ReistTrans: Reist standardization
In Pstat: Assessing Pst Statistics
Description
Usage
Arguments
Value
Note
Author(s)
References
Examples
Description
'ReistTrans' calculates residuals (size adjusted measurements) from Reist tranformations to eliminate any variation resulting from allometric growth. There is a single regressor (one of the quantitative traits).
Usage
1
ReistTrans(data, reg, Rp = 0, Ri = 0)
Arguments
data
a dataframe with as many rows as individuals. The first column contains the name of the population to which the individual belongs, the others contain quantitative variables.
reg
the name (or the rank) of the variable chosen as the explanatory variable.
Rp
a vector containing the names of the populations to be deleted.
Ri
a vector containing each number of individual to be deleted. The vector Ri must contain existent individuals, each of them once.
Value
the data frame of adjusted variables, the column containing the quantitative trait used as a regressor being deleted.
Note
dispensable quantitative measures can easily be deleted in the main functions of R.
Author(s)
Blondeau Da Silva Stephane - Da Silva Anne.
References
Reist J.D., 1985. An empirical evaluation of several univariate methods that adjust for size variation in morphometric data. Canadian Journal Zoology 63, 1429-1439.
Kaeuffer R. et al., 2012. Parallel and nonparallel aspects of ecological, phenotypic, and genetic divergence across replicate population pairs of lake and stream stickleback. Evolution 66(2), 402-418.
He Y. et al., 2013. Morphological Variation Among Wild Populations of Chinese Rare Minnow (Gobiocypris rarus): Deciphering the Role of Evolutionary Processes. Zoological Science 30, 475-483.
Examples
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data(test)
names(test)[9]
ReistTrans(test,reg=9)
## The function is currently defined as
function (data, reg, Rp = 0, Ri = 0)
{
dat.rem.ind.pop <- function(data, ind = 0, pop = 0) {
data = as.data.frame(data)
dat.rem.ind <- function(dat, ind) {
nb.rem.ind = length(ind)
nb.ind = dim(dat)[1]
for (i in 1:nb.rem.ind) dat = dat[row.names(dat)[1:(nb.ind -
i + 1)] != ind[i], ]
return(dat)
}
dat.rem.pop <- function(dat, pop) {
nb.rem.pop = length(pop)
for (i in 1:nb.rem.pop) dat = dat[dat[, 1] != pop[i],
]
return(dat)
}
if (ind[1] != 0)
data = dat.rem.ind(data, ind)
if (pop[1] != 0)
data = dat.rem.pop(data, pop)
return(data)
}
Reitra.va <- function(dat, clm, re) {
dat = dat[is.finite(dat[, re]), ]
log.dat = dat
mea = mean(dat[is.finite(dat[, clm]), re])
log.dat[, clm] = log(dat[, clm], base = 10)
log.dat[, re] = log(dat[, re], base = 10)
mea.clm = mean(log.dat[is.finite(log.dat[, clm]), clm],
na.rm = TRUE)
mea.reg = mean(log.dat[is.finite(log.dat[, clm]), re],
na.rm = TRUE)
a = sum((log.dat[is.finite(log.dat[, clm]), re] - mea.reg) *
log.dat[is.finite(log.dat[, clm]), clm])/sum((log.dat[is.finite(log.dat[,
clm]), re] - mea.reg) * (log.dat[is.finite(log.dat[,
clm]), re] - mea.reg))
dat[, clm] = log.dat[, clm] - a * (log.dat[, re] - log(mea,
base = 10))
return(dat)
}
nb.var = dim(data)[2] - 1
for (i in 1:nb.var) {
if (names(data)[i + 1] == reg)
reg = i
}
if (is.numeric(reg) == FALSE)
return("reg value does not exist!")
data = dat.rem.ind.pop(data, ind = Ri, pop = Rp)
if (reg == 1)
for (i in 2:nb.var) data = Reitra.va(data, clm = i +
1, re = 2)
else {
for (i in 2:reg) data = Reitra.va(data, clm = i, re = reg +
1)
if (reg < nb.var)
for (j in (reg + 1):nb.var) data = Reitra.va(data,
clm = j + 1, re = reg + 1)
}
return(data[-(reg + 1)])
}
Example output
[1] "Body_length"
Population QM1 QM2 QM3 QM4 QM5 QM6
1 A -0.7590259 -0.3951344 -0.7721667 1.569443 3.178918 1.823581
2 B -0.6460305 -0.3235728 -0.6629609 1.607328 3.379570 2.055754
3 C -0.6440391 -0.3276897 -0.6867095 1.366948 2.874679 1.827251
4 B -0.6955804 -0.4257444 -0.7338634 1.693202 2.970462 1.782825
5 C -0.6640926 -0.3147925 -0.6704503 1.320057 2.897293 1.692427
6 C -0.5770896 -0.4307417 -0.7223309 1.595669 3.309544 2.026347
7 C -0.7481464 -0.3004923 -0.6646057 1.372876 2.759956 1.756231
8 C -0.7453724 -0.3890565 -0.7537607 1.238766 3.062241 1.898475
9 C -0.8428386 -0.4068218 -0.7803727 1.325506 3.165749 1.898410
10 C -0.7777228 -0.3937156 -0.6868270 1.500305 3.448639 2.136530
11 C -0.8073174 -0.4081834 -0.7016917 1.358492 2.998838 1.747399
12 C -0.6976097 -0.3514724 -0.7087975 1.179881 3.218276 1.918657
13 C -0.7483115 -0.3808272 -0.7417273 1.376855 3.246367 2.071985
14 B -0.7815328 -0.4246299 -0.7793228 1.718582 3.852398 2.014777
15 C -0.6860165 -0.3351921 -0.6445173 1.437821 3.191525 1.894472
16 C -0.7104967 -0.3959264 -0.8004555 1.275770 2.856214 1.979147
17 B -0.6828507 -0.3436423 -0.6890728 1.642839 3.412060 1.974568
18 C -0.7608641 -0.3389340 -0.8129668 1.421813 2.547371 1.748794
19 A -0.7625689 -0.4504744 -0.7167801 1.414355 3.494346 1.969817
20 D NA -0.4200603 -0.7223319 1.531013 3.916594 2.154077
21 C -0.8056447 -0.3511445 -0.7134932 1.399458 3.098619 1.936670
22 C -0.8500376 -0.4059354 -0.7224476 1.175625 3.304756 1.904376
23 C -0.8259392 -0.4042531 -0.7639690 1.390645 2.920882 2.047240
24 C -0.8068229 -0.3717029 -0.7803494 1.465267 3.096126 2.191951
25 D -0.9619204 -0.3890197 -0.6329213 1.696196 3.517378 2.178976
26 C -0.9686718 -0.4032990 -0.7103929 1.298259 3.460825 2.122836
27 B -1.0005477 -0.3693215 -0.6819476 1.583707 3.295793 2.152527
28 C -1.0570196 -0.4093236 -0.7366735 1.482826 3.166535 2.019729
29 B -0.9467467 -0.3911789 -0.7255979 1.811491 3.441518 2.196966
30 C -1.0725824 -0.4118915 -0.7660842 1.418457 3.386840 2.029349
31 B -0.9892142 -0.4211008 -0.6900800 1.577291 3.419210 2.173526
32 B -1.0783525 -0.4349488 -0.8195825 1.721720 3.103766 2.130619
33 C -0.8638121 -0.3226918 -0.7431994 1.378899 3.125398 1.973622
34 C -0.7343324 -0.3901229 -0.7861187 1.408104 3.215272 1.912273
35 B -0.7919520 -0.3761059 -0.6789350 1.626969 3.192516 1.930886
36 C -0.9029725 -0.3925416 -0.8046770 1.439609 3.819275 2.145081
37 C -0.9591781 -0.3709245 -0.7830686 1.374193 2.947440 1.850673
38 C -0.7725225 -0.3994928 -0.7400946 1.249829 2.700035 1.655330
39 C -0.9108243 -0.3936586 -0.7544808 1.252924 2.383422 1.305578
40 C -0.9667331 -0.3501839 -0.6755846 1.401348 3.139865 2.019093
41 C -0.8941013 -0.3619764 -0.7900345 1.351949 2.823791 1.867868
42 B -0.8814940 -0.3710108 -0.6878111 1.669248 2.967117 1.946501
43 C -0.9306927 -0.4050953 -0.7572396 1.271322 2.492618 1.510157
44 B -0.8816475 -0.3910433 -0.7648788 1.584722 3.119980 1.904455
45 C -0.9190739 -0.3585301 -0.8007738 1.316148 2.769259 1.821829
46 B -0.9590637 -0.3371163 -0.6698991 1.533000 2.830847 1.881459
47 C -0.8404451 -0.3644979 -0.7902017 1.368105 2.882172 1.836777
