I trained my neural network with a sigmoid activation function so that the predicted values lie in the range [0,1). However, the range of real data in which the z-score transformation has been performed goes beyond [0,1). In this case what would be the appropriate way to evaluate my model. Should I rescale as well the original test data to the same range and then evaluate with criteria like mean square forecast error?
> real_predicted_neural
predicted real
1 1.909219e-07 -3.57877473
2 4.161819e-08 -2.28704595
3 1.754706e-11 -1.08509429
4 1.149891e-13 -0.46573114
5 7.777560e-02 0.42381300
6 4.173448e-07 -0.44060297
7 1.119703e-01 0.21075550
8 8.682557e-01 -0.01292402
9 4.736056e-08 -0.29830701
10 7.506821e-08 -1.20302227
11 7.341235e-01 -0.03986571
12 7.501776e-05 -0.94315815
13 1.145697e-04 0.49730175
14 2.214929e-13 0.04252241
15 4.597199e-01 -0.38539901
16 2.324931e-03 -0.74468628
17 4.366025e-06 -0.77037244
18 1.394450e-06 0.16679048
19 5.869884e-11 -0.75876486
20 1.817941e-04 0.04303387
21 7.060773e-04 0.06099372
22 8.267170e-06 -1.21687318
23 9.388680e-02 0.61135319
24 1.099290e-01 0.55715201
25 9.757236e-01 -0.33480226
26 9.544055e-01 0.09061006
27 7.322074e-07 0.09290822
28 1.014327e-06 -0.61658893
29 7.848382e-08 -0.78739456
30 1.791908e-04 -0.44073540
31 1.357918e-03 -0.22099008
32 5.192233e-06 -0.32744703
33 2.624779e-06 -0.37644068
34 6.414216e-02 -0.36947939
35 1.388143e-06 -0.00994845
36 3.010872e-05 -0.05984833
37 9.873201e-03 -0.21815268
38 3.896163e-04 -0.24009094
39 2.718760e-02 0.33383333
40 1.025650e-02 0.09779867
envelope of the K funcition (and its derivative such as L) is very useful for validating a fitted spatial points process model. for instance, I fit a poisson model for a data J1a2, which is as following:
J1a2.points:
# X.1 X Y
1 1 118.544 1638.445
2 2 325.995 1761.223
3 3 681.625 1553.771
4 4 677.392 1816.261
5 5 986.451 1685.016
6 6 1469.093 1354.787
7 7 1608.805 1625.744
8 8 1994.071 1782.391
9 9 1968.669 1375.955
10 10 2362.403 1337.852
11 11 2701.099 1773.924
12 12 2900.083 1820.495
13 13 2963.588 1668.081
14 14 3412.360 1676.549
15 15 3378.490 1456.396
16 16 3721.420 1464.863
17 17 3823.028 1701.951
18 18 4072.817 1790.859
19 19 4089.751 1388.656
20 20 97.375 715.497
21 21 376.799 1033.025
22 22 563.082 1126.166
23 23 935.647 1206.607
24 24 512.277 486.876
25 25 935.647 757.834
26 26 1409.821 410.670
27 27 1435.223 639.290
28 28 1706.180 1045.726
29 29 1968.669 876.378
30 30 2307.365 711.263
31 31 2624.892 897.546
32 32 2654.528 1236.243
33 33 2857.746 423.371
34 34 3039.795 639.290
35 35 3298.050 707.029
36 36 3111.767 1011.856
37 37 3361.555 1227.775
38 38 4047.414 1185.438
39 39 3569.007 508.045
40 40 4250.632 469.942
41 41 4386.110 872.144
42 42 93.141 237.088
43 43 554.614 186.283
44 44 757.832 148.180
45 45 965.283 220.153
46 46 1723.115 296.360
47 47 1744.283 423.371
48 48 1913.631 203.218
49 49 2167.653 292.126
50 50 2629.126 211.685
51 51 3217.610 283.658
52 52 3827.262 325.996
and:
J1a2.Win<-owin(c(0, 4500.42),c(0, 1917.87))
if you draw evelope for the data with Lest:
library(spatstat)
env.data<-envelope(J1a2, Lest,correction="border",
nsim=19, global=TRUE)
plot(env.data,.-r~r, shade=NULL, legend=FALSE,
xlab=expression(paste("r(",mu,"m)")),ylab="L(r)-r", main = "")
the Lest() curve goes out of the envelope. however, if you use Linhom instead of Lest, you will find the Linhom() are all inside of the envelope.
