has an answer here:
Closed 11 years ago.
Possible Duplicate:
Comparing svd and princomp in R
How to perform PCA using 2 methods (princomp() and svd of correlation matrix ) in R
I have a data set like:
438,498,3625,3645,5000,2918,5000,2351,2332,2643,1698,1687,1698,1717,1744,593,502,493,504,445,431,444,440,429,10
438,498,3625,3648,5000,2918,5000,2637,2332,2649,1695,1687,1695,1720,1744,592,502,493,504,449,431,444,443,429,10
438,498,3625,3629,5000,2918,5000,2637,2334,2643,1696,1687,1695,1717,1744,593,502,493,504,449,431,444,446,429,10
437,501,3625,3626,5000,2918,5000,2353,2334,2642,1730,1687,1695,1717,1744,593,502,493,504,449,431,444,444,429,10
438,498,3626,3629,5000,2918,5000,2640,2334,2639,1696,1687,1695,1717,1744,592,502,493,504,449,431,444,441,429,10
439,498,3626,3629,5000,2918,5000,2633,2334,2645,1705,1686,1694,1719,1744,589,502,493,504,446,431,444,444,430,10
440,5000,3627,3628,5000,2919,3028,2346,2330,2638,1727,1684,1692,1714,1745,588,501,492,504,451,433,446,444,432,10
444,5021,3631,3634,5000,2919,5000,2626,2327,2638,1698,1680,1688,1709,1740,595,500,491,503,453,436,448,444,436,10
451,5025,3635,3639,5000,2920,3027,2620,2323,2632,1706,1673,1681,1703,753,595,499,491,502,457,440,453,454,442,20
458,5022,3640,3644,5000,2922,5000,2346,2321,2628,1688,1666,1674,1696,744,590,496,490,498,462,444,458,461,449,20
465,525,3646,3670,5000,2923,5000,2611,2315,2631,1674,1658,1666,1688,735,593,495,488,497,467,449,462,469,457,20
473,533,3652,3676,5000,2925,5000,2607,2310,2623,1669,1651,1659,1684,729,578,496,487,498,469,454,467,476,465,20
481,544,3658,3678,5000,2926,5000,2606,2303,2619,1668,1643,1651,1275,723,581,495,486,497,477,459,472,484,472,20
484,544,3661,3665,5000,2928,5000,2321,2304,5022,1647,1639,1646,1270,757,623,493,484,495,480,461,474,485,476,20
484,532,3669,3662,2945,2926,5000,2326,2306,2620,1648,1639,1646,1270,760,533,493,483,494,507,461,473,486,476,20
482,520,3685,3664,2952,2927,5000,2981,2307,2329,1650,1640,1644,1268,757,533,492,482,492,513,459,474,485,474,20
481,522,3682,3661,2955,2927,2957,2984,1700,2622,1651,1641,1645,1272,761,530,492,482,492,513,462,486,483,473,20
480,525,3694,3664,2948,2926,2950,2995,1697,2619,1651,1642,1646,1269,762,530,493,482,492,516,462,486,483,473,20
481,515,5018,3664,2956,2927,2947,2993,1697,2622,1651,1641,1645,1269,765,592,489,482,495,531,462,499,483,473,20
479,5000,3696,3661,2953,2927,2944,2993,1702,2622,1649,1642,1645,1269,812,588,489,481,491,510,462,481,483,473,20
480,506,5019,3665,2941,2929,2945,2981,1700,2616,1652,1642,1645,1271,814,643,491,480,493,524,461,469,484,473,20
