Extract predictions of the genotypic value from an object of class
fitMod.
Usage
getGenoPred(
fitMod,
timePoints = names(fitMod),
predictChecks = FALSE,
outFile = NULL
)Arguments
- fitMod
An object of class
fitMod.- timePoints
A character or numeric vector indicating the time point(s) for which the predictions should be extracted. When using a character string to reference a time point, the value has to be an exact match to one of the existing time points. When using a number it will be matched by its number ("timeNumber") in the timePoints attribute of the TP object.
- predictChecks
Should predictions of the check genotypes be included in the ouptut. If
TRUEa list of twodata.framesis returned from the function, one with the predictions for the regular genotypes and one with the predictions for the checks.- outFile
A character string indicating the .csv file to which the results should be written. If
NULLno file is written.
Value
A list of two data.frames with predicted genotypic values per time
point. genoPred with the predicted values for the genotypes and
checkPred with the predicted values for the checks. If
predictChecks = FALSE the latter will be NULL.
See also
Other functions for spatial modeling:
fitModels(),
getCorrected(),
getEffDims(),
getHerit(),
getVar(),
plot.fitMod(),
summary.fitMod()
Examples
## Using the first example dataset (PhenovatorDat1).
# \donttest{
phenoTP <- createTimePoints(dat = PhenovatorDat1,
experimentName = "Phenovator",
genotype = "Genotype",
timePoint = "timepoints",
repId = "Replicate",
plotId = "pos",
rowNum = "y", colNum = "x",
addCheck = TRUE,
checkGenotypes = c("check1", "check2",
"check3", "check4"))
#> Warning: The following plotIds have observations for less than 50% of the time points:
#> c24r41, c7r18, c7r49
## Fit a SpATS model on few time points.
modPhenoSp <- fitModels(TP = phenoTP,
trait = "EffpsII",
timePoints = c(1, 6, 20))
#> 2018-05-31 16:37:00
#> 2018-06-02 09:07:00
#> 2018-06-05 14:37:00
## Extract the genotypic predictions for one time point:
genoPredSp <- getGenoPred(modPhenoSp,
timePoints = 6)
head(genoPredSp)
#> $genoPred
#> timeNumber timePoint genotype predicted.values standard.errors
#> 1 6 2018-06-02 09:07:00 G001 0.6664379 0.007700058
#> 2 6 2018-06-02 09:07:00 G002 0.6649805 0.007700359
#> 3 6 2018-06-02 09:07:00 G003 0.6569831 0.007704902
#> 4 6 2018-06-02 09:07:00 G004 0.6122083 0.007729850
#> 5 6 2018-06-02 09:07:00 G005 0.6576721 0.007697154
#> 6 6 2018-06-02 09:07:00 G006 0.6442406 0.007711890
#> 7 6 2018-06-02 09:07:00 G007 0.6620636 0.007709637
#> 8 6 2018-06-02 09:07:00 G008 0.6592120 0.007709473