it seems that this suggest a inhomogenous density kernel of the data. so I use y as covariate in fitting:
poisson.J1a2<-ppm(J1a2~1,Poisson(),correction="border")
y1.J1a2<-ppm(J1a2~y,correction="border")
anova(poisson.J1a2,y.J1a2,test="LR") #p=0.6484
I don't find any evidence of a spatial trend of density along y, or x, or their combinations.
then why the Linhom() outperform the Lest() in this case?
furthermore, when should one decide to use Linhom() instead of Lest?
You should first decide whether or not the intensity can be assumed to be constant. To help you with this you can look at kernel density estimates or do formal tests such as a quadrat test etc. If you decide that the intensity can be assumed to be constant you use Lest() if this is not the case you use Linhom().
My first question here :)
My goal is: Given a data frame with predictors (each column a predictor / rows observations) fit a regression using lm and then predict the value using the last observation using a rolling window.
The data frame looks like:
> DfPredictor[1:40,]
Y X1 X2 X3 X4 X5
1 3.2860 192.5115 2.1275 83381 11.4360 8.7440
2 3.2650 190.1462 2.0050 88720 11.4359 8.8971
3 3.2213 192.9773 2.0500 74130 11.4623 8.8380
4 3.1991 193.7058 2.1050 73930 11.3366 8.7536
5 3.2224 193.5407 2.0275 80875 11.3534 8.7555
6 3.2000 190.6049 2.0950 86606 11.3290 8.8555
7 3.1939 191.1390 2.0975 91402 11.2960 8.8433
8 3.1971 192.2921 2.2700 88181 11.2930 8.8681
9 3.1873 194.9700 2.3300 115959 1.9477 8.5245
10 3.2182 194.5396 2.4200 134754 11.3200 8.4990
11 3.2409 194.5396 2.2025 136685 1.9649 8.4192
12 3.2112 195.1362 2.1900 136316 1.9750 8.3752
13 3.2231 193.3560 2.2475 140295 1.9691 8.3546
14 3.2015 192.9649 2.2575 139474 1.9500 8.3116
15 3.1744 194.0154 2.1900 146202 1.8476 8.2225
16 3.1646 194.4423 2.2650 142983 1.8600 8.1948
17 3.1708 194.9473 2.2425 141377 1.8522 8.2589
18 3.1675 193.9788 2.2400 141377 1.8600 8.2600
19 3.1744 194.2563 2.3000 149875 1.8718 8.2899
20 3.1410 193.4316 2.2300 129561 1.8480 8.2395
21 3.1266 191.2633 2.2550 122636 1.8440 8.2396
22 3.1486 192.0354 2.3600 130996 1.8570 8.8640
23 3.1282 194.3351 2.4825 92430 1.7849 8.1291
24 3.1214 193.5196 2.4750 94814 1.7624 8.1991
25 3.1230 193.2017 2.3725 87590 1.7660 8.2310
26 3.1182 192.1642 2.4475 87715 1.6955 8.2414
27 3.1203 191.3744 2.3775 89857 1.6539 8.2480
28 3.1156 192.2646 2.3725 92159 1.5976 8.1676
29 3.1270 192.7555 2.3675 97425 1.5896 8.1162
30 3.1154 194.0375 2.3725 87598 1.5277 8.2640
31 3.1104 192.0596 2.3850 93236 1.5132 7.9999
32 3.0846 192.2792 2.2900 94608 1.4990 8.1600
33 3.0569 193.2573 2.3050 84663 1.4715 8.2200
34 3.0893 192.7632 2.2550 67149 1.4955 7.9590
35 3.0991 192.1229 2.3050 75519 1.4280 7.9183
36 3.0879 192.1229 2.3100 76756 1.3839 7.9133
37 3.0965 192.0502 2.2175 61748 1.3130 7.8750
38 3.0655 191.2274 2.2300 41490 1.2823 7.8656
39 3.0636 191.6342 2.1925 51049 1.1492 7.7447
40 3.1097 190.9312 2.2150 21934 1.1626 7.6895
For instance using the rolling window with width = 10 the regression should be estimate and then predict the 'Y' correspondent to the X1,X2,...,X5.