48 C -0.9597835 -0.3793101 -0.6999402 1.223017 3.517338 2.134658
49 C NA -0.3830301 -0.8407464 1.381216 2.893305 1.897279
50 B -0.6140882 -0.4315887 -0.7765801 1.614428 3.487698 2.162679
51 C -0.7960680 -0.4207385 -0.7069342 1.327912 3.739782 2.213908
52 C -0.6937369 -0.3103980 -0.7130876 1.255638 3.900186 NA
53 C -0.7259460 -0.3507698 -0.7408208 1.263884 3.173107 2.058867
54 C -0.8986347 -0.3587543 -0.7063756 1.213707 3.722397 2.166333
55 C -1.0295976 -0.3941556 -0.6866039 1.379839 2.919430 1.878423
56 B -0.9478070 -0.4338145 -0.7776806 1.708201 4.177139 2.428601
57 C -0.9095962 -0.4616379 -0.7229030 1.394959 3.664355 2.307852
58 C -0.6168341 -0.4110634 -0.8064352 1.491690 3.623841 2.386264
59 C -0.7502251 -0.4014228 -0.7602673 1.426587 3.386773 2.250840
60 A -0.8962022 -0.3585420 -0.6857937 1.621386 3.290260 2.015227
61 C -0.7509504 -0.4258805 -0.7942989 1.476382 3.164635 2.103320
62 C NA -0.3760105 -0.7597204 1.442051 3.136912 2.021558
63 B -0.8732821 -0.4235510 -0.7483974 1.597521 3.520043 2.154109
64 C -0.7234784 -0.3620013 -0.7906425 1.230460 2.882492 2.064857
65 B -0.8060689 -0.4125184 -0.7198180 1.636458 3.724366 2.180524
66 B -0.8529520 -0.4647064 -0.7943736 1.645437 3.517154 2.165093
67 B -1.0432811 -0.4155598 -0.6997293 1.691173 3.699615 2.332843
68 C -0.7057272 -0.3742712 -0.7666012 1.473054 3.113194 2.018166
69 B -0.7339590 -0.3779371 -0.6957950 1.702123 3.791689 2.275370
70 B -0.8618488 -0.4019713 -0.7061525 1.653417 3.573178 2.243941
71 C -0.8979207 -0.3435581 -0.7107614 1.342697 3.625965 1.911590
72 C -0.9714988 -0.4181825 -0.8294199 1.383102 3.127147 2.046322
73 A -0.9311343 -0.3339285 -0.7277864 1.667552 3.367072 2.098011
74 C -0.9983369 -0.4127272 -0.7537223 1.508009 3.042904 2.091543
75 B -0.8425332 -0.4508940 -0.6815014 1.539355 3.390069 1.910459
76 C -0.9942300 -0.3700034 -0.6734641 1.294237 2.892068 1.862271
77 C -0.9183472 -0.3999953 -0.7202354 1.355145 2.720290 1.988324
78 C -0.8031948 -0.3740600 -0.6962159 1.464632 3.506855 2.269956
79 C -0.7833394 -0.3743033 -0.6953714 1.495240 2.883231 2.274431
80 B -0.7008309 -0.4193737 -0.7520027 1.758198 3.888379 2.198125
81 B -0.7912027 -0.4154184 -0.6790003 1.649903 2.781322 1.959156
82 B -0.9142669 -0.4087950 -0.6886602 1.645507 3.496307 2.100667
83 C -0.8763244 -0.4028004 -0.7709171 1.408529 2.702658 2.076631
84 C -0.7538363 -0.3139253 -0.6828325 1.400696 3.955822 2.284554
85 B -0.6600969 -0.4269418 -0.7660405 1.692185 4.502465 2.356454
86 C -0.7929989 -0.4116336 -0.7379311 1.204174 3.186346 2.037152
87 B -0.7449942 -0.4845227 -0.7851283 1.684982 4.540643 2.332709
88 A -0.8702745 -0.3720318 -0.8173183 1.588813 3.586418 2.096597
89 C -1.0447555 -0.3847242 -0.7270040 1.410897 2.442834 1.963081
90 C -0.8989025 -0.3788955 -0.7872292 1.261320 3.053650 2.113438
91 C -0.9466336 -0.3895887 -0.8273049 1.368911 3.031070 2.080764
92 D -0.9782193 -0.4457062 -0.7060653 1.681225 3.708815 2.297930
93 A -0.6600856 -0.3922845 -0.7582847 1.514347 4.058741 2.271012
94 E -0.7401867 -0.3184420 -0.6375921 1.664276 3.646811 2.066630
95 A -0.7025699 -0.4061909 -0.7208184 1.550251 3.663914 2.249341
96 A -0.6482602 -0.3615996 -0.7134261 1.552538 3.829352 2.251730
97 A -0.9000377 -0.3387984 -0.6897922 1.717697 3.361225 2.172189
98 A -0.9771293 -0.3894172 -0.7647202 1.489849 3.158529 1.908035
99 B -0.9638461 -0.3938150 -0.7651983 1.653794 3.558604 2.089396
100 C -0.9910257 -0.3447437 -0.7656910 1.504417 2.592988 1.810647
101 B -0.7902041 -0.4022844 -0.6891214 1.818787 3.471932 2.154688
102 B -0.9024824 -0.3790003 -0.6929349 1.801225 3.540681 2.044620
103 D -0.7857136 -0.4035825 -0.7544587 1.741282 3.362304 1.873395
104 B -0.8690280 -0.4029010 -0.7622345 1.695160 3.368250 2.097816
105 C -0.8934354 -0.4174098 -0.7877601 1.300509 3.236241 1.846168
106 C -1.0227260 -0.3543612 -0.6753400 1.183298 2.600647 1.839214
107 B -0.9179009 -0.3961974 -0.6650298 1.630275 2.713875 1.909834
108 C -0.7246494 -0.3819585 -0.7351477 1.410557 3.359059 2.040389
109 C -0.5940952 -0.3426013 -0.7497155 1.242445 3.143118 1.965562
110 E -0.5484003 -0.3683209 -0.6992916 1.716015 3.473756 2.164752
111 A -0.7023891 -0.3805961 -0.7277786 1.519097 3.122604 1.929666
112 B -0.6144901 -0.4142297 -0.7788816 1.618035 4.593133 2.279809
113 B -0.6271228 -0.4201209 -0.7873389 1.489125 3.747837 2.064001
114 B -0.9374338 -0.4493552 -0.7743012 1.781543 3.108606 2.037455
115 B -0.7998778 -0.3722895 -0.6970747 1.801473 3.132465 2.113559
116 C -0.9806839 -0.4039749 -0.8034511 1.357546 2.712769 1.876571
117 C -0.7040628 -0.3759114 -0.6621059 1.343174 2.678387 1.805838
118 C -0.7327413 -0.3729065 -0.6689486 1.248727 2.855726 1.771723
119 D -0.7147009 -0.4197368 -0.7778149 1.649145 3.424511 2.117672
120 C -0.9401997 -0.4195720 -0.7407069 1.390796 2.530110 1.889284
121 D -0.8326032 -0.4529377 -0.7351390 1.552748 2.798165 1.833049
122 C -1.0316787 -0.3238433 -0.6584312 1.295587 2.721084 1.775981
123 C NA -0.4054600 -0.7157939 1.237120 2.370099 1.557720
124 B -0.9681795 -0.4344302 -0.7535611 1.580779 2.303277 1.547693
125 C -0.8271119 -0.3433707 -0.6857333 1.329947 2.427966 1.539553
126 C -0.9382645 -0.3595852 -0.6709830 1.462201 3.084361 1.995462
127 D -0.9430933 -0.3663446 -0.6575747 1.513870 2.447233 1.772063
128 C -0.9656474 -0.3672694 -0.7868488 1.399111 2.781081 1.873877
129 D -0.9901482 -0.4171422 -0.7266887 1.695713 3.271073 1.975386
130 B -0.7399145 -0.4319037 -0.8293470 1.475544 2.636848 1.857653
131 B -0.9047358 -0.4113785 -0.7562850 1.793118 3.134161 2.047376
132 D -0.8169973 -0.4059113 -0.7119989 1.710995 3.877139 2.172283
133 C -0.9346004 -0.3247644 -0.7280448 1.342307 2.602518 1.772204
134 B -0.8270418 -0.4220870 -0.7859609 1.488570 2.841400 1.884408
135 B -0.8512009 -0.3400516 -0.7127701 1.671447 3.174653 2.068574
136 B -0.8534620 -0.3788833 -0.7592261 1.513307 2.934532 1.877398
137 C -0.9841095 -0.4069943 -0.6709240 1.404291 3.007007 2.010746
138 C -1.0477981 -0.3704666 -0.6997512 1.285939 3.074708 2.047092
139 B -0.8654257 -0.3978385 -0.7794363 1.618378 2.984531 2.035712
140 B -0.9262619 -0.3659393 -0.7605195 1.667439 2.830062 1.935640
141 D -0.7860189 -0.3744966 -0.6836144 1.613002 4.395341 2.320702
142 B -0.7207703 -0.3431397 -0.6905097 1.725272 3.493837 2.106486
143 C -1.0088532 -0.4210804 -0.8053397 1.262503 2.770824 1.923547
144 D -0.7544585 -0.4177477 -0.7170721 1.434969 3.691441 2.337105
145 D -1.0134058 -0.4165725 -0.7180139 1.683975 3.004423 2.008032
146 B -0.9606298 -0.3992524 -0.7495242 1.780356 3.317118 2.028899
147 B -0.8134629 -0.4472239 -0.7166747 1.629266 3.309058 1.865842
148 D NA -0.4572582 -0.7515089 1.476247 3.130523 2.095423
149 D -0.7894909 -0.3810340 -0.7318774 1.709746 3.662477 2.087767