479,5000,5019,3661,2943,2930,2942,2996,1698,2312,1653,1642,1644,1274,811,617,491,479,491,575,461,465,484,473,20
479,5000,5020,3662,2945,2931,2942,2997,1700,2313,1654,1642,1644,1270,908,616,490,478,489,503,460,460,478,473,10
481,508,5021,3660,2954,2936,2946,2966,1705,2313,1654,1643,1643,1270,1689,678,493,477,483,497,467,459,476,473,10
486,510,522,3662,2958,2938,2939,2627,1707,2314,1659,1643,1639,1665,1702,696,516,476,477,547,465,457,470,474,10
479,521,520,3663,2954,2938,2941,2957,1712,2314,1660,1643,1638,1660,1758,688,534,475,475,489,461,456,465,474,10
480,554,521,3664,2954,2938,2941,2632,1715,2313,1660,1643,1637,1656,1761,687,553,475,474,558,462,453,465,476,10
481,511,5023,3665,2954,2937,2941,2627,1707,2312,1660,1641,1636,1655,1756,687,545,475,475,504,463,458,470,477,10
482,528,524,3665,2953,2937,2940,2629,1706,2312,1657,1640,1635,1654,1756,566,549,475,476,505,464,459,468,477,10
So I am doing this:
x <- read.csv("C:\\data_25_1000.txt",header=F,row.names=NULL)
p1 <- princomp(x, cor = TRUE) ## using correlation matrix
p1
Call:
princomp(x = x, cor = TRUE)
Standard deviations:
Comp.1 Comp.2 Comp.3 Comp.4 Comp.5 Comp.6 Comp.7 Comp.8 Comp.9 Comp.10 Comp.11 Comp.12 Comp.13 Comp.14 Comp.15 Comp.16
1.9800328 1.8321498 1.4147367 1.3045541 1.2016116 1.1708212 1.1424120 1.0134829 1.0045317 0.9078734 0.8442308 0.8093044 0.7977656 0.7661921 0.7370972 0.7075442
Comp.17 Comp.18 Comp.19 Comp.20 Comp.21 Comp.22 Comp.23 Comp.24 Comp.25
0.7011462 0.6779179 0.6671614 0.6407627 0.6077336 0.5767217 0.5659030 0.5526520 0.5191375
25 variables and 1000 observations.
For the second method suppose I have the correlation matrix of "C:\data_25_1000.txt"
which is:
1.0 0.3045 0.1448 -0.0714 -0.038 -0.0838 -0.1433 -0.1071 -0.1988 -0.1076 -0.0313 -0.157 -0.1032 -0.137 -0.0802 0.1244 0.0701 0.0457 -0.0634 0.0401 0.1643 0.3056 0.3956 0.4533 0.1557
0.3045 0.9999 0.3197 0.1328 0.093 -0.0846 -0.132 0.0046 -0.004 -0.0197 -0.1469 -0.1143 -0.2016 -0.1 -0.0316 0.0044 -0.0589 -0.0589 0.0277 0.0314 0.078 0.0104 0.0692 0.1858 0.0217
0.1448 0.3197 1 0.3487 0.2811 0.0786 -0.1421 -0.1326 -0.2056 -0.1109 0.0385 -0.1993 -0.1975 -0.1858 -0.1546 -0.0297 -0.0629 -0.0997 -0.0624 -0.0583 0.0316 0.0594 0.0941 0.0813 -0.1211
-0.0714 0.1328 0.3487 1 0.6033 0.2866 -0.246 -0.1201 -0.1975 -0.0929 -0.1071 -0.212 -0.3018 -0.3432 -0.2562 0.0277 -0.1363 -0.2218 -0.1443 -0.0322 -0.012 0.1741 -0.0725 -0.0528 -0.0937