The predictions should be included in a new column 'Ypred'.
There's some way to do that using rollapply + lm/predict + mudate??
Many thanks!!
Using the data in the Note at the end and assuming that in a window of width 10 we want to predict the last Y (i..e. the 10th), then:
library(zoo)
pred <- function(x) tail(fitted(lm(Y ~., as.data.frame(x))), 1)
transform(DF, pred = rollapplyr(DF, 10, pred, by.column = FALSE, fill = NA))
giving:
Y X1 X2 X3 X4 X5 pred
1 3.2860 192.5115 2.1275 83381 11.4360 8.7440 NA
2 3.2650 190.1462 2.0050 88720 11.4359 8.8971 NA
3 3.2213 192.9773 2.0500 74130 11.4623 8.8380 NA
4 3.1991 193.7058 2.1050 73930 11.3366 8.7536 NA
5 3.2224 193.5407 2.0275 80875 11.3534 8.7555 NA
6 3.2000 190.6049 2.0950 86606 11.3290 8.8555 NA
7 3.1939 191.1390 2.0975 91402 11.2960 8.8433 NA
8 3.1971 192.2921 2.2700 88181 11.2930 8.8681 NA
9 3.1873 194.9700 2.3300 115959 1.9477 8.5245 NA
10 3.2182 194.5396 2.4200 134754 11.3200 8.4990 3.219764
11 3.2409 194.5396 2.2025 136685 1.9649 8.4192 3.241614
12 3.2112 195.1362 2.1900 136316 1.9750 8.3752 3.225423
13 3.2231 193.3560 2.2475 140295 1.9691 8.3546 3.217797
14 3.2015 192.9649 2.2575 139474 1.9500 8.3116 3.205856
15 3.1744 194.0154 2.1900 146202 1.8476 8.2225 3.177928
16 3.1646 194.4423 2.2650 142983 1.8600 8.1948 3.156405
17 3.1708 194.9473 2.2425 141377 1.8522 8.2589 3.176243
18 3.1675 193.9788 2.2400 141377 1.8600 8.2600 3.177165
19 3.1744 194.2563 2.3000 149875 1.8718 8.2899 3.177211
20 3.1410 193.4316 2.2300 129561 1.8480 8.2395 3.145533
21 3.1266 191.2633 2.2550 122636 1.8440 8.2396 3.127410
22 3.1486 192.0354 2.3600 130996 1.8570 8.8640 3.148792
23 3.1282 194.3351 2.4825 92430 1.7849 8.1291 3.124913
24 3.1214 193.5196 2.4750 94814 1.7624 8.1991 3.124992
25 3.1230 193.2017 2.3725 87590 1.7660 8.2310 3.117981
26 3.1182 192.1642 2.4475 87715 1.6955 8.2414 3.117679
27 3.1203 191.3744 2.3775 89857 1.6539 8.2480 3.119898
28 3.1156 192.2646 2.3725 92159 1.5976 8.1676 3.121039
29 3.1270 192.7555 2.3675 97425 1.5896 8.1162 3.123903
30 3.1154 194.0375 2.3725 87598 1.5277 8.2640 3.119438
31 3.1104 192.0596 2.3850 93236 1.5132 7.9999 3.113963
32 3.0846 192.2792 2.2900 94608 1.4990 8.1600 3.101229
33 3.0569 193.2573 2.3050 84663 1.4715 8.2200 3.076817
34 3.0893 192.7632 2.2550 67149 1.4955 7.9590 3.083266
35 3.0991 192.1229 2.3050 75519 1.4280 7.9183 3.089377
36 3.0879 192.1229 2.3100 76756 1.3839 7.9133 3.084225
37 3.0965 192.0502 2.2175 61748 1.3130 7.8750 3.075252
38 3.0655 191.2274 2.2300 41490 1.2823 7.8656 3.063025
39 3.0636 191.6342 2.1925 51049 1.1492 7.7447 3.068808
40 3.1097 190.9312 2.2150 21934 1.1626 7.6895 3.091819
Note: Input DF in reproducible form is:
Lines <- " Y X1 X2 X3 X4 X5
1 3.2860 192.5115 2.1275 83381 11.4360 8.7440
2 3.2650 190.1462 2.0050 88720 11.4359 8.8971
3 3.2213 192.9773 2.0500 74130 11.4623 8.8380
4 3.1991 193.7058 2.1050 73930 11.3366 8.7536