150 B -0.8702802 -0.4212836 -0.7717762 1.675687 2.945328 1.782699
151 B -0.8959982 -0.4532867 -0.7575234 1.696700 3.340246 2.112242
152 B -0.8727787 NA NA 1.609505 3.165334 1.941069
153 B -0.7287816 -0.4411923 -0.8199154 1.820119 3.378737 2.030202
154 D -0.8306826 -0.3879402 -0.7126316 1.532213 3.665380 2.288818
155 B -1.1035728 -0.4166814 -0.7499951 1.733416 3.148637 2.077005
157 D -1.1656831 -0.4094766 -0.6568059 1.486265 3.057721 2.019742
158 B -0.8287520 -0.3778382 -0.6684581 1.860627 4.197227 2.346329
159 B -1.0108128 -0.4274124 -0.6683326 1.687959 2.955737 1.866986
160 D -1.0676344 -0.4162911 -0.7196688 1.662679 3.395881 2.220870
161 B -0.8034156 -0.3972215 -0.7568217 1.654154 3.590133 2.124283
162 B -0.8067777 -0.3983574 -0.7548814 1.706613 2.910784 2.017589
163 B NA -0.4187882 -0.7777367 1.606034 3.350810 2.121179
164 A -0.7776935 -0.3117567 -0.6716249 1.393005 3.041405 1.932921
165 D -0.9247607 -0.4777367 -0.6807628 1.583539 3.371228 2.069870
166 B -0.9998227 -0.4333877 -0.7197409 1.735350 4.131078 2.419954
167 D -1.0122711 -0.3927440 -0.6912370 1.632277 4.077273 2.337147
168 D -0.9892242 -0.3966510 -0.6997499 1.685257 3.782106 2.227818
169 B -1.0485016 -0.4178416 -0.6747679 1.672606 3.451951 2.136452
170 D -1.0501030 -0.3429475 -0.6190308 1.627386 3.097127 2.138686
171 B -1.1421587 -0.3846310 -0.6926803 1.605234 3.474970 2.235099
172 B -0.7444711 NA NA NA 2.997583 1.830673
173 B -0.6144327 -0.3990264 -0.7692508 1.532591 3.243063 1.626133
174 D -1.1170238 -0.4617040 -0.7928825 1.566525 3.689704 2.264072
175 D -0.9306243 -0.4272194 -0.7384463 1.509637 3.452680 2.217999
176 B -0.9165866 -0.4520131 -0.8190213 1.849186 3.243496 2.170018
177 B -0.6972554 -0.4309818 -0.7637556 1.610883 3.053707 1.938808
178 B -0.7013150 -0.3362897 -0.7372289 1.638397 3.298661 1.901148
179 D -0.8281413 -0.3883881 -0.7581800 1.511371 3.412672 2.082485
180 B -0.6173049 -0.3490039 -0.7318502 1.544584 3.776039 2.083347
181 B -0.6332665 -0.4129741 -0.7730550 1.618777 3.633055 2.201951
182 D -0.7560403 -0.4546400 -0.7936337 1.784590 4.199218 2.222232
183 B -0.6424603 -0.4523366 -0.7872121 1.722039 3.592274 2.359482
184 B NA -0.4342184 -0.7012054 1.768107 3.217109 1.944042
185 B -0.7443035 -0.3814828 -0.7519820 1.561112 3.267657 2.089002
186 B -0.7150350 -0.3669770 -0.7480748 1.570603 2.952830 1.832626
187 B -0.8129544 -0.4390137 -0.7225952 1.662577 3.873245 2.232115
188 B -0.7661273 -0.4153849 -0.7902126 1.705512 3.545173 2.121416
189 B -0.8765039 -0.3834105 -0.7063492 1.680270 4.077351 2.381777
190 B -0.9835638 -0.3847323 -0.6966527 1.682053 3.218837 1.903897
191 E -0.7773198 -0.3844451 -0.7043883 1.771925 3.208751 2.109849
192 B -0.7437660 -0.4684617 -0.7252402 1.766230 3.499189 1.964891
193 B -0.8043471 -0.4030203 -0.7084004 1.782507 3.666152 2.186683
194 E -0.8126684 -0.3785103 -0.6970862 1.799606 3.497210 2.304553
195 D -0.9890023 -0.4416312 -0.7597366 1.654785 3.072736 2.207125
196 D -0.8286560 -0.3949620 -0.7228262 1.526753 NA NA
197 D -0.9018886 -0.4109795 -0.6854056 1.491055 3.671315 2.160054
198 D -0.9321159 -0.3959975 -0.7021804 1.588221 3.714907 2.267305
199 D -0.9026825 -0.3852335 -0.7255204 1.492403 3.363116 2.062329
200 D -0.9484733 -0.4037686 -0.7293312 1.557575 3.573282 2.130919
QM7 Body_length QM9 QM10
1 -1.3544756 2.178029 2.286888 2.232889
2 -1.3229031 2.047586 2.438588 2.245106
3 -1.0472996 2.242912 2.204588 2.235096
4 -1.1880424 2.161376 2.434301 2.249078
5 -1.2070595 2.284468 2.353749 2.242091
6 -1.2888322 2.068618 2.510134 2.244866
7 -1.0037864 2.351616 2.301464 2.235670
8 -1.1657454 2.031124 2.360295 2.233850
9 -1.2689914 2.119810 2.198816 2.240463
10 -1.3174251 2.071396 2.384901 2.246452
11 -1.2548662 2.100637 2.351607 2.245809
12 -1.3006073 2.195875 2.160748 2.238461
13 -1.1751416 2.251024 2.071947 2.222440
14 -1.8375370 2.067709 2.374918 2.237733
15 -1.2981265 2.121731 2.324746 2.238719
16 -0.8778376 2.318556 2.394811 2.230209
17 -1.4374193 2.108677 2.329224 2.247638
18 -0.7996628 2.278862 2.437393 2.233706
19 -1.5216358 2.206300 2.328605 2.226763
20 -1.7585603 2.124160 2.422909 2.277770
21 -1.1628645 2.134833 2.352795 2.233192
22 -1.3979351 2.268689 2.167248 2.228117
23 -0.8754369 2.249301 2.331565 2.233295
24 -0.9056235 2.239813 2.264019 2.224517
25 -1.3371102 2.202751 2.370695 2.248816
26 -1.3402364 2.242712 2.314913 2.226924
27 -1.1428633 2.210510 2.304876 2.234269
28 -1.1473983 2.312915 2.419622 2.208738
29 -1.2455891 2.156014 2.481547 2.250982
30 -1.3607990 2.078430 2.257885 2.216920
31 -1.2441122 2.150327 2.465993 2.262216
32 -0.9731639 2.093950 2.432639 2.235534
33 -1.1520306 2.332512 2.284118 2.243719
34 -1.3053549 2.273078 2.309536 2.250048
35 -1.2629523 2.042835 2.391433 2.251841
36 -1.6775612 2.305502 2.136273 2.245630
37 -1.0986537 2.213806 2.339551 2.248635
38 -1.0479391 2.164846 2.230341 2.252695
39 -1.0794323 2.128667 2.330005 2.240269
40 -1.1235304 2.298153 2.438553 2.246299
41 -0.9577446 2.300407 2.281162 2.243474
42 -1.0184582 2.178015 2.397740 2.241357
43 -0.9830881 2.267401 2.482623 2.237376
44 -1.2151547 2.051180 2.488607 2.246741
45 -0.9468333 2.317466 2.248506 2.233685
46 -0.9495071 2.010695 2.481792 2.235840
47 -1.0470865 2.228967 2.340516 2.240579
48 -1.3833074 2.253238 2.239235 2.237376
49 -0.9981378 2.263227 2.146464 2.234251
50 -1.3252741 2.189517 2.236693 2.253479
51 -1.5269227 2.205367 2.222656 2.238645
52 NA 2.150606 2.308638 2.238029
53 -1.1132327 2.274693 2.265525 2.227401
54 -1.5555958 2.224105 2.226970 2.229023
55 -1.0444042 2.212192 2.325325 2.245719
56 -1.7524681 1.936528 2.361509 2.259700
57 -1.3626513 2.162648 2.208090 2.243852
58 -1.2426158 2.213938 2.313742 2.222137
59 -1.1382890 2.182328 2.330957 2.232422
60 -1.2758398 2.234656 2.207798 2.250288
61 -1.0621581 2.225157 2.353809 2.209492
62 -1.1165634 2.183262 2.312964 2.239129
63 -1.3670078 2.237455 2.351198 2.251093
64 -0.8185019 2.265147 2.279401 2.209565
65 -1.5454692 2.101852 2.394100 2.240385
66 -1.3517778 2.237449 2.355155 2.247004
67 -1.3688582 2.279920 2.238835 2.241767
68 -1.0983072 2.273765 2.340869 2.216831
69 -1.5178557 1.927517 2.436899 2.252489
70 -1.3275673 2.167196 2.389590 2.242828
71 -1.7196917 2.209698 2.321514 2.258969
72 -1.0843272 2.293464 2.375972 2.246035
73 -1.2681065 2.251774 2.427411 2.249833
74 -0.9569245 2.227600 2.315435 2.242088
75 -1.4829479 2.003880 2.537013 2.262767
76 -1.0335574 2.259468 2.406532 2.246814
77 -0.7345697 2.320557 2.267533 2.233171
78 -1.2404763 2.103638 2.364771 2.238665
79 -0.6112097 2.080351 2.446873 2.235149
80 -1.6935925 2.156847 2.485070 2.257914
81 -0.8220263 2.077150 2.403594 2.235063
82 -1.3959526 2.147630 2.408632 2.248800