-0.038 0.093 0.2811 0.6033 1 0.4613 0.016 0.0655 -0.1094 0.0026 -0.1152 -0.1692 -0.2047 -0.2508 -0.319 -0.0528 -0.1839 -0.2758 -0.2657 -0.1136 -0.0699 0.1433 -0.0136 -0.0409 -0.1538
-0.0838 -0.0846 0.0786 0.2866 0.4613 0.9999 0.2615 0.2449 0.1471 0.0042 -0.1496 -0.2025 -0.1669 -0.142 -0.1746 -0.1984 -0.2197 -0.2631 -0.2675 -0.1999 -0.1315 0.0469 0.0003 -0.1113 -0.1217
-0.1433 -0.132 -0.1421 -0.246 0.016 0.2615 1 0.3979 0.3108 0.1622 -0.0539 0.0231 0.1801 0.2129 0.1331 -0.1325 -0.0669 -0.0922 -0.1236 -0.1463 -0.1452 -0.2422 -0.0768 -0.1457 0.036
-0.1071 0.0046 -0.1326 -0.1201 0.0655 0.2449 0.3979 1 0.4244 0.3821 0.119 -0.0666 0.0163 0.0963 -0.0078 -0.1202 -0.204 -0.2257 -0.2569 -0.2334 -0.234 -0.2004 -0.138 -0.0735 -0.1442
-0.1988 -0.004 -0.2056 -0.1975 -0.1094 0.1471 0.3108 0.4244 0.9999 0.5459 0.0498 -0.052 0.0987 0.186 0.2576 -0.052 -0.1921 -0.2222 -0.1792 -0.0154 -0.058 -0.1868 -0.2232 -0.3118 0.0186
-0.1076 -0.0197 -0.1109 -0.0929 0.0026 0.0042 0.1622 0.3821 0.5459 0.9999 0.2416 0.0183 0.063 0.0252 0.186 0.0519 -0.1943 -0.2241 -0.2635 -0.0498 -0.0799 -0.0553 -0.1567 -0.2281 -0.0263
-0.0313 -0.1469 0.0385 -0.1071 -0.1152 -0.1496 -0.0539 0.119 0.0498 0.2416 1 0.2601 0.1625 -0.0091 -0.0633 0.0355 0.0397 -0.0288 -0.0768 -0.2144 -0.2581 0.1062 0.0469 -0.0608 -0.0578
-0.157 -0.1143 -0.1993 -0.212 -0.1692 -0.2025 0.0231 -0.0666 -0.052 0.0183 0.2601 0.9999 0.3685 0.3059 0.1269 -0.0302 0.1417 0.1678 0.2219 -0.0392 -0.2391 -0.2504 -0.2743 -0.1827 -0.0496
-0.1032 -0.2016 -0.1975 -0.3018 -0.2047 -0.1669 0.1801 0.0163 0.0987 0.063 0.1625 0.3685 1 0.6136 0.2301 -0.1158 0.0366 0.0965 0.1334 -0.0449 -0.1923 -0.2321 -0.1848 -0.1109 0.1007
-0.137 -0.1 -0.1858 -0.3432 -0.2508 -0.142 0.2129 0.0963 0.186 0.0252 -0.0091 0.3059 0.6136 1 0.4078 -0.0615 0.0607 0.1223 0.1379 0.0072 -0.1377 -0.3633 -0.2905 -0.1867 0.0277
-0.0802 -0.0316 -0.1546 -0.2562 -0.319 -0.1746 0.1331 -0.0078 0.2576 0.186 -0.0633 0.1269 0.2301 0.4078 1 0.0521 -0.0345 0.0444 0.0778 0.0925 0.0596 -0.2551 -0.1499 -0.2211 0.244
0.1244 0.0044 -0.0297 0.0277 -0.0528 -0.1984 -0.1325 -0.1202 -0.052 0.0519 0.0355 -0.0302 -0.1158 -0.0615 0.0521 1 0.295 0.2421 -0.06 0.0921 0.243 0.0953 0.0886 0.0518 -0.0032
0.0701 -0.0589 -0.0629 -0.1363 -0.1839 -0.2197 -0.0669 -0.204 -0.1921 -0.1943 0.0397 0.1417 0.0366 0.0607 -0.0345 0.295 0.9999 0.4832 0.2772 0.0012 0.1198 0.0411 0.1213 0.1409 0.0368
0.0457 -0.0589 -0.0997 -0.2218 -0.2758 -0.2631 -0.0922 -0.2257 -0.2222 -0.2241 -0.0288 0.1678 0.0965 0.1223 0.0444 0.2421 0.4832 1 0.2632 0.0576 0.0965 -0.0043 0.0818 0.102 0.0915