5 3.2224 193.5407 2.0275 80875 11.3534 8.7555
6 3.2000 190.6049 2.0950 86606 11.3290 8.8555
7 3.1939 191.1390 2.0975 91402 11.2960 8.8433
8 3.1971 192.2921 2.2700 88181 11.2930 8.8681
9 3.1873 194.9700 2.3300 115959 1.9477 8.5245
10 3.2182 194.5396 2.4200 134754 11.3200 8.4990
11 3.2409 194.5396 2.2025 136685 1.9649 8.4192
12 3.2112 195.1362 2.1900 136316 1.9750 8.3752
13 3.2231 193.3560 2.2475 140295 1.9691 8.3546
14 3.2015 192.9649 2.2575 139474 1.9500 8.3116
15 3.1744 194.0154 2.1900 146202 1.8476 8.2225
16 3.1646 194.4423 2.2650 142983 1.8600 8.1948
17 3.1708 194.9473 2.2425 141377 1.8522 8.2589
18 3.1675 193.9788 2.2400 141377 1.8600 8.2600
19 3.1744 194.2563 2.3000 149875 1.8718 8.2899
20 3.1410 193.4316 2.2300 129561 1.8480 8.2395
21 3.1266 191.2633 2.2550 122636 1.8440 8.2396
22 3.1486 192.0354 2.3600 130996 1.8570 8.8640
23 3.1282 194.3351 2.4825 92430 1.7849 8.1291
24 3.1214 193.5196 2.4750 94814 1.7624 8.1991
25 3.1230 193.2017 2.3725 87590 1.7660 8.2310
26 3.1182 192.1642 2.4475 87715 1.6955 8.2414
27 3.1203 191.3744 2.3775 89857 1.6539 8.2480
28 3.1156 192.2646 2.3725 92159 1.5976 8.1676
29 3.1270 192.7555 2.3675 97425 1.5896 8.1162
30 3.1154 194.0375 2.3725 87598 1.5277 8.2640
31 3.1104 192.0596 2.3850 93236 1.5132 7.9999
32 3.0846 192.2792 2.2900 94608 1.4990 8.1600
33 3.0569 193.2573 2.3050 84663 1.4715 8.2200
34 3.0893 192.7632 2.2550 67149 1.4955 7.9590
35 3.0991 192.1229 2.3050 75519 1.4280 7.9183
36 3.0879 192.1229 2.3100 76756 1.3839 7.9133
37 3.0965 192.0502 2.2175 61748 1.3130 7.8750
38 3.0655 191.2274 2.2300 41490 1.2823 7.8656
39 3.0636 191.6342 2.1925 51049 1.1492 7.7447
40 3.1097 190.9312 2.2150 21934 1.1626 7.6895"
DF <- read.table(text = Lines, header = TRUE)
I'm trying to add error bars to a second curve (using dataset "pmfprofbs01"), but I'm having problems and I couldn't fix this.
There are a few threads on this error, but unfortunately it looks like every other answer is case specific, and I'm not able to overcome this error in my code. I am able to plot a first smoothed curve (stat_smooth) and overlapping errorbars (using geom_errobar). The problem rises when I try to add a second curve to the same graph, for comparison purposes.
With following code, I get the following error: "Error: Aesthetics must be either length 1 or the same as the data (35): ymin, ymax, x, y, colour"
I am looking to add additional errorbars to the second smoothed curve (corresponding to datasets pmfprof01 and pmfprofbs01).
Could someone explain why I keep getting this error? The code works until using the second call of geom_errorbar().
These are my 4 datasets (all used as data frames):
- pmfprof1 and pmfprof01 are the two datasets used for applying the smoothing method.
- pmfprofbs1 and pmfprofbs01 contain additional information based on an error analysis for plotting error bars.