83 -0.6283965 2.137523 2.302691 2.242623
84 -1.6727923 2.222963 2.360919 2.240077
85 -2.1475217 2.085076 2.473123 2.257265
86 -1.1519249 2.327553 2.194406 2.236113
87 -2.2086333 2.046198 2.393731 2.249964
88 -1.4895818 2.171379 2.231365 2.242230
89 -0.4799622 2.296836 2.307262 2.207583
90 -0.9391233 2.279360 2.193349 2.224606
91 -0.9520233 2.229483 2.312790 2.225328
92 -1.4106349 2.074945 2.479220 2.266197
93 -1.7902634 2.160717 2.377898 2.243121
94 -1.5810965 2.076841 2.503607 2.255468
95 -1.4168876 2.193576 2.403861 2.259685
96 -1.5772523 2.331659 2.321264 2.234367
97 -1.1929354 2.280954 2.329253 2.247233
98 -1.2532385 2.196163 2.390357 2.256127
99 -1.4710548 2.159775 2.454125 2.272517
100 -0.7840844 2.310070 2.348922 2.248202
101 -1.3243894 2.146815 2.437549 2.257013
102 -1.5007800 2.163570 2.455136 2.262077
103 -1.4914155 2.143649 2.437968 2.274504
104 -1.2736095 2.118285 2.387982 2.262278
105 -1.3940344 2.352124 2.295371 2.259794
106 -0.7616310 2.294474 2.423081 2.243547
107 -0.8061662 2.038286 2.575125 2.254262
108 -1.3245233 2.236551 2.209293 2.265492
109 -1.1752130 2.272714 2.277676 2.240796
110 -1.3098704 1.949719 2.380859 2.255322
111 -1.1966216 2.153453 2.304394 2.258957
112 -2.3140233 1.960768 2.242031 2.254817
113 -1.6817913 2.126918 2.176343 2.246550
114 -1.0752391 2.068918 2.430315 2.247799
115 -1.0233464 2.195482 2.441990 2.266087
116 -0.8403490 2.196194 2.365134 2.232660
117 -0.8747690 2.289780 2.365533 2.249639
118 -1.0891966 2.095294 2.260508 2.251135
119 -1.3078884 2.075852 2.507499 2.283901
120 -0.6393933 2.302743 2.256692 2.231167
121 -0.9670814 2.039293 2.460445 2.295617
122 -0.9480606 2.181942 2.446387 2.256771
123 -0.8143049 2.335336 2.275245 2.241287
124 -0.7572370 2.037196 2.334695 2.252837
125 -0.8902087 2.174188 2.280137 2.253266
126 -1.0912822 2.188949 2.431258 2.250131
127 -0.6754713 2.089408 2.484932 2.290601
128 -0.9086778 2.221948 2.141738 2.247390
129 -1.2956365 2.112352 2.532816 2.280586
130 -0.7791110 2.209236 2.350688 2.252457
131 -1.0881330 2.171280 2.345842 2.256769
132 -1.7052956 2.156164 2.541392 2.291020
133 -0.8318254 2.263614 2.172093 2.240038
134 -0.9564806 1.886639 2.481817 2.251170
135 -1.1052492 2.136730 2.286195 2.232983
136 -1.0555037 2.111861 2.248930 2.242946
137 -0.9997635 2.243247 2.204501 2.240985
138 -1.0279981 2.172495 2.299666 2.236635
139 -0.9492010 2.124190 2.217131 2.236635
140 -0.8919685 2.034423 2.281843 2.240463
141 -2.0748485 2.163297 2.515153 2.267581
142 -1.3877338 2.111225 2.331851 2.249009
143 -0.8469057 2.200942 2.233082 2.234367
144 -1.3521036 2.217230 2.494879 2.274012
145 -0.9962294 2.172922 2.459930 2.280251
146 -1.2896290 1.886231 2.601763 2.271199
147 -1.4407711 2.110326 2.230418 2.245343
148 -1.0319273 2.246034 2.496152 2.280132
149 -1.5797494 1.964418 2.498977 2.286780
150 -1.1642175 2.128667 2.463544 2.271736
151 -1.2305799 2.109991 2.436997 2.274713
152 -1.2264578 2.013562 2.254117 2.249557
153 -1.3514645 2.045812 2.351161 2.244310
154 -1.3759014 2.115965 2.379976 2.278747
155 -1.0750731 2.185257 2.542684 2.263081
157 -1.0391395 2.099603 2.517313 2.270446
158 -1.8551277 2.116667 2.422767 2.279696
159 -1.0895460 2.119462 2.406052 2.250252
160 -1.1749941 2.186809 2.460088 2.280688
161 -1.4639478 2.159922 2.371926 2.246980
162 -0.8929782 2.099268 2.426420 2.252056
163 -1.2286767 2.194421 2.376259 2.249833
164 -1.1057500 2.153766 2.321609 2.222195
165 -1.2979713 2.036010 2.319310 2.256746
166 -1.7123464 2.107789 2.469443 2.239166
167 -1.7438244 2.043619 2.354907 2.278096
168 -1.5533854 2.088860 2.313158 2.264230
169 -1.3186303 2.045529 2.223135 2.244920
170 -0.9572907 2.063876 2.427931 2.263485
171 -1.2369154 1.992223 2.389591 2.226577
172 -1.1649323 2.150379 2.276308 2.246750
173 -1.6148851 2.121203 2.325641 2.246550
174 -1.4246771 2.064342 2.311118 2.286817
175 -1.2325797 2.244291 2.481777 2.274408
176 -1.0729670 2.029730 2.484342 2.265410
177 -1.1135058 2.075809 2.427781 2.262754
178 -1.3975979 1.938953 2.393159 2.267205
179 -1.3277970 2.234187 2.395190 2.273538
180 -1.6907053 2.147483 2.343389 2.260962
181 -1.4318275 2.190580 2.484952 2.269129
182 -1.9778288 2.142863 2.620877 2.283278
183 -1.2335864 2.078069 2.460210 2.240381
184 -1.2753409 1.957828 2.490476 2.273802
185 -1.1785594 2.010511 2.417705 2.252423
186 -1.1184185 2.087263 2.285623 2.247329
187 -1.6392471 2.002365 2.466704 2.261279
188 -1.4286609 2.054019 2.473051 2.281726
189 -1.6979428 2.160647 2.486164 2.274090
190 -1.3164261 2.017008 2.446569 2.271428
191 -1.0991118 2.080628 2.493337 2.267581
192 -1.5376066 1.924107 2.537426 2.276918
193 -1.4816888 2.197590 2.507098 2.273639
194 -1.1964786 2.013543 2.512895 2.283111
195 -0.8645124 2.188979 2.566886 2.286382
196 NA 2.228525 2.405353 2.276064
197 -1.5096509 2.118202 2.427094 2.275886
198 -1.4470152 2.075130 2.371709 2.287927
199 -1.2971241 2.179437 2.533704 2.278657
200 -1.4401583 2.145861 2.420358 2.283052
function (data, reg, Rp = 0, Ri = 0)
{
dat.rem.ind.pop <- function(data, ind = 0, pop = 0) {
data = as.data.frame(data)
dat.rem.ind <- function(dat, ind) {
nb.rem.ind = length(ind)
nb.ind = dim(dat)[1]
for (i in 1:nb.rem.ind) dat = dat[row.names(dat)[1:(nb.ind -
i + 1)] != ind[i], ]
return(dat)
}
dat.rem.pop <- function(dat, pop) {
nb.rem.pop = length(pop)
for (i in 1:nb.rem.pop) dat = dat[dat[, 1] != pop[i],
]
return(dat)
}
if (ind[1] != 0)
data = dat.rem.ind(data, ind)
if (pop[1] != 0)
data = dat.rem.pop(data, pop)
return(data)
}
Reitra.va <- function(dat, clm, re) {
dat = dat[is.finite(dat[, re]), ]
log.dat = dat
mea = mean(dat[is.finite(dat[, clm]), re])
log.dat[, clm] = log(dat[, clm], base = 10)
log.dat[, re] = log(dat[, re], base = 10)
mea.clm = mean(log.dat[is.finite(log.dat[, clm]), clm],
na.rm = TRUE)
mea.reg = mean(log.dat[is.finite(log.dat[, clm]), re],
na.rm = TRUE)
a = sum((log.dat[is.finite(log.dat[, clm]), re] - mea.reg) *
log.dat[is.finite(log.dat[, clm]), clm])/sum((log.dat[is.finite(log.dat[,
clm]), re] - mea.reg) * (log.dat[is.finite(log.dat[,
clm]), re] - mea.reg))
dat[, clm] = log.dat[, clm] - a * (log.dat[, re] - log(mea,
base = 10))
return(dat)
}
nb.var = dim(data)[2] - 1
for (i in 1:nb.var) {
if (names(data)[i + 1] == reg)
reg = i
}
if (is.numeric(reg) == FALSE)
return("reg value does not exist!")
data = dat.rem.ind.pop(data, ind = Ri, pop = Rp)
if (reg == 1)
for (i in 2:nb.var) data = Reitra.va(data, clm = i +
1, re = 2)
else {
for (i in 2:reg) data = Reitra.va(data, clm = i, re = reg +
1)
if (reg < nb.var)
for (j in (reg + 1):nb.var) data = Reitra.va(data,
clm = j + 1, re = reg + 1)
}
return(data[-(reg + 1)])
}
Pstat documentation built on May 2, 2019, 5:56 a.m.