#> 9 6 2018-06-02 09:07:00 G009 0.6386014 0.007697191
#> 10 6 2018-06-02 09:07:00 G010 0.6516471 0.007705202
#> 11 6 2018-06-02 09:07:00 G011 0.6750342 0.007708246
#> 12 6 2018-06-02 09:07:00 G012 0.6498224 0.007707951
#> 13 6 2018-06-02 09:07:00 G013 0.6605911 0.007700541
#> 14 6 2018-06-02 09:07:00 G014 0.6554624 0.007703979
#> 15 6 2018-06-02 09:07:00 G015 0.6597110 0.007705703
#> 16 6 2018-06-02 09:07:00 G016 0.6567955 0.007703997
#> 17 6 2018-06-02 09:07:00 G017 0.6591929 0.007695574
#> 18 6 2018-06-02 09:07:00 G018 0.6762427 0.007702262
#> 19 6 2018-06-02 09:07:00 G019 0.6659143 0.007707118
#> 20 6 2018-06-02 09:07:00 G020 0.6645302 0.007709326
#> 21 6 2018-06-02 09:07:00 G021 0.6846686 0.007701105
#> 22 6 2018-06-02 09:07:00 G022 0.6509674 0.008658303
#> 23 6 2018-06-02 09:07:00 G023 0.6830110 0.007702653
#> 24 6 2018-06-02 09:07:00 G024 0.6600209 0.007699111
#> 25 6 2018-06-02 09:07:00 G025 0.6445336 0.007702148
#> 26 6 2018-06-02 09:07:00 G026 0.6768089 0.007709682
#> 27 6 2018-06-02 09:07:00 G027 0.6544579 0.007699560
#> 28 6 2018-06-02 09:07:00 G028 0.6445496 0.007705877
#> 29 6 2018-06-02 09:07:00 G029 0.6693540 0.007699365
#> 30 6 2018-06-02 09:07:00 G030 0.6630166 0.007697679
#> 31 6 2018-06-02 09:07:00 G031 0.6601530 0.007701743
#> 32 6 2018-06-02 09:07:00 G032 0.6633195 0.007727830
#> 33 6 2018-06-02 09:07:00 G033 0.6645295 0.007703311
#> 34 6 2018-06-02 09:07:00 G034 0.6708713 0.007731471
#> 35 6 2018-06-02 09:07:00 G035 0.6536753 0.007729132
#> 36 6 2018-06-02 09:07:00 G036 0.6802631 0.007704726
#> 37 6 2018-06-02 09:07:00 G037 0.6612019 0.007698814
#> 38 6 2018-06-02 09:07:00 G038 0.6602141 0.007700083
#> 39 6 2018-06-02 09:07:00 G039 0.6735273 0.007700494
#> 40 6 2018-06-02 09:07:00 G040 0.6530825 0.007694335
#> 41 6 2018-06-02 09:07:00 G041 0.6621874 0.007707950
#> 42 6 2018-06-02 09:07:00 G042 0.6722508 0.008124089
#> 43 6 2018-06-02 09:07:00 G043 0.6612456 0.007701214
#> 44 6 2018-06-02 09:07:00 G044 0.6609375 0.007703963
#> 45 6 2018-06-02 09:07:00 G045 0.6787019 0.007702768
#> 46 6 2018-06-02 09:07:00 G046 0.6677625 0.007704307
#> 47 6 2018-06-02 09:07:00 G047 0.6654780 0.007698372
#> 48 6 2018-06-02 09:07:00 G048 0.6549039 0.007704991
#> 49 6 2018-06-02 09:07:00 G049 0.6449453 0.007711530
#> 50 6 2018-06-02 09:07:00 G050 0.6663340 0.007705456
#> 51 6 2018-06-02 09:07:00 G051 0.6611572 0.007727261
#> 52 6 2018-06-02 09:07:00 G052 0.6550151 0.007706797
#> 53 6 2018-06-02 09:07:00 G053 0.6585780 0.007705182
#> 54 6 2018-06-02 09:07:00 G054 0.6680242 0.007751794
#> 55 6 2018-06-02 09:07:00 G055 0.6703971 0.007729620
#> 56 6 2018-06-02 09:07:00 G056 0.6118391 0.007701664