> pmfprof1
Z correctedpmfprof1
1 -1.1023900 -8.025386e-22
2 -1.0570000 6.257110e-02
3 -1.0116000 1.251420e-01
4 -0.9662020 2.143170e-01
5 -0.9208040 3.300960e-01
6 -0.8754060 4.658550e-01
7 -0.8300090 6.113410e-01
8 -0.7846110 4.902430e-01
9 -0.7392140 3.344200e-01
10 -0.6938160 4.002040e-01
11 -0.6484190 1.215460e-01
12 -0.6030210 -1.724360e-01
13 -0.5576240 -6.077170e-01
14 -0.5122260 -1.513420e+00
15 -0.4668290 -2.075330e+00
16 -0.4214310 -2.617160e+00
17 -0.3760340 -3.350500e+00
18 -0.3306360 -4.076220e+00
19 -0.2852380 -4.926540e+00
20 -0.2398410 -5.826390e+00
21 -0.1944430 -6.761300e+00
22 -0.1490460 -7.301530e+00
23 -0.1036480 -7.303880e+00
24 -0.0582507 -7.026800e+00
25 -0.0128532 -6.627960e+00
26 0.0325444 -6.651490e+00
27 0.0779419 -6.919830e+00
28 0.1233390 -6.686490e+00
29 0.1687370 -6.129060e+00
30 0.2141350 -6.120890e+00
31 0.2595320 -6.455160e+00
32 0.3049300 -6.554560e+00
33 0.3503270 -6.983390e+00
34 0.3957250 -7.413500e+00
35 0.4411220 -6.697370e+00
36 0.4865200 -5.477230e+00
37 0.5319170 -4.552890e+00
38 0.5773150 -3.393060e+00
39 0.6227120 -2.449930e+00
40 0.6681100 -2.183190e+00
41 0.7135080 -1.673980e+00
42 0.7589050 -8.003740e-01
43 0.8043030 -2.918780e-01
44 0.8497000 -1.159710e-01
45 0.8950980 9.123767e-22
> pmfprof01
Z correctedpmfprof01
1 -1.25634000 -1.878749e-21
2 -1.20387000 -1.750190e-01
3 -1.15141000 -3.500380e-01
4 -1.09894000 -6.005650e-01
5 -1.04647000 -7.935110e-01
6 -0.99400600 -8.626150e-01
7 -0.94153900 -1.313880e+00
8 -0.88907200 -2.067770e+00
9 -0.83660500 -2.662440e+00
10 -0.78413800 -4.514190e+00
11 -0.73167100 -7.989510e+00
12 -0.67920400 -1.186870e+01
13 -0.62673800 -1.535970e+01
14 -0.57427100 -1.829150e+01
15 -0.52180400 -2.067170e+01
16 -0.46933700 -2.167890e+01
17 -0.41687000 -2.069820e+01
18 -0.36440300 -1.662640e+01
19 -0.31193600 -1.265950e+01
20 -0.25946900 -1.182580e+01
21 -0.20700200 -1.213370e+01
22 -0.15453500 -1.233680e+01
23 -0.10206800 -1.235160e+01
24 -0.04960160 -1.123630e+01
25 0.00286531 -9.086940e+00
26 0.05533220 -6.562710e+00
27 0.10779900 -4.185860e+00
28 0.16026600 -3.087430e+00
29 0.21273300 -2.005150e+00
30 0.26520000 -9.295540e-02
31 0.31766700 1.450360e+00
32 0.37013400 1.123910e+00
33 0.42260100 2.426750e-01
34 0.47506700 1.213370e-01
35 0.52753400 5.265226e-21
> pmfprofbs1
Z correctedpmfprof01 bsmean bssd bsse bsci
1 -1.1023900 -8.025386e-22 0.00000000 0.0000000 0.00000000 0.0000000
2 -1.0570000 6.257110e-02 1.46519200 0.6691245 0.09974719 0.2010273
3 -1.0116000 1.251420e-01 1.62453300 0.6368053 0.09492933 0.1913175
4 -0.9662020 2.143170e-01 1.62111600 0.7200497 0.10733867 0.2163269
5 -0.9208040 3.300960e-01 1.44754700 0.7236743 0.10787900 0.2174158
6 -0.8754060 4.658550e-01 1.67509800 0.7148755 0.10656735 0.2147724
7 -0.8300090 6.113410e-01 1.78144200 0.7374481 0.10993227 0.2215539
8 -0.7846110 4.902430e-01 1.73058700 0.7701354 0.11480501 0.2313743