R Package Documentation
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Description Usage Arguments Value Note Author(s) References Examples
Description
'ReistTrans' calculates residuals (size adjusted measurements) from Reist tranformations to eliminate any variation resulting from allometric growth. There is a single regressor (one of the quantitative traits).
Usage
1 | ReistTrans(data, reg, Rp = 0, Ri = 0)
|
Arguments
data |
a dataframe with as many rows as individuals. The first column contains the name of the population to which the individual belongs, the others contain quantitative variables. |
reg |
the name (or the rank) of the variable chosen as the explanatory variable. |
Rp |
a vector containing the names of the populations to be deleted. |
Ri |
a vector containing each number of individual to be deleted. The vector Ri must contain existent individuals, each of them once. |
Value
the data frame of adjusted variables, the column containing the quantitative trait used as a regressor being deleted.
Note
dispensable quantitative measures can easily be deleted in the main functions of R.
Author(s)
Blondeau Da Silva Stephane - Da Silva Anne.
References
Reist J.D., 1985. An empirical evaluation of several univariate methods that adjust for size variation in morphometric data. Canadian Journal Zoology 63, 1429-1439.
Kaeuffer R. et al., 2012. Parallel and nonparallel aspects of ecological, phenotypic, and genetic divergence across replicate population pairs of lake and stream stickleback. Evolution 66(2), 402-418.
He Y. et al., 2013. Morphological Variation Among Wild Populations of Chinese Rare Minnow (Gobiocypris rarus): Deciphering the Role of Evolutionary Processes. Zoological Science 30, 475-483.
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 | data(test)
names(test)[9]
ReistTrans(test,reg=9)
## The function is currently defined as
function (data, reg, Rp = 0, Ri = 0)
{
dat.rem.ind.pop <- function(data, ind = 0, pop = 0) {
data = as.data.frame(data)
dat.rem.ind <- function(dat, ind) {
nb.rem.ind = length(ind)
nb.ind = dim(dat)[1]
for (i in 1:nb.rem.ind) dat = dat[row.names(dat)[1:(nb.ind -
i + 1)] != ind[i], ]
return(dat)
}
dat.rem.pop <- function(dat, pop) {
nb.rem.pop = length(pop)
for (i in 1:nb.rem.pop) dat = dat[dat[, 1] != pop[i],
]
return(dat)
}
if (ind[1] != 0)
data = dat.rem.ind(data, ind)
if (pop[1] != 0)
data = dat.rem.pop(data, pop)
return(data)
}
Reitra.va <- function(dat, clm, re) {
dat = dat[is.finite(dat[, re]), ]
log.dat = dat
mea = mean(dat[is.finite(dat[, clm]), re])
log.dat[, clm] = log(dat[, clm], base = 10)
log.dat[, re] = log(dat[, re], base = 10)
mea.clm = mean(log.dat[is.finite(log.dat[, clm]), clm],
na.rm = TRUE)
mea.reg = mean(log.dat[is.finite(log.dat[, clm]), re],
na.rm = TRUE)
a = sum((log.dat[is.finite(log.dat[, clm]), re] - mea.reg) *
log.dat[is.finite(log.dat[, clm]), clm])/sum((log.dat[is.finite(log.dat[,
clm]), re] - mea.reg) * (log.dat[is.finite(log.dat[,
clm]), re] - mea.reg))
dat[, clm] = log.dat[, clm] - a * (log.dat[, re] - log(mea,
base = 10))
return(dat)
}
nb.var = dim(data)[2] - 1
for (i in 1:nb.var) {
if (names(data)[i + 1] == reg)
reg = i
}
if (is.numeric(reg) == FALSE)
return("reg value does not exist!")
data = dat.rem.ind.pop(data, ind = Ri, pop = Rp)
if (reg == 1)
for (i in 2:nb.var) data = Reitra.va(data, clm = i +
1, re = 2)
else {
for (i in 2:reg) data = Reitra.va(data, clm = i, re = reg +
1)
if (reg < nb.var)
for (j in (reg + 1):nb.var) data = Reitra.va(data,
clm = j + 1, re = reg + 1)
}
return(data[-(reg + 1)])
}
|
Example output
[1] "Body_length"
Population QM1 QM2 QM3 QM4 QM5 QM6
1 A -0.7590259 -0.3951344 -0.7721667 1.569443 3.178918 1.823581
2 B -0.6460305 -0.3235728 -0.6629609 1.607328 3.379570 2.055754
3 C -0.6440391 -0.3276897 -0.6867095 1.366948 2.874679 1.827251
4 B -0.6955804 -0.4257444 -0.7338634 1.693202 2.970462 1.782825
5 C -0.6640926 -0.3147925 -0.6704503 1.320057 2.897293 1.692427
6 C -0.5770896 -0.4307417 -0.7223309 1.595669 3.309544 2.026347
7 C -0.7481464 -0.3004923 -0.6646057 1.372876 2.759956 1.756231
8 C -0.7453724 -0.3890565 -0.7537607 1.238766 3.062241 1.898475
9 C -0.8428386 -0.4068218 -0.7803727 1.325506 3.165749 1.898410
10 C -0.7777228 -0.3937156 -0.6868270 1.500305 3.448639 2.136530
11 C -0.8073174 -0.4081834 -0.7016917 1.358492 2.998838 1.747399
12 C -0.6976097 -0.3514724 -0.7087975 1.179881 3.218276 1.918657
13 C -0.7483115 -0.3808272 -0.7417273 1.376855 3.246367 2.071985
14 B -0.7815328 -0.4246299 -0.7793228 1.718582 3.852398 2.014777
15 C -0.6860165 -0.3351921 -0.6445173 1.437821 3.191525 1.894472
16 C -0.7104967 -0.3959264 -0.8004555 1.275770 2.856214 1.979147
17 B -0.6828507 -0.3436423 -0.6890728 1.642839 3.412060 1.974568
18 C -0.7608641 -0.3389340 -0.8129668 1.421813 2.547371 1.748794
19 A -0.7625689 -0.4504744 -0.7167801 1.414355 3.494346 1.969817
20 D NA -0.4200603 -0.7223319 1.531013 3.916594 2.154077
21 C -0.8056447 -0.3511445 -0.7134932 1.399458 3.098619 1.936670
22 C -0.8500376 -0.4059354 -0.7224476 1.175625 3.304756 1.904376
23 C -0.8259392 -0.4042531 -0.7639690 1.390645 2.920882 2.047240
24 C -0.8068229 -0.3717029 -0.7803494 1.465267 3.096126 2.191951
25 D -0.9619204 -0.3890197 -0.6329213 1.696196 3.517378 2.178976
26 C -0.9686718 -0.4032990 -0.7103929 1.298259 3.460825 2.122836
27 B -1.0005477 -0.3693215 -0.6819476 1.583707 3.295793 2.152527
28 C -1.0570196 -0.4093236 -0.7366735 1.482826 3.166535 2.019729
29 B -0.9467467 -0.3911789 -0.7255979 1.811491 3.441518 2.196966
30 C -1.0725824 -0.4118915 -0.7660842 1.418457 3.386840 2.029349
31 B -0.9892142 -0.4211008 -0.6900800 1.577291 3.419210 2.173526
32 B -1.0783525 -0.4349488 -0.8195825 1.721720 3.103766 2.130619
33 C -0.8638121 -0.3226918 -0.7431994 1.378899 3.125398 1.973622
34 C -0.7343324 -0.3901229 -0.7861187 1.408104 3.215272 1.912273
35 B -0.7919520 -0.3761059 -0.6789350 1.626969 3.192516 1.930886
36 C -0.9029725 -0.3925416 -0.8046770 1.439609 3.819275 2.145081
37 C -0.9591781 -0.3709245 -0.7830686 1.374193 2.947440 1.850673
38 C -0.7725225 -0.3994928 -0.7400946 1.249829 2.700035 1.655330
39 C -0.9108243 -0.3936586 -0.7544808 1.252924 2.383422 1.305578
40 C -0.9667331 -0.3501839 -0.6755846 1.401348 3.139865 2.019093
41 C -0.8941013 -0.3619764 -0.7900345 1.351949 2.823791 1.867868
42 B -0.8814940 -0.3710108 -0.6878111 1.669248 2.967117 1.946501
43 C -0.9306927 -0.4050953 -0.7572396 1.271322 2.492618 1.510157
44 B -0.8816475 -0.3910433 -0.7648788 1.584722 3.119980 1.904455
45 C -0.9190739 -0.3585301 -0.8007738 1.316148 2.769259 1.821829
46 B -0.9590637 -0.3371163 -0.6698991 1.533000 2.830847 1.881459
47 C -0.8404451 -0.3644979 -0.7902017 1.368105 2.882172 1.836777