#> 57 6 2018-06-02 09:07:00 G057 0.6645530 0.007723636
#> 58 6 2018-06-02 09:07:00 G058 0.6595585 0.007700130
#> 59 6 2018-06-02 09:07:00 G059 0.6652163 0.007705836
#> 60 6 2018-06-02 09:07:00 G060 0.6667614 0.007753973
#> 61 6 2018-06-02 09:07:00 G061 0.6642653 0.007699283
#> 62 6 2018-06-02 09:07:00 G062 0.6645500 0.007706543
#> 63 6 2018-06-02 09:07:00 G063 0.6699651 0.008116854
#> 64 6 2018-06-02 09:07:00 G064 0.6619514 0.007703589
#> 65 6 2018-06-02 09:07:00 G065 0.6651044 0.007733521
#> 66 6 2018-06-02 09:07:00 G066 0.6724889 0.007699851
#> 67 6 2018-06-02 09:07:00 G067 0.6611455 0.007701246
#> 68 6 2018-06-02 09:07:00 G068 0.6507050 0.008127772
#> 69 6 2018-06-02 09:07:00 G069 0.6613007 0.007739806
#> 70 6 2018-06-02 09:07:00 G070 0.6574314 0.008616607
#> 71 6 2018-06-02 09:07:00 G071 0.6694904 0.007703818
#> 72 6 2018-06-02 09:07:00 G072 0.6690957 0.007698006
#> 73 6 2018-06-02 09:07:00 G073 0.6632111 0.007702209
#> 74 6 2018-06-02 09:07:00 G074 0.6481942 0.007707940
#> 75 6 2018-06-02 09:07:00 G075 0.6686951 0.007707523
#> 76 6 2018-06-02 09:07:00 G076 0.6711070 0.007701188
#> 77 6 2018-06-02 09:07:00 G077 0.6612662 0.007697369
#> 78 6 2018-06-02 09:07:00 G078 0.6532985 0.007723672
#> 79 6 2018-06-02 09:07:00 G079 0.6640932 0.007694946
#> 80 6 2018-06-02 09:07:00 G080 0.6702728 0.007726926
#> 81 6 2018-06-02 09:07:00 G081 0.6760972 0.007696653
#> 82 6 2018-06-02 09:07:00 G082 0.6710345 0.007730372
#> 83 6 2018-06-02 09:07:00 G083 0.6488169 0.007710044
#> 84 6 2018-06-02 09:07:00 G084 0.6713796 0.007725933
#> 85 6 2018-06-02 09:07:00 G085 0.6744627 0.007699481
#> 86 6 2018-06-02 09:07:00 G086 0.6757281 0.007731798
#> 87 6 2018-06-02 09:07:00 G087 0.6509790 0.007732842
#> 88 6 2018-06-02 09:07:00 G088 0.6576374 0.007699586
#> 89 6 2018-06-02 09:07:00 G089 0.6605186 0.007699723
#> 90 6 2018-06-02 09:07:00 G090 0.6553467 0.007699184
#> 91 6 2018-06-02 09:07:00 G091 0.6703697 0.007704221
#> 92 6 2018-06-02 09:07:00 G092 0.6539418 0.007700623
#> 93 6 2018-06-02 09:07:00 G093 0.6604147 0.007715465
#> 94 6 2018-06-02 09:07:00 G094 0.6592644 0.008120315
#> 95 6 2018-06-02 09:07:00 G095 0.6711211 0.007699168
#> 96 6 2018-06-02 09:07:00 G096 0.6567808 0.007754300
#> 97 6 2018-06-02 09:07:00 G097 0.6612442 0.008126946
#> 98 6 2018-06-02 09:07:00 G098 0.6550896 0.007707885
#> 99 6 2018-06-02 09:07:00 G099 0.6607817 0.008193340
#> 100 6 2018-06-02 09:07:00 G100 0.6770290 0.010959465
#> 101 6 2018-06-02 09:07:00 G101 0.6775766 0.007700139
#> 102 6 2018-06-02 09:07:00 G102 0.6706355 0.007703304
#> 103 6 2018-06-02 09:07:00 G103 0.6615825 0.007697344