9 -0.7392140 3.344200e-01 0.97430090 0.7809477 0.11641681 0.2346227
10 -0.6938160 4.002040e-01 1.26812000 0.8033838 0.11976139 0.2413632
11 -0.6484190 1.215460e-01 0.93601510 0.7927926 0.11818254 0.2381813
12 -0.6030210 -1.724360e-01 0.63201080 0.8210839 0.12239996 0.2466809
13 -0.5576240 -6.077170e-01 0.05952252 0.8653050 0.12899205 0.2599664
14 -0.5122260 -1.513420e+00 0.57893690 0.8858471 0.13205429 0.2661379
15 -0.4668290 -2.075330e+00 -0.08164613 0.8921298 0.13299086 0.2680255
16 -0.4214310 -2.617160e+00 -1.08074600 0.8906925 0.13277660 0.2675937
17 -0.3760340 -3.350500e+00 -1.67279700 0.9081813 0.13538367 0.2728479
18 -0.3306360 -4.076220e+00 -2.50074900 1.0641550 0.15863486 0.3197076
19 -0.2852380 -4.926540e+00 -3.12062200 1.0639080 0.15859804 0.3196333
20 -0.2398410 -5.826390e+00 -4.47060100 1.1320770 0.16876008 0.3401136
21 -0.1944430 -6.761300e+00 -5.40812700 1.1471780 0.17101120 0.3446504
22 -0.1490460 -7.301530e+00 -6.42419100 1.1685490 0.17419700 0.3510710
23 -0.1036480 -7.303880e+00 -5.79613500 1.1935850 0.17792915 0.3585926
24 -0.0582507 -7.026800e+00 -5.85496900 1.2117630 0.18063896 0.3640539
25 -0.0128532 -6.627960e+00 -6.70480400 1.1961400 0.17831002 0.3593602
26 0.0325444 -6.651490e+00 -8.27106200 1.3376870 0.19941060 0.4018857
27 0.0779419 -6.919830e+00 -8.79402900 1.3582760 0.20247983 0.4080713
28 0.1233390 -6.686490e+00 -8.35947700 1.3673080 0.20382624 0.4107848
29 0.1687370 -6.129060e+00 -8.04437600 1.3921620 0.20753126 0.4182518
30 0.2141350 -6.120890e+00 -8.18588300 1.5220550 0.22689456 0.4572759
31 0.2595320 -6.455160e+00 -8.37217600 1.5436800 0.23011823 0.4637728
32 0.3049300 -6.554560e+00 -8.59346400 1.6276880 0.24264140 0.4890116
33 0.3503270 -6.983390e+00 -8.88378700 1.6557140 0.24681927 0.4974316
34 0.3957250 -7.413500e+00 -9.72709800 1.6569390 0.24700188 0.4977996
35 0.4411220 -6.697370e+00 -9.46033400 1.6378470 0.24415582 0.4920637
36 0.4865200 -5.477230e+00 -8.37590600 1.6262700 0.24243002 0.4885856
37 0.5319170 -4.552890e+00 -7.52867000 1.6617010 0.24771176 0.4992302
38 0.5773150 -3.393060e+00 -6.89192300 1.6667330 0.24846189 0.5007420
39 0.6227120 -2.449930e+00 -6.25115300 1.6670390 0.24850750 0.5008340
40 0.6681100 -2.183190e+00 -6.05373800 1.6720180 0.24924973 0.5023298
41 0.7135080 -1.673980e+00 -5.10526700 1.6668400 0.24847784 0.5007742
42 0.7589050 -8.003740e-01 -4.42001600 1.6561830 0.24688918 0.4975725
43 0.8043030 -2.918780e-01 -4.26640200 1.6588970 0.24729376 0.4983878
44 0.8497000 -1.159710e-01 -4.46318500 1.6533830 0.24647179 0.4967312
45 0.8950980 9.123767e-22 -5.17173200 1.6557990 0.24683194 0.4974571
> pmfprofbs01
Z correctedpmfprof01 bsmean bssd bsse bsci
1 -1.25634000 -1.878749e-21 0.000000 0.0000000 0.00000000 0.0000000
2 -1.20387000 -1.750190e-01 2.316589 0.4646486 0.07853995 0.1596124
3 -1.15141000 -3.500380e-01 2.320647 0.4619668 0.07808664 0.1586911