48 C -0.9597835 -0.3793101 -0.6999402 1.223017 3.517338 2.134658
49 C NA -0.3830301 -0.8407464 1.381216 2.893305 1.897279
50 B -0.6140882 -0.4315887 -0.7765801 1.614428 3.487698 2.162679
51 C -0.7960680 -0.4207385 -0.7069342 1.327912 3.739782 2.213908
52 C -0.6937369 -0.3103980 -0.7130876 1.255638 3.900186 NA
53 C -0.7259460 -0.3507698 -0.7408208 1.263884 3.173107 2.058867
54 C -0.8986347 -0.3587543 -0.7063756 1.213707 3.722397 2.166333
55 C -1.0295976 -0.3941556 -0.6866039 1.379839 2.919430 1.878423
56 B -0.9478070 -0.4338145 -0.7776806 1.708201 4.177139 2.428601
57 C -0.9095962 -0.4616379 -0.7229030 1.394959 3.664355 2.307852
58 C -0.6168341 -0.4110634 -0.8064352 1.491690 3.623841 2.386264
59 C -0.7502251 -0.4014228 -0.7602673 1.426587 3.386773 2.250840
60 A -0.8962022 -0.3585420 -0.6857937 1.621386 3.290260 2.015227
61 C -0.7509504 -0.4258805 -0.7942989 1.476382 3.164635 2.103320
62 C NA -0.3760105 -0.7597204 1.442051 3.136912 2.021558
63 B -0.8732821 -0.4235510 -0.7483974 1.597521 3.520043 2.154109
64 C -0.7234784 -0.3620013 -0.7906425 1.230460 2.882492 2.064857
65 B -0.8060689 -0.4125184 -0.7198180 1.636458 3.724366 2.180524
66 B -0.8529520 -0.4647064 -0.7943736 1.645437 3.517154 2.165093
67 B -1.0432811 -0.4155598 -0.6997293 1.691173 3.699615 2.332843
68 C -0.7057272 -0.3742712 -0.7666012 1.473054 3.113194 2.018166
69 B -0.7339590 -0.3779371 -0.6957950 1.702123 3.791689 2.275370
70 B -0.8618488 -0.4019713 -0.7061525 1.653417 3.573178 2.243941
71 C -0.8979207 -0.3435581 -0.7107614 1.342697 3.625965 1.911590
72 C -0.9714988 -0.4181825 -0.8294199 1.383102 3.127147 2.046322
73 A -0.9311343 -0.3339285 -0.7277864 1.667552 3.367072 2.098011
74 C -0.9983369 -0.4127272 -0.7537223 1.508009 3.042904 2.091543
75 B -0.8425332 -0.4508940 -0.6815014 1.539355 3.390069 1.910459
76 C -0.9942300 -0.3700034 -0.6734641 1.294237 2.892068 1.862271
77 C -0.9183472 -0.3999953 -0.7202354 1.355145 2.720290 1.988324
78 C -0.8031948 -0.3740600 -0.6962159 1.464632 3.506855 2.269956
79 C -0.7833394 -0.3743033 -0.6953714 1.495240 2.883231 2.274431
80 B -0.7008309 -0.4193737 -0.7520027 1.758198 3.888379 2.198125
81 B -0.7912027 -0.4154184 -0.6790003 1.649903 2.781322 1.959156
82 B -0.9142669 -0.4087950 -0.6886602 1.645507 3.496307 2.100667
83 C -0.8763244 -0.4028004 -0.7709171 1.408529 2.702658 2.076631
84 C -0.7538363 -0.3139253 -0.6828325 1.400696 3.955822 2.284554
85 B -0.6600969 -0.4269418 -0.7660405 1.692185 4.502465 2.356454
86 C -0.7929989 -0.4116336 -0.7379311 1.204174 3.186346 2.037152
87 B -0.7449942 -0.4845227 -0.7851283 1.684982 4.540643 2.332709
88 A -0.8702745 -0.3720318 -0.8173183 1.588813 3.586418 2.096597
89 C -1.0447555 -0.3847242 -0.7270040 1.410897 2.442834 1.963081
90 C -0.8989025 -0.3788955 -0.7872292 1.261320 3.053650 2.113438
91 C -0.9466336 -0.3895887 -0.8273049 1.368911 3.031070 2.080764
92 D -0.9782193 -0.4457062 -0.7060653 1.681225 3.708815 2.297930
93 A -0.6600856 -0.3922845 -0.7582847 1.514347 4.058741 2.271012
94 E -0.7401867 -0.3184420 -0.6375921 1.664276 3.646811 2.066630
95 A -0.7025699 -0.4061909 -0.7208184 1.550251 3.663914 2.249341
96 A -0.6482602 -0.3615996 -0.7134261 1.552538 3.829352 2.251730
97 A -0.9000377 -0.3387984 -0.6897922 1.717697 3.361225 2.172189
98 A -0.9771293 -0.3894172 -0.7647202 1.489849 3.158529 1.908035
99 B -0.9638461 -0.3938150 -0.7651983 1.653794 3.558604 2.089396
100 C -0.9910257 -0.3447437 -0.7656910 1.504417 2.592988 1.810647
101 B -0.7902041 -0.4022844 -0.6891214 1.818787 3.471932 2.154688
102 B -0.9024824 -0.3790003 -0.6929349 1.801225 3.540681 2.044620
103 D -0.7857136 -0.4035825 -0.7544587 1.741282 3.362304 1.873395
104 B -0.8690280 -0.4029010 -0.7622345 1.695160 3.368250 2.097816
105 C -0.8934354 -0.4174098 -0.7877601 1.300509 3.236241 1.846168
106 C -1.0227260 -0.3543612 -0.6753400 1.183298 2.600647 1.839214
107 B -0.9179009 -0.3961974 -0.6650298 1.630275 2.713875 1.909834
108 C -0.7246494 -0.3819585 -0.7351477 1.410557 3.359059 2.040389
109 C -0.5940952 -0.3426013 -0.7497155 1.242445 3.143118 1.965562
110 E -0.5484003 -0.3683209 -0.6992916 1.716015 3.473756 2.164752
111 A -0.7023891 -0.3805961 -0.7277786 1.519097 3.122604 1.929666
112 B -0.6144901 -0.4142297 -0.7788816 1.618035 4.593133 2.279809
113 B -0.6271228 -0.4201209 -0.7873389 1.489125 3.747837 2.064001
114 B -0.9374338 -0.4493552 -0.7743012 1.781543 3.108606 2.037455
115 B -0.7998778 -0.3722895 -0.6970747 1.801473 3.132465 2.113559
116 C -0.9806839 -0.4039749 -0.8034511 1.357546 2.712769 1.876571
117 C -0.7040628 -0.3759114 -0.6621059 1.343174 2.678387 1.805838
118 C -0.7327413 -0.3729065 -0.6689486 1.248727 2.855726 1.771723
119 D -0.7147009 -0.4197368 -0.7778149 1.649145 3.424511 2.117672
120 C -0.9401997 -0.4195720 -0.7407069 1.390796 2.530110 1.889284
121 D -0.8326032 -0.4529377 -0.7351390 1.552748 2.798165 1.833049
122 C -1.0316787 -0.3238433 -0.6584312 1.295587 2.721084 1.775981
123 C NA -0.4054600 -0.7157939 1.237120 2.370099 1.557720
124 B -0.9681795 -0.4344302 -0.7535611 1.580779 2.303277 1.547693
125 C -0.8271119 -0.3433707 -0.6857333 1.329947 2.427966 1.539553
126 C -0.9382645 -0.3595852 -0.6709830 1.462201 3.084361 1.995462
127 D -0.9430933 -0.3663446 -0.6575747 1.513870 2.447233 1.772063
128 C -0.9656474 -0.3672694 -0.7868488 1.399111 2.781081 1.873877
129 D -0.9901482 -0.4171422 -0.7266887 1.695713 3.271073 1.975386
130 B -0.7399145 -0.4319037 -0.8293470 1.475544 2.636848 1.857653
131 B -0.9047358 -0.4113785 -0.7562850 1.793118 3.134161 2.047376
132 D -0.8169973 -0.4059113 -0.7119989 1.710995 3.877139 2.172283
133 C -0.9346004 -0.3247644 -0.7280448 1.342307 2.602518 1.772204
134 B -0.8270418 -0.4220870 -0.7859609 1.488570 2.841400 1.884408
135 B -0.8512009 -0.3400516 -0.7127701 1.671447 3.174653 2.068574
136 B -0.8534620 -0.3788833 -0.7592261 1.513307 2.934532 1.877398
137 C -0.9841095 -0.4069943 -0.6709240 1.404291 3.007007 2.010746
138 C -1.0477981 -0.3704666 -0.6997512 1.285939 3.074708 2.047092
139 B -0.8654257 -0.3978385 -0.7794363 1.618378 2.984531 2.035712
140 B -0.9262619 -0.3659393 -0.7605195 1.667439 2.830062 1.935640
141 D -0.7860189 -0.3744966 -0.6836144 1.613002 4.395341 2.320702
142 B -0.7207703 -0.3431397 -0.6905097 1.725272 3.493837 2.106486
143 C -1.0088532 -0.4210804 -0.8053397 1.262503 2.770824 1.923547
144 D -0.7544585 -0.4177477 -0.7170721 1.434969 3.691441 2.337105
145 D -1.0134058 -0.4165725 -0.7180139 1.683975 3.004423 2.008032
146 B -0.9606298 -0.3992524 -0.7495242 1.780356 3.317118 2.028899
147 B -0.8134629 -0.4472239 -0.7166747 1.629266 3.309058 1.865842
148 D NA -0.4572582 -0.7515089 1.476247 3.130523 2.095423