#> 104 6 2018-06-02 09:07:00 G104 0.6687181 0.007705662
#> 105 6 2018-06-02 09:07:00 G105 0.6643059 0.007729564
#> 106 6 2018-06-02 09:07:00 G106 0.6601783 0.007704042
#> 107 6 2018-06-02 09:07:00 G107 0.6385798 0.007701669
#> 108 6 2018-06-02 09:07:00 G108 0.6645371 0.007753134
#> 109 6 2018-06-02 09:07:00 G109 0.6566105 0.007701133
#> 110 6 2018-06-02 09:07:00 G110 0.6747622 0.007701680
#> 111 6 2018-06-02 09:07:00 G111 0.6409722 0.007703590
#> 112 6 2018-06-02 09:07:00 G112 0.6695963 0.007699623
#> 113 6 2018-06-02 09:07:00 G113 0.6679433 0.007701223
#> 114 6 2018-06-02 09:07:00 G114 0.6707194 0.007702253
#> 115 6 2018-06-02 09:07:00 G115 0.6768654 0.007698791
#> 116 6 2018-06-02 09:07:00 G116 0.6605405 0.007699775
#> 117 6 2018-06-02 09:07:00 G117 0.6751478 0.007700256
#> 118 6 2018-06-02 09:07:00 G118 0.6622331 0.007699093
#> 119 6 2018-06-02 09:07:00 G119 0.6529363 0.007709090
#> 120 6 2018-06-02 09:07:00 G120 0.6599894 0.007702553
#> 121 6 2018-06-02 09:07:00 G121 0.6705033 0.007702127
#> 122 6 2018-06-02 09:07:00 G122 0.6682551 0.007706948
#> 123 6 2018-06-02 09:07:00 G123 0.6475131 0.007707386
#> 124 6 2018-06-02 09:07:00 G124 0.6411380 0.007699575
#> 125 6 2018-06-02 09:07:00 G125 0.6691985 0.007703873
#> 126 6 2018-06-02 09:07:00 G126 0.6667264 0.007704937
#> 127 6 2018-06-02 09:07:00 G127 0.6678950 0.007697067
#> 128 6 2018-06-02 09:07:00 G128 0.6548751 0.007700656
#> 129 6 2018-06-02 09:07:00 G129 0.6650380 0.007727470
#> 130 6 2018-06-02 09:07:00 G130 0.6624278 0.007709811
#> 131 6 2018-06-02 09:07:00 G131 0.6713800 0.007707018
#> 132 6 2018-06-02 09:07:00 G132 0.6530011 0.007698864
#> 133 6 2018-06-02 09:07:00 G133 0.6638719 0.007700631
#> 134 6 2018-06-02 09:07:00 G134 0.6688086 0.007699578
#> 135 6 2018-06-02 09:07:00 G135 0.6665965 0.008118718
#> 136 6 2018-06-02 09:07:00 G136 0.6612019 0.007726583
#> 137 6 2018-06-02 09:07:00 G137 0.6625749 0.007698220
#> 138 6 2018-06-02 09:07:00 G138 0.6612678 0.007700833
#> 139 6 2018-06-02 09:07:00 G139 0.6768107 0.007703699
#> 140 6 2018-06-02 09:07:00 G140 0.6662416 0.007696663
#> 141 6 2018-06-02 09:07:00 G141 0.6781536 0.007699923
#> 142 6 2018-06-02 09:07:00 G142 0.6586183 0.008619330
#> 143 6 2018-06-02 09:07:00 G143 0.6677179 0.007715456
#> 144 6 2018-06-02 09:07:00 G144 0.6655668 0.007697878
#> 145 6 2018-06-02 09:07:00 G145 0.6626089 0.007709919
#> 146 6 2018-06-02 09:07:00 G146 0.6630299 0.007705597
#> 147 6 2018-06-02 09:07:00 G147 0.6621096 0.007700863
#> 148 6 2018-06-02 09:07:00 G148 0.6637336 0.007711971
#> 149 6 2018-06-02 09:07:00 G149 0.6623033 0.007725988
#> 150 6 2018-06-02 09:07:00 G150 0.6611395 0.007701117