4 -1.09894000 -6.005650e-01 2.635883 0.6519826 0.11020517 0.2239639
5 -1.04647000 -7.935110e-01 2.814679 0.6789875 0.11476983 0.2332404
6 -0.99400600 -8.626150e-01 2.588038 0.7324196 0.12380151 0.2515949
7 -0.94153900 -1.313880e+00 2.033736 0.7635401 0.12906183 0.2622852
8 -0.88907200 -2.067770e+00 2.394285 0.8120181 0.13725611 0.2789380
9 -0.83660500 -2.662440e+00 2.465425 0.9485307 0.16033095 0.3258317
10 -0.78413800 -4.514190e+00 0.998115 1.0177400 0.17202946 0.3496059
11 -0.73167100 -7.989510e+00 -1.585430 1.0502190 0.17751941 0.3607628
12 -0.67920400 -1.186870e+01 -5.740894 1.2281430 0.20759406 0.4218819
13 -0.62673800 -1.535970e+01 -9.325951 1.3289330 0.22463068 0.4565045
14 -0.57427100 -1.829150e+01 -12.010540 1.3279860 0.22447060 0.4561792
15 -0.52180400 -2.067170e+01 -14.672770 1.3296720 0.22475559 0.4567583
16 -0.46933700 -2.167890e+01 -14.912250 1.3192610 0.22299581 0.4531820
17 -0.41687000 -2.069820e+01 -12.850570 1.3288470 0.22461614 0.4564749
18 -0.36440300 -1.662640e+01 -6.093746 1.3497100 0.22814263 0.4636416
19 -0.31193600 -1.265950e+01 -5.210692 1.3602240 0.22991982 0.4672533
20 -0.25946900 -1.182580e+01 -6.041660 1.3818700 0.23357866 0.4746890
21 -0.20700200 -1.213370e+01 -5.765808 1.3854680 0.23418683 0.4759249
22 -0.15453500 -1.233680e+01 -6.985883 1.4025360 0.23707185 0.4817880
23 -0.10206800 -1.235160e+01 -7.152865 1.4224030 0.24042999 0.4886125
24 -0.04960160 -1.123630e+01 -3.600538 1.4122650 0.23871635 0.4851300
25 0.00286531 -9.086940e+00 -0.751673 1.5764920 0.26647578 0.5415439
26 0.05533220 -6.562710e+00 2.852910 1.5535620 0.26259991 0.5336672
27 0.10779900 -4.185860e+00 5.398850 1.5915640 0.26902342 0.5467214
28 0.16026600 -3.087430e+00 6.262459 1.6137360 0.27277117 0.5543377
29 0.21273300 -2.005150e+00 8.047920 1.6283340 0.27523868 0.5593523
30 0.26520000 -9.295540e-02 11.168640 1.6267620 0.27497297 0.5588123
31 0.31766700 1.450360e+00 12.345900 1.6363310 0.27659042 0.5620994
32 0.37013400 1.123910e+00 12.124650 1.6289230 0.27533824 0.5595546
33 0.42260100 2.426750e-01 11.279890 1.6137100 0.27276677 0.5543288
34 0.47506700 1.213370e-01 11.531670 1.6311490 0.27571450 0.5603193
35 0.52753400 5.265226e-21 11.284980 1.6662890 0.28165425 0.5723903
The code for plotting both curves is:
deltamean01<-pmfprofbs01[,"bsmean"]-
pmfprofbs01[,"correctedpmfprof01"]
correctmean01<-pmfprofbs01[,"bsmean"]-deltamean01
deltamean1<-pmfprofbs1[,"bsmean"]-
pmfprofbs1[,"correctedpmfprof1"]
correctmean1<-pmfprofbs1[,"bsmean"]-deltamean1
pl<- ggplot(pmfprof1, aes(x=pmfprof1[,1], y=pmfprof1[,2],
colour="red")) +
list(
stat_smooth(method = "gam", formula = y ~ s(x), size = 1,
colour="chartreuse3",fill="chartreuse3", alpha = 0.3),
geom_line(data=pmfprof1,linetype=4, size=0.5,colour="chartreuse3"),
geom_errorbar(aes(ymin=correctmean1-pmfprofbs1[,"bsci"],
ymax=correctmean1+pmfprofbs1[,"bsci"]),
data=pmfprofbs1,colour="chartreuse3",
width=0.02,size=0.9),