149 D -0.7894909 -0.3810340 -0.7318774 1.709746 3.662477 2.087767
150 B -0.8702802 -0.4212836 -0.7717762 1.675687 2.945328 1.782699
151 B -0.8959982 -0.4532867 -0.7575234 1.696700 3.340246 2.112242
152 B -0.8727787 NA NA 1.609505 3.165334 1.941069
153 B -0.7287816 -0.4411923 -0.8199154 1.820119 3.378737 2.030202
154 D -0.8306826 -0.3879402 -0.7126316 1.532213 3.665380 2.288818
155 B -1.1035728 -0.4166814 -0.7499951 1.733416 3.148637 2.077005
157 D -1.1656831 -0.4094766 -0.6568059 1.486265 3.057721 2.019742
158 B -0.8287520 -0.3778382 -0.6684581 1.860627 4.197227 2.346329
159 B -1.0108128 -0.4274124 -0.6683326 1.687959 2.955737 1.866986
160 D -1.0676344 -0.4162911 -0.7196688 1.662679 3.395881 2.220870
161 B -0.8034156 -0.3972215 -0.7568217 1.654154 3.590133 2.124283
162 B -0.8067777 -0.3983574 -0.7548814 1.706613 2.910784 2.017589
163 B NA -0.4187882 -0.7777367 1.606034 3.350810 2.121179
164 A -0.7776935 -0.3117567 -0.6716249 1.393005 3.041405 1.932921
165 D -0.9247607 -0.4777367 -0.6807628 1.583539 3.371228 2.069870
166 B -0.9998227 -0.4333877 -0.7197409 1.735350 4.131078 2.419954
167 D -1.0122711 -0.3927440 -0.6912370 1.632277 4.077273 2.337147
168 D -0.9892242 -0.3966510 -0.6997499 1.685257 3.782106 2.227818
169 B -1.0485016 -0.4178416 -0.6747679 1.672606 3.451951 2.136452
170 D -1.0501030 -0.3429475 -0.6190308 1.627386 3.097127 2.138686
171 B -1.1421587 -0.3846310 -0.6926803 1.605234 3.474970 2.235099
172 B -0.7444711 NA NA NA 2.997583 1.830673
173 B -0.6144327 -0.3990264 -0.7692508 1.532591 3.243063 1.626133
174 D -1.1170238 -0.4617040 -0.7928825 1.566525 3.689704 2.264072
175 D -0.9306243 -0.4272194 -0.7384463 1.509637 3.452680 2.217999
176 B -0.9165866 -0.4520131 -0.8190213 1.849186 3.243496 2.170018
177 B -0.6972554 -0.4309818 -0.7637556 1.610883 3.053707 1.938808
178 B -0.7013150 -0.3362897 -0.7372289 1.638397 3.298661 1.901148
179 D -0.8281413 -0.3883881 -0.7581800 1.511371 3.412672 2.082485
180 B -0.6173049 -0.3490039 -0.7318502 1.544584 3.776039 2.083347
181 B -0.6332665 -0.4129741 -0.7730550 1.618777 3.633055 2.201951
182 D -0.7560403 -0.4546400 -0.7936337 1.784590 4.199218 2.222232
183 B -0.6424603 -0.4523366 -0.7872121 1.722039 3.592274 2.359482
184 B NA -0.4342184 -0.7012054 1.768107 3.217109 1.944042
185 B -0.7443035 -0.3814828 -0.7519820 1.561112 3.267657 2.089002
186 B -0.7150350 -0.3669770 -0.7480748 1.570603 2.952830 1.832626
187 B -0.8129544 -0.4390137 -0.7225952 1.662577 3.873245 2.232115
188 B -0.7661273 -0.4153849 -0.7902126 1.705512 3.545173 2.121416
189 B -0.8765039 -0.3834105 -0.7063492 1.680270 4.077351 2.381777
190 B -0.9835638 -0.3847323 -0.6966527 1.682053 3.218837 1.903897
191 E -0.7773198 -0.3844451 -0.7043883 1.771925 3.208751 2.109849
192 B -0.7437660 -0.4684617 -0.7252402 1.766230 3.499189 1.964891
193 B -0.8043471 -0.4030203 -0.7084004 1.782507 3.666152 2.186683
194 E -0.8126684 -0.3785103 -0.6970862 1.799606 3.497210 2.304553
195 D -0.9890023 -0.4416312 -0.7597366 1.654785 3.072736 2.207125
196 D -0.8286560 -0.3949620 -0.7228262 1.526753 NA NA
197 D -0.9018886 -0.4109795 -0.6854056 1.491055 3.671315 2.160054
198 D -0.9321159 -0.3959975 -0.7021804 1.588221 3.714907 2.267305
199 D -0.9026825 -0.3852335 -0.7255204 1.492403 3.363116 2.062329
200 D -0.9484733 -0.4037686 -0.7293312 1.557575 3.573282 2.130919
QM7 Body_length QM9 QM10
1 -1.3544756 2.178029 2.286888 2.232889
2 -1.3229031 2.047586 2.438588 2.245106
3 -1.0472996 2.242912 2.204588 2.235096
4 -1.1880424 2.161376 2.434301 2.249078
5 -1.2070595 2.284468 2.353749 2.242091
6 -1.2888322 2.068618 2.510134 2.244866
7 -1.0037864 2.351616 2.301464 2.235670
8 -1.1657454 2.031124 2.360295 2.233850
9 -1.2689914 2.119810 2.198816 2.240463
10 -1.3174251 2.071396 2.384901 2.246452
11 -1.2548662 2.100637 2.351607 2.245809
12 -1.3006073 2.195875 2.160748 2.238461
13 -1.1751416 2.251024 2.071947 2.222440
14 -1.8375370 2.067709 2.374918 2.237733
15 -1.2981265 2.121731 2.324746 2.238719
16 -0.8778376 2.318556 2.394811 2.230209
17 -1.4374193 2.108677 2.329224 2.247638
18 -0.7996628 2.278862 2.437393 2.233706
19 -1.5216358 2.206300 2.328605 2.226763
20 -1.7585603 2.124160 2.422909 2.277770
21 -1.1628645 2.134833 2.352795 2.233192
22 -1.3979351 2.268689 2.167248 2.228117
23 -0.8754369 2.249301 2.331565 2.233295
24 -0.9056235 2.239813 2.264019 2.224517
25 -1.3371102 2.202751 2.370695 2.248816
26 -1.3402364 2.242712 2.314913 2.226924
27 -1.1428633 2.210510 2.304876 2.234269
28 -1.1473983 2.312915 2.419622 2.208738
29 -1.2455891 2.156014 2.481547 2.250982
30 -1.3607990 2.078430 2.257885 2.216920
31 -1.2441122 2.150327 2.465993 2.262216
32 -0.9731639 2.093950 2.432639 2.235534
33 -1.1520306 2.332512 2.284118 2.243719
34 -1.3053549 2.273078 2.309536 2.250048
35 -1.2629523 2.042835 2.391433 2.251841
36 -1.6775612 2.305502 2.136273 2.245630
37 -1.0986537 2.213806 2.339551 2.248635
38 -1.0479391 2.164846 2.230341 2.252695
39 -1.0794323 2.128667 2.330005 2.240269
40 -1.1235304 2.298153 2.438553 2.246299
41 -0.9577446 2.300407 2.281162 2.243474
42 -1.0184582 2.178015 2.397740 2.241357
43 -0.9830881 2.267401 2.482623 2.237376
44 -1.2151547 2.051180 2.488607 2.246741
45 -0.9468333 2.317466 2.248506 2.233685
46 -0.9495071 2.010695 2.481792 2.235840
47 -1.0470865 2.228967 2.340516 2.240579
48 -1.3833074 2.253238 2.239235 2.237376
49 -0.9981378 2.263227 2.146464 2.234251
50 -1.3252741 2.189517 2.236693 2.253479
51 -1.5269227 2.205367 2.222656 2.238645
52 NA 2.150606 2.308638 2.238029
53 -1.1132327 2.274693 2.265525 2.227401
54 -1.5555958 2.224105 2.226970 2.229023
55 -1.0444042 2.212192 2.325325 2.245719
56 -1.7524681 1.936528 2.361509 2.259700
57 -1.3626513 2.162648 2.208090 2.243852
58 -1.2426158 2.213938 2.313742 2.222137
59 -1.1382890 2.182328 2.330957 2.232422
60 -1.2758398 2.234656 2.207798 2.250288
61 -1.0621581 2.225157 2.353809 2.209492
62 -1.1165634 2.183262 2.312964 2.239129
63 -1.3670078 2.237455 2.351198 2.251093
64 -0.8185019 2.265147 2.279401 2.209565
65 -1.5454692 2.101852 2.394100 2.240385
66 -1.3517778 2.237449 2.355155 2.247004
67 -1.3688582 2.279920 2.238835 2.241767
68 -1.0983072 2.273765 2.340869 2.216831
69 -1.5178557 1.927517 2.436899 2.252489
70 -1.3275673 2.167196 2.389590 2.242828
71 -1.7196917 2.209698 2.321514 2.258969
72 -1.0843272 2.293464 2.375972 2.246035
73 -1.2681065 2.251774 2.427411 2.249833
74 -0.9569245 2.227600 2.315435 2.242088
75 -1.4829479 2.003880 2.537013 2.262767
76 -1.0335574 2.259468 2.406532 2.246814
77 -0.7345697 2.320557 2.267533 2.233171
78 -1.2404763 2.103638 2.364771 2.238665
79 -0.6112097 2.080351 2.446873 2.235149
80 -1.6935925 2.156847 2.485070 2.257914
81 -0.8220263 2.077150 2.403594 2.235063
82 -1.3959526 2.147630 2.408632 2.248800