#> 151 6 2018-06-02 09:07:00 G151 0.6703583 0.008137396
#> 152 6 2018-06-02 09:07:00 G152 0.6602543 0.007701790
#> 153 6 2018-06-02 09:07:00 G153 0.6561635 0.007710115
#> 154 6 2018-06-02 09:07:00 G154 0.6629187 0.007702880
#> 155 6 2018-06-02 09:07:00 G155 0.6705896 0.007703185
#> 156 6 2018-06-02 09:07:00 G156 0.6844003 0.007705869
#> 157 6 2018-06-02 09:07:00 G157 0.6610507 0.007715084
#> 158 6 2018-06-02 09:07:00 G158 0.6683279 0.007729605
#> 159 6 2018-06-02 09:07:00 G159 0.6661457 0.007698585
#> 160 6 2018-06-02 09:07:00 G160 0.6728815 0.008151421
#> 161 6 2018-06-02 09:07:00 G161 0.6682824 0.007727406
#> 162 6 2018-06-02 09:07:00 G162 0.6661318 0.007702443
#> 163 6 2018-06-02 09:07:00 G163 0.6678264 0.007726285
#> 164 6 2018-06-02 09:07:00 G164 0.6735394 0.007702346
#> 165 6 2018-06-02 09:07:00 G165 0.6563783 0.007703739
#> 166 6 2018-06-02 09:07:00 G166 0.6707537 0.007701172
#> 167 6 2018-06-02 09:07:00 G167 0.6440117 0.007705528
#> 168 6 2018-06-02 09:07:00 G168 0.6529146 0.007734770
#> 169 6 2018-06-02 09:07:00 G169 0.6684723 0.007704579
#> 170 6 2018-06-02 09:07:00 G170 0.6651630 0.007712559
#> 171 6 2018-06-02 09:07:00 G171 0.6648108 0.007699813
#> 172 6 2018-06-02 09:07:00 G172 0.6599931 0.007707282
#> 173 6 2018-06-02 09:07:00 G173 0.6546251 0.007731448
#> 174 6 2018-06-02 09:07:00 G174 0.6774589 0.007706590
#> 175 6 2018-06-02 09:07:00 G175 0.6486491 0.007703446
#> 176 6 2018-06-02 09:07:00 G176 0.6592223 0.007698616
#> 177 6 2018-06-02 09:07:00 G177 0.6538269 0.007712652
#> 178 6 2018-06-02 09:07:00 G178 0.6531421 0.008119709
#> 179 6 2018-06-02 09:07:00 G179 0.6588950 0.007711187
#> 180 6 2018-06-02 09:07:00 G180 0.6670155 0.007704359
#> 181 6 2018-06-02 09:07:00 G181 0.6094924 0.008125642
#> 182 6 2018-06-02 09:07:00 G182 0.6753670 0.007701206
#> 183 6 2018-06-02 09:07:00 G183 0.6561471 0.007698872
#> 184 6 2018-06-02 09:07:00 G184 0.6638217 0.007699844
#> 185 6 2018-06-02 09:07:00 G185 0.6596904 0.007737100
#> 186 6 2018-06-02 09:07:00 G186 0.6537197 0.007729561
#> 187 6 2018-06-02 09:07:00 G187 0.6612610 0.008122376
#> 188 6 2018-06-02 09:07:00 G188 0.6583949 0.007698748
#> 189 6 2018-06-02 09:07:00 G189 0.6565257 0.007735060
#> 190 6 2018-06-02 09:07:00 G190 0.6707160 0.007737670
#> 191 6 2018-06-02 09:07:00 G191 0.6566763 0.007703687
#> 192 6 2018-06-02 09:07:00 G192 0.6732723 0.007707968
#> 193 6 2018-06-02 09:07:00 check1 0.6659502 0.004303533
#> 194 6 2018-06-02 09:07:00 check2 0.5895666 0.005915225
#> 195 6 2018-06-02 09:07:00 check3 0.6675627 0.005784187
#> 196 6 2018-06-02 09:07:00 check4 0.6745496 0.004242575
#>
#> $checkPred
#> NULL
#>
# }