Vignettes are long form documentation commonly included in packages. Because they are
# test
library(Dark)
data(dark)
tmp<-dark
names(tmp)
## [1] "time" "thrs" "fit" "resid" "R2"
## [6] "Bootstrap" "weight" "valid" "opt" "Mod"
## [11] "Pn" "AIC" "val" "call"
Some text about the data
par(las=1, bty='n',mfrow=c(1,1))
plot(tmp$time, tmp$thrs)
P<-Start(tmp, 2000)
MSC<-ModelSelect(tmp,P)
tmp<-BestFit(tmp,MSC, T)
Some text
par(las=1, bty='n')
tmp<-MultiStart(tmp,repeats = 25)
tmp<-BootDark(tmp,R = 150, T)
the output
tmp
## $time
## [1] -0.049385871 0.001365711 0.052117293 0.150250233 0.251753397
## [6] 0.251753397 0.402223906 0.404008141 0.678780376 0.754114755
## [11] 0.857402153 0.942252454 1.207508767 1.210878989 1.408730858
## [16] 1.420229263 1.590722858 1.647620139 1.891663877 1.929331066
## [21] 2.170004582 2.371226673 2.444776816 2.597031561 3.204464553
## [26] 3.582524186 3.631491533 4.022635558 4.336859217 4.449860786
## [31] 5.050355085 5.565800835 5.640936966 6.092546743 6.457521984
## [36] 6.709693905 7.138505119 7.527864909 7.956676124 8.158096463
## [41] 8.233232594 8.648959416 9.028803285 9.054972069 9.343026944
## [46] 9.357697323 9.860256930 10.069408956 10.144743334 10.156043491
## [51] 10.332881033 10.422885791 10.848326784 11.000581529 11.000581529
## [56] 11.139751881 11.301720796 11.455759776 11.593145893 11.743616403
## [61] 12.041187199 12.172427617 12.283644950 12.450768323 12.638906021
## [66] 12.840128112 12.977514230 13.154351772 13.506242621 13.568294359
## [71] 13.818682045 13.846635064 14.458429521 14.509181102 14.672934252
## [76] 14.759568788 14.813690592 15.060708055 15.388016107 15.436983453
## [81] 15.878879060 16.040847974 16.270023085 16.723417097 17.301112834
## [86] 17.374662978 17.865525931 17.878808571 18.183318061 18.371455760
## [91] 18.670810792 18.682110949 19.174956385 19.511780358 19.624781927
## [96] 20.155096305 20.395769820 20.709993480 20.873548381 21.742669216
## [101] 21.742669216 22.559254234 22.596723175 22.897862442 24.553831040
## [106] 25.268912894 26.286720003 26.587859270 26.789081361 27.103305021
## [111] 27.882222849 27.919890038 28.361785645 29.391091159 29.466425538
## [116] 29.994955680 30.836123496 31.387452200 31.626341481 32.015899519
## [121] 32.469095283 32.932203465 34.063012142 34.301901422 34.578457892
## [126] 35.417841472 36.550236136 36.651739299 37.533944526 37.974254146
## [131] 38.993845490 39.749964756 41.456486687 41.898580542 42.954054840
## [136] 44.423471725 46.495167145 49.483166511
##
## $thrs
## [1] -0.5733348 -0.2487572 -0.7428293 -0.8499813 -0.9795381 -1.0313200
## [7] -0.3260362 -1.1478657 -0.8167534 -0.9202880 -1.0609305 -1.2682622
## [13] -1.3662831 -1.5487887 -1.4917266 -1.2162470 -1.5877929 -1.3366727
## [19] -1.5191783 -1.6376494 -1.6711398 -1.7171163 -1.6265637 -1.7522697
## [25] -1.7390252 -1.7500817 -1.8406343 -1.7702985 -1.7888525 -1.8572337
## [31] -1.9244480 -1.8782090 -1.8259312 -1.9596306 -1.9186718 -1.9906705
## [37] -1.9516372 -2.0031565 -1.9660778 -2.0306082 -1.9528041 -2.0065114
## [43] -2.0585558 -2.1363308 -2.2528764 -2.1548847 -2.0790352 -2.3308264
## [49] -2.2465751 -2.1760059 -2.4069385 -2.5063889 -2.3402201 -2.1435365
## [55] -2.6614428 -2.5246803 -2.5894441 -2.7286571 -2.6542371 -2.5969123
## [61] -2.3789909 -2.7342000 -2.6896530 -2.7211889 -2.7823644 -2.9188935
## [67] -2.9781145 -3.0335138 -3.0226907 -3.2035042 -3.0999697 -3.2668678
## [73] -3.3427173 -3.2762614 -3.0775649 -3.4662353 -3.2131605 -3.5565254
## [79] -3.6362257 -3.4147160 -3.7525380 -3.6046898 -3.8322676 -3.9449624
## [85] -3.9468878 -4.0648630 -4.1700896 -4.0629376 -4.0150065 -4.0687138
## [91] -4.1866890 -4.2606131 -4.1111020 -4.2924115 -4.3591299 -4.2514820
## [97] -4.3832268 -4.2888233 -4.4236604 -4.4754423 -4.5532172 -4.5898000
## [103] -4.4070318 -4.5565721 -4.6692669 -4.6692669 -4.7431910 -4.7952063
## [109] -4.7229742 -4.8655421 -4.9450091 -4.8506056 -4.8893764 -4.9035544
## [115] -4.9871348 -4.9685808 -5.0425049 -4.9647300 -5.1140077 -5.0862934
## [121] -5.0752369 -5.1436181 -5.0973791 -5.2172797 -5.2615933 -5.1525159
## [127] -5.1948749 -5.2948212 -5.3299746 -5.3299746 -5.3632025 -5.4003104
## [133] -5.3468365 -5.3986184 -5.5151641 -5.4561765 -5.5539348 -5.5893507
##
## $fit
## [1] -0.5334183 -0.5778374 -0.6208805 -0.7003631 -0.7776425 -0.7776425
## [7] -0.8836157 -0.8848140 -1.0543848 -1.0960476 -1.1500967 -1.1919799
## [13] -1.3095655 -1.3109386 -1.3867182 -1.3908429 -1.4486740 -1.4666523
## [19] -1.5369595 -1.5468944 -1.6051778 -1.6476569 -1.6619079 -1.6894219
## [25] -1.7766391 -1.8164874 -1.8209986 -1.8525128 -1.8728394 -1.8792337
## [31] -1.9066222 -1.9232310 -1.9252386 -1.9355201 -1.9419636 -1.9456362
## [37] -1.9507026 -1.9542704 -1.9573210 -1.9584969 -1.9588993 -1.9581964
## [43] -2.0355673 -2.0416084 -2.1080223 -2.1114009 -2.2269493 -2.2749436
## [49] -2.2922192 -2.2948100 -2.3353387 -2.3559557 -2.4533240 -2.4881399
## [55] -2.4881399 -2.5199518 -2.5569621 -2.5921486 -2.6235223 -2.6578753
## [61] -2.7257879 -2.7557311 -2.7811021 -2.8192205 -2.8621239 -2.9080029
## [67] -2.9393228 -2.9796317 -3.0598290 -3.0739691 -3.1310222 -3.1373911
## [73] -3.2767674 -3.2883281 -3.3256283 -3.3453615 -3.3576889 -3.4139505
## [79] -3.4884950 -3.4996469 -3.6002816 -3.6371660 -3.6893538 -3.7925974
## [85] -3.9241412 -3.9408886 -4.0526566 -4.0556810 -4.1250159 -4.1678533
## [91] -4.2360136 -4.2385865 -4.3508017 -4.4134018 -4.4171669 -4.4421832
## [97] -4.4535361 -4.4683584 -4.4760735 -4.5170702 -4.5170702 -4.5555882
## [103] -4.5573556 -4.5715601 -4.6496706 -4.6834002 -4.7314089 -4.7456133
## [109] -4.7551047 -4.7699262 -4.8066668 -4.8084435 -4.8292871 -4.8778382
## [115] -4.8813916 -4.9063217 -4.9459985 -4.9720039 -4.9832720 -5.0016470
## [121] -5.0230236 -5.0448678 -5.0982066 -5.1094747 -5.1225195 -5.1621121
## [127] -5.2155257 -5.2203135 -5.2619259 -5.2826948 -5.3307876 -5.3664527
## [133] -5.4469471 -5.4678001 -5.5175855 -5.5868959 -5.6846151 -5.8255551
##
## $resid
## [1] -0.0399165373 0.3290801315 -0.1219488335 -0.1496181806 -0.2018956296
## [6] -0.2536775098 0.5575795000 -0.2630517602 0.2376314093 0.1757596385
## [11] 0.0891662210 -0.0762823011 -0.0567175952 -0.2378501329 -0.1050083325
## [16] 0.1745959685 -0.1391189123 0.1299796661 0.0177812323 -0.0907550087
## [21] -0.0659620559 -0.0694593973 0.0353442414 -0.0628477157 0.0376139495
## [26] 0.0664057492 -0.0196357707 0.0822143454 0.0839869382 0.0219999549
## [31] -0.0178258249 0.0450219708 0.0993074100 -0.0241104797 0.0232917430
## [36] -0.0450343029 -0.0009345801 -0.0488860793 -0.0087567262 -0.0721112468
## [41] 0.0060952374 -0.0483150070 -0.0229885370 -0.0947223900 -0.1448541578
## [46] -0.0434838508 0.1479141448 -0.0558827946 0.0456440962 0.1188041634
## [51] -0.0715998073 -0.1504331851 0.1131039688 0.3446033967 -0.1733029233
## [56] -0.0047284632 -0.0324819661 -0.1365085023 -0.0307147507 0.0609629294
## [61] 0.3467970537 0.0215311594 0.0914491833 0.0980316004 0.0797595055
## [66] -0.0108906244 -0.0387917096 -0.0538821357 0.0371382893 -0.1295351384
## [71] 0.0310525010 -0.1294766751 -0.0659498680 0.0120666818 0.2480634401
## [76] -0.1208737515 0.1445284747 -0.1425748709 -0.1477307272 0.0849309766
## [81] -0.1522563935 0.0324761865 -0.1429137602 -0.1523650202 -0.0227466368
## [86] -0.1239744352 -0.1174329708 -0.0072565567 0.1100093587 0.0991394917
## [91] 0.0493245982 -0.0220265774 0.2396997022 0.1209902738 0.0580369442
## [96] 0.1907011702 0.0703093743 0.1795351597 0.0524130878 0.0416278903
## [101] -0.0361470350 -0.0342118182 0.1503237269 0.0149880326 -0.0195963561
## [106] 0.0141332432 -0.0117821259 -0.0495930233 0.0321304475 -0.0956159322
## [111] -0.1383423212 -0.0421621354 -0.0600892575 -0.0257162697 -0.1057431751
## [116] -0.0622591356 -0.0965064470 0.0072739356 -0.1307356475 -0.0846464568
## [121] -0.0522132781 -0.0987503238 0.0008274772 -0.1078050060 -0.1390738185
## [126] 0.0095962459 0.0206507875 -0.0745077627 -0.0680486265 -0.0472797966
## [131] -0.0324149259 -0.0338576836 0.1001106358 0.0691817457 0.0024213939
## [136] 0.1307194541 0.1306802673 0.2362044077
##
## $R2
## [1] 0.9929571
##
## $Bootstrap
## 2.5% 50% 97.5%
## CT -2.028 -1.963 -1.887
## CC 1.271 1.391 1.489
## Tau 0.516 0.634 0.758
## S2 -0.238 -0.228 -0.217
## Alpha 8.318 8.698 8.981
## *S3* 0.169 0.181 0.192
## Beta 18.955 19.467 19.924
##
## $weight
## CT CC Tau S2 Alpha *S3* Beta
## 7.092199 4.587156 4.132231 47.619048 1.508296 43.478261 1.031992
##
## $valid
## [1] 1 1 1 1 1 1 1
##
## $Mod
## [1] "P7c"
##
## $Pn
## [1] 7
##
## $AIC
## [1] 0.0000 0.0000 -347.6882 0.0000 -359.3740 0.0000 -561.6973
##
## $opt
## [1] -1.9673371 1.3906768 0.6200271 -0.2276815 8.7065001 0.1805128
## [7] 19.4250502
##
## $val
## [1] 2.115328
##
## $call
## BootDark(obj = tmp, R = 150, graph = T)
##
## attr(,"class")
## [1] "dark"