83 -0.6283965 2.137523 2.302691 2.242623
84 -1.6727923 2.222963 2.360919 2.240077
85 -2.1475217 2.085076 2.473123 2.257265
86 -1.1519249 2.327553 2.194406 2.236113
87 -2.2086333 2.046198 2.393731 2.249964
88 -1.4895818 2.171379 2.231365 2.242230
89 -0.4799622 2.296836 2.307262 2.207583
90 -0.9391233 2.279360 2.193349 2.224606
91 -0.9520233 2.229483 2.312790 2.225328
92 -1.4106349 2.074945 2.479220 2.266197
93 -1.7902634 2.160717 2.377898 2.243121
94 -1.5810965 2.076841 2.503607 2.255468
95 -1.4168876 2.193576 2.403861 2.259685
96 -1.5772523 2.331659 2.321264 2.234367
97 -1.1929354 2.280954 2.329253 2.247233
98 -1.2532385 2.196163 2.390357 2.256127
99 -1.4710548 2.159775 2.454125 2.272517
100 -0.7840844 2.310070 2.348922 2.248202
101 -1.3243894 2.146815 2.437549 2.257013
102 -1.5007800 2.163570 2.455136 2.262077
103 -1.4914155 2.143649 2.437968 2.274504
104 -1.2736095 2.118285 2.387982 2.262278
105 -1.3940344 2.352124 2.295371 2.259794
106 -0.7616310 2.294474 2.423081 2.243547
107 -0.8061662 2.038286 2.575125 2.254262
108 -1.3245233 2.236551 2.209293 2.265492
109 -1.1752130 2.272714 2.277676 2.240796
110 -1.3098704 1.949719 2.380859 2.255322
111 -1.1966216 2.153453 2.304394 2.258957
112 -2.3140233 1.960768 2.242031 2.254817
113 -1.6817913 2.126918 2.176343 2.246550
114 -1.0752391 2.068918 2.430315 2.247799
115 -1.0233464 2.195482 2.441990 2.266087
116 -0.8403490 2.196194 2.365134 2.232660
117 -0.8747690 2.289780 2.365533 2.249639
118 -1.0891966 2.095294 2.260508 2.251135
119 -1.3078884 2.075852 2.507499 2.283901
120 -0.6393933 2.302743 2.256692 2.231167
121 -0.9670814 2.039293 2.460445 2.295617
122 -0.9480606 2.181942 2.446387 2.256771
123 -0.8143049 2.335336 2.275245 2.241287
124 -0.7572370 2.037196 2.334695 2.252837
125 -0.8902087 2.174188 2.280137 2.253266
126 -1.0912822 2.188949 2.431258 2.250131
127 -0.6754713 2.089408 2.484932 2.290601
128 -0.9086778 2.221948 2.141738 2.247390
129 -1.2956365 2.112352 2.532816 2.280586
130 -0.7791110 2.209236 2.350688 2.252457
131 -1.0881330 2.171280 2.345842 2.256769
132 -1.7052956 2.156164 2.541392 2.291020
133 -0.8318254 2.263614 2.172093 2.240038
134 -0.9564806 1.886639 2.481817 2.251170
135 -1.1052492 2.136730 2.286195 2.232983
136 -1.0555037 2.111861 2.248930 2.242946
137 -0.9997635 2.243247 2.204501 2.240985
138 -1.0279981 2.172495 2.299666 2.236635
139 -0.9492010 2.124190 2.217131 2.236635
140 -0.8919685 2.034423 2.281843 2.240463
141 -2.0748485 2.163297 2.515153 2.267581
142 -1.3877338 2.111225 2.331851 2.249009
143 -0.8469057 2.200942 2.233082 2.234367
144 -1.3521036 2.217230 2.494879 2.274012
145 -0.9962294 2.172922 2.459930 2.280251
146 -1.2896290 1.886231 2.601763 2.271199
147 -1.4407711 2.110326 2.230418 2.245343
148 -1.0319273 2.246034 2.496152 2.280132
149 -1.5797494 1.964418 2.498977 2.286780
150 -1.1642175 2.128667 2.463544 2.271736
151 -1.2305799 2.109991 2.436997 2.274713
152 -1.2264578 2.013562 2.254117 2.249557
153 -1.3514645 2.045812 2.351161 2.244310
154 -1.3759014 2.115965 2.379976 2.278747
155 -1.0750731 2.185257 2.542684 2.263081
157 -1.0391395 2.099603 2.517313 2.270446
158 -1.8551277 2.116667 2.422767 2.279696
159 -1.0895460 2.119462 2.406052 2.250252
160 -1.1749941 2.186809 2.460088 2.280688
161 -1.4639478 2.159922 2.371926 2.246980
162 -0.8929782 2.099268 2.426420 2.252056
163 -1.2286767 2.194421 2.376259 2.249833
164 -1.1057500 2.153766 2.321609 2.222195
165 -1.2979713 2.036010 2.319310 2.256746
166 -1.7123464 2.107789 2.469443 2.239166
167 -1.7438244 2.043619 2.354907 2.278096
168 -1.5533854 2.088860 2.313158 2.264230
169 -1.3186303 2.045529 2.223135 2.244920
170 -0.9572907 2.063876 2.427931 2.263485
171 -1.2369154 1.992223 2.389591 2.226577
172 -1.1649323 2.150379 2.276308 2.246750
173 -1.6148851 2.121203 2.325641 2.246550
174 -1.4246771 2.064342 2.311118 2.286817
175 -1.2325797 2.244291 2.481777 2.274408
176 -1.0729670 2.029730 2.484342 2.265410
177 -1.1135058 2.075809 2.427781 2.262754
178 -1.3975979 1.938953 2.393159 2.267205
179 -1.3277970 2.234187 2.395190 2.273538
180 -1.6907053 2.147483 2.343389 2.260962
181 -1.4318275 2.190580 2.484952 2.269129
182 -1.9778288 2.142863 2.620877 2.283278
183 -1.2335864 2.078069 2.460210 2.240381
184 -1.2753409 1.957828 2.490476 2.273802
185 -1.1785594 2.010511 2.417705 2.252423
186 -1.1184185 2.087263 2.285623 2.247329
187 -1.6392471 2.002365 2.466704 2.261279
188 -1.4286609 2.054019 2.473051 2.281726
189 -1.6979428 2.160647 2.486164 2.274090
190 -1.3164261 2.017008 2.446569 2.271428
191 -1.0991118 2.080628 2.493337 2.267581
192 -1.5376066 1.924107 2.537426 2.276918
193 -1.4816888 2.197590 2.507098 2.273639
194 -1.1964786 2.013543 2.512895 2.283111
195 -0.8645124 2.188979 2.566886 2.286382
196 NA 2.228525 2.405353 2.276064
197 -1.5096509 2.118202 2.427094 2.275886
198 -1.4470152 2.075130 2.371709 2.287927
199 -1.2971241 2.179437 2.533704 2.278657
200 -1.4401583 2.145861 2.420358 2.283052
function (data, reg, Rp = 0, Ri = 0)
{
dat.rem.ind.pop <- function(data, ind = 0, pop = 0) {
data = as.data.frame(data)
dat.rem.ind <- function(dat, ind) {
nb.rem.ind = length(ind)
nb.ind = dim(dat)[1]
for (i in 1:nb.rem.ind) dat = dat[row.names(dat)[1:(nb.ind -
i + 1)] != ind[i], ]
return(dat)
}
dat.rem.pop <- function(dat, pop) {
nb.rem.pop = length(pop)
for (i in 1:nb.rem.pop) dat = dat[dat[, 1] != pop[i],
]
return(dat)
}
if (ind[1] != 0)
data = dat.rem.ind(data, ind)
if (pop[1] != 0)
data = dat.rem.pop(data, pop)
return(data)
}
Reitra.va <- function(dat, clm, re) {
dat = dat[is.finite(dat[, re]), ]
log.dat = dat
mea = mean(dat[is.finite(dat[, clm]), re])
log.dat[, clm] = log(dat[, clm], base = 10)
log.dat[, re] = log(dat[, re], base = 10)
mea.clm = mean(log.dat[is.finite(log.dat[, clm]), clm],
na.rm = TRUE)
mea.reg = mean(log.dat[is.finite(log.dat[, clm]), re],
na.rm = TRUE)
a = sum((log.dat[is.finite(log.dat[, clm]), re] - mea.reg) *
log.dat[is.finite(log.dat[, clm]), clm])/sum((log.dat[is.finite(log.dat[,
clm]), re] - mea.reg) * (log.dat[is.finite(log.dat[,
clm]), re] - mea.reg))
dat[, clm] = log.dat[, clm] - a * (log.dat[, re] - log(mea,
base = 10))
return(dat)
}
nb.var = dim(data)[2] - 1
for (i in 1:nb.var) {
if (names(data)[i + 1] == reg)
reg = i
}
if (is.numeric(reg) == FALSE)
return("reg value does not exist!")
data = dat.rem.ind.pop(data, ind = Ri, pop = Rp)
if (reg == 1)
for (i in 2:nb.var) data = Reitra.va(data, clm = i +
1, re = 2)
else {
for (i in 2:reg) data = Reitra.va(data, clm = i, re = reg +
1)
if (reg < nb.var)
for (j in (reg + 1):nb.var) data = Reitra.va(data,
clm = j + 1, re = reg + 1)
}
return(data[-(reg + 1)])
}
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