-0.0634 0.0277 -0.0624 -0.1443 -0.2657 -0.2675 -0.1236 -0.2569 -0.1792 -0.2635 -0.0768 0.2219 0.1334 0.1379 0.0778 -0.06 0.2772 0.2632 1 0.2036 -0.0452 -0.142 -0.0696 -0.0367 0.3039
0.0401 0.0314 -0.0583 -0.0322 -0.1136 -0.1999 -0.1463 -0.2334 -0.0154 -0.0498 -0.2144 -0.0392 -0.0449 0.0072 0.0925 0.0921 0.0012 0.0576 0.2036 0.9999 0.2198 0.1268 0.0294 0.0261 0.3231
0.1643 0.078 0.0316 -0.012 -0.0699 -0.1315 -0.1452 -0.234 -0.058 -0.0799 -0.2581 -0.2391 -0.1923 -0.1377 0.0596 0.243 0.1198 0.0965 -0.0452 0.2198 1 0.2667 0.2833 0.2467 0.0288
0.3056 0.0104 0.0594 0.1741 0.1433 0.0469 -0.2422 -0.2004 -0.1868 -0.0553 0.1062 -0.2504 -0.2321 -0.3633 -0.2551 0.0953 0.0411 -0.0043 -0.142 0.1268 0.2667 1 0.4872 0.3134 0.1663
0.3956 0.0692 0.0941 -0.0725 -0.0136 0.0003 -0.0768 -0.138 -0.2232 -0.1567 0.0469 -0.2743 -0.1848 -0.2905 -0.1499 0.0886 0.1213 0.0818 -0.0696 0.0294 0.2833 0.4872 0.9999 0.4208 0.1317
0.4533 0.1858 0.0813 -0.0528 -0.0409 -0.1113 -0.1457 -0.0735 -0.3118 -0.2281 -0.0608 -0.1827 -0.1109 -0.1867 -0.2211 0.0518 0.1409 0.102 -0.0367 0.0261 0.2467 0.3134 0.4208 1 0.0592
0.1557 0.0217 -0.1211 -0.0937 -0.1538 -0.1217 0.036 -0.1442 0.0186 -0.0263 -0.0578 -0.0496 0.1007 0.0277 0.244 -0.0032 0.0368 0.0915 0.3039 0.3231 0.0288 0.1663 0.1317 0.0592 0.9999
I have also computed svd of this correlation matrix and got:
> s = svd(Correlation_25_1000)
$d
[1] 3.9205298 3.3567729 2.0014799 1.7018614 1.4438704 1.3708223 1.3051053 1.0271475 1.0090840 0.8242341 0.7127256 0.6549736 0.6364299 0.5870503 0.5433123 0.5006188 0.4916060
[18] 0.4595726 0.4451043 0.4105769 0.3693401 0.3326079 0.3202462 0.3054243 0.2695037
$u
matrix
$v
matrix
My question is, how can I use $d, $u and $v to get principal components
Could I use prcomp() ?? If, so how?
Try this one princomp princomp(USArrests, cor = TRUE)$loadings Loadings: Comp.1 Comp.2 Comp.3 Comp.4 Murder -0.536 0.418 -0.341 0.649 Assault -0.583 0.188 -0.268 -0.743 UrbanPop -0.278 -0.873 -0.378 0.134 Rape -0.543 -0.167 0.818 svd svd(cor(USArrests))$u [,1] [,2] [,3] [,4] [1,] -0.5358995 0.4181809 -0.3412327 0.64922780 [2,] -0.5831836 0.1879856 -0.2681484 -0.74340748 [3,] -0.2781909 -0.8728062 -0.3780158 0.13387773 [4,] -0.5434321 -0.1673186 0.8177779 0.08902432 eigen eigen(cor(USArrests))$vectors [,1] [,2] [,3] [,4] [1,] -0.5358995 0.4181809 -0.3412327 0.64922780 [2,] -0.5831836 0.1879856 -0.2681484 -0.74340748 [3,] -0.2781909 -0.8728062 -0.3780158 0.13387773 [4,] -0.5434321 -0.1673186 0.8177779 0.08902432 For cor matrix, all princomp, svd, and eigen produces same results.