geom_point(data=pmfprof1,size=1,colour="chartreuse3"),
xlab(expression(xi*(nm))),
ylab("PMF (KJ/mol)"),
## GCD
geom_errorbar(aes(ymin=correctmean01-pmfprofbs01[,"bsci"],
ymax=correctmean01+pmfprofbs01[,"bsci"]),
data=pmfprofbs01,
width=0.02,size=0.9),
geom_line(data=pmfprof01,aes(x=pmfprof01[,1],y=pmfprof01[,2]),
linetype=4, size=0.5,colour="darkgreen"),
stat_smooth(data=pmfprof01,method = "gam",aes(x=pmfprof01[,1],pmfprof01[,2]),
formula = y ~ s(x), size = 1,
colour="darkgreen",fill="darkgreen", alpha = 0.3),
theme(text = element_text(size=20),
axis.text.x = element_text(size=20,colour="black"),
axis.text.y = element_text(size=20,colour="black")),
scale_x_continuous(breaks=number_ticks(8)),
scale_y_continuous(breaks=number_ticks(8)),
theme(panel.background = element_rect(fill ='white',
colour='gray')),
theme(plot.background = element_rect(fill='white',
colour='white')),
theme(legend.position="none"),
theme(legend.key = element_blank()),
theme(legend.title = element_text(colour='gray', size=20)),
NULL
)
pl
This is the result of using pl,
[enter image description here][1]
[1]: https://i.stack.imgur.com/x8FjY.png
Thanks in advance for any suggestion,
Im trying Moran's I and respective plot in r. But the plot has only one point. I have no idea of what is going wrong. The code is based on<
http://rstudio-pubs-static.s3.amazonaws.com/9688_a49c681fab974bbca889e3eae9fbb837.html>
my data called "coordenata"
resid x y
1 0.07785411 -53.20342 -22.66700
2 -0.28358702 -53.20389 -22.66864
3 -0.64011338 -53.21392 -22.68122
4 1.22071249 -53.21311 -22.72369
5 0.95734778 -53.28469 -22.75289
6 0.35345302 -53.25822 -22.74850
7 -0.68357738 -53.28344 -22.70694
8 -1.24596010 -53.32950 -22.72872
9 -0.19944162 -53.33669 -22.73561
10 0.67544909 -53.36756 -22.80767
11 0.64002961 -53.35947 -22.79958
12 0.04564233 -53.21889 -22.67419
13 0.01618436 -53.24522 -22.70144
14 -2.65436794 -53.23017 -22.69292
15 0.72096256 -53.25539 -22.69978
16 0.89656515 -53.28489 -22.72222
17 1.85358579 -53.33069 -22.79161
18 -0.03590077 -53.33200 -22.78336
19 0.32348975 -53.33494 -22.78586
20 2.06771402 -53.37781 -22.77869
21 -1.02190709 -53.30492 -22.77244
22 -2.02813250 -53.53917 -22.79856
23 -1.20702445 -53.53858 -22.79406
24 -1.24091732 -53.55272 -22.80536
25 -1.13491596 -53.56181 -22.82914
26 -0.82934613 -53.56422 -22.83417
27 1.23418758 -53.60017 -22.85531
28 -1.72808514 -53.65900 -22.97828
29 -0.02144049 -53.65908 -22.97497
30 0.49174568 -53.64597 -22.95439
31 -0.54408149 -53.64217 -22.91033
32 -0.37111342 -53.61447 -22.86269
33 -0.31121931 -53.27153 -22.70036
34 0.32419211 -53.30308 -22.72183
35 1.57980287 -53.33053 -22.72947
36 -1.91156060 -53.34633 -22.74722
37 -0.79036645 -53.23667 -22.68925
the code
coordinates(coordenata)<-c("x","y")
fit2<-correlog(coordenata$x,coordenata$y,coordenata$resid,increment=5,resamp=100,quiet=T)
plot(fit2)
Thanks in advance for any help!