问题描述
我想知道 glmmTMB 是否添加了 exp(coordinates + 0 | SITES ) 作为空间自相关结构仍然保持空间自相关。我接下来该怎么做。这是我的公式 glmmTMB：
df$coordinates = numFactor(df$Longitude,df$Latitude)
M <- glmmTMB(lgDouYa ~ MFS*CD*SNC +
I(MFS^2)+I(CD^2)+I(SNC^2) +(1|SITES/YEAR) +
exp(coordinates + 0 | SITES ),ziformula=~1,dispformula=~0,data = df
)
然后，我尝试使用 DHARMa 测试空间自相关。
library(DHARMa)
recalculateResiduals(simulateResiduals(M,n = 1000),group = df$SITES) %>%
testSpatialAutocorrelation(x = aggregate(df$Latitude,list(df$SITES),mean)$x,y = aggregate(df$Longitude,mean)$x)
但结果对于空间自相关是显着的。
DHARMa Moran's I test for spatial
autocorrelation
data: .
observed = -0.109366,expected =
-0.023810,sd = 0.036913,p-value =
0.02046
alternative hypothesis: Spatial autocorrelation
那么我应该怎么做才能解决空间自相关问题？ 感谢所有关注我问题的人。谢谢。
这是我的数据集：
df <-
structure(list(YEAR = structure(c(1L,1L,2L,3L,3L),.Label = c("2017","2018","2019"
),class = "factor"),SITES = structure(c(1L,4L,5L,6L,7L,8L,9L,10L,11L,12L,13L,14L,15L,16L,17L,18L,19L,20L,21L,22L,23L,24L,25L,28L,30L,33L,35L,36L,37L,38L,39L,43L,44L,46L,47L,48L,49L,50L,52L,53L,55L,55L),.Label = c("CA1","CA10","CA11","CA12","CA13","CA14","CA15","CA17","CA18","CA19","CA2","CA20","CA3","CA4","CA5","CA6","CA7","CA9","CB1","CB10","CB11","CB12","CB13","CB14","CB15","CB16","CB17","CB18","CB19","CB2","CB20","CB3","CB4","CB5","CB6","CB7","CB8","CB9","CC1","CC10","CC11","CC12","CC13","CC14","CC15","CC16","CC17","CC18","CC2","CC3","CC4","CC5","CC6","CC7","CC8","CC9","CA16","CA8"),lgDouYa = c(0.869423773288886,0.0965586152896391,-0.647230897017041,2.30836181466664,1.6906216295849,0.348755695517045,0.492483444930366,0.68000152309815,0.275129454289906,0.376838393944666,0.414754435392883,0.463010775531561,1.0653594780622,0.658075667360263,0.615141104595973,0.783103333893848,0.921779971361295,0.18510477917444,1.16318304340856,1.40225483961546,1.27362258886383,0.948927783595636,0.573311845426998,1.76882503851871,0.433934970416483,0.702259280165173,1.0200762327862,1.31410405776748,0.532462663541631,0.724870518877707,0.747858594763302,0.819348843909036,1.19837970230692,0.895295078198926,1.85963585496984,0.395725295814487,0.512370678114162,0.636461718809469,0.844121707593991,1.50289108284423,1.09680356209351,1.96901778371413,0.976793633267482,1.12937124274826,1.55948717001655,2.10876310243032,1.45073686181061,1.3568616481425,2.69717709201565,1.23512706836797,1.62157161294753,-0.647230897017041),DouYa = c(0.826666666666667,0.0133333333333333,13.56,5.62666666666667,0.0533333333333333,0.186666666666667,0.32,0.04,0.0666666666666667,0.0933333333333333,0.12,1.61333333333333,0.293333333333333,0.24,0.506666666666667,1.17333333333333,0.0266666666666667,1.86666666666667,2.88,2.28,1.18666666666667,0.226666666666667,6.02666666666667,0.106666666666667,0.346666666666667,1.50666666666667,2.36,0.213333333333333,0.4,0.453333333333333,0.533333333333333,1.93333333333333,0.84,7.34666666666667,0.08,0.2,0.28,0.8,4,1.64,7.68,1.24,1.78666666666667,4.96,8.77333333333333,2.92,2.6,14.2,2,5.08,0),MFS = structure(c(-0.704470454018713,-0.704470454018713,-0.49219727458324,0.527968407082596,2.61289211033616,0.973964696600823,0.810053831748292,-0.646038990797124,-0.0405740424844551,-0.608003192334688,0.365588661218839,1.27085722552215,-0.348247043875247,-1.34256604272275,-0.442366256663233,0.590527862041596,0.425429474000678,0.867288135599791,2.45848921736224,-0.316682761074777,1.27997422497702,0.929231872203228,0.810280534910473,0.708521487075458,1.74376310922201,-0.638866315394154,-1.04054218648781,-0.910039293047068,-0.376862291489762,-0.92230815650878,-1.38047124297597,-0.674768565361297,-0.673581308608378,-0.595112731354483,-1.2473400909545,-1.14108242285356,-1.06398632494527,-1.09717275254042,0.23200886760946,0.199500012511306,-0.930127869136063,-1.39138211207404,0.340576705522566,1.41673194858262,1.41673194858262),"`scaled:center`" = 0.531172306358715,"`scaled:scale`" = 0.1321853801893,.Dim = c(143L,1L)),CD = structure(c(0.571325446748364,0.571325446748364,0.0487947267179488,-1.20061533945842,-1.65920875929318,0.0776291954336383,-1.24474461331896,-0.423839825708794,-0.398515640141102,1.34634581892399,0.413111970577926,0.353938626083119,0.856661319778408,1.39047509278453,1.20016759926097,0.478302943326443,-0.172353111605864,-0.0244197503688467,-0.767596839701932,-0.454680170509054,-1.04390627035141,-0.0161455115199964,1.04370926466454,0.579850420107785,-1.08126571242652,1.39523904848538,0.810526169833304,0.659834728980003,-0.139256156210463,-0.786652662505345,0.0738681777750704,-0.313015172036317,-0.789410742121628,1.39298243789024,0.301785847884306,-1.60780818462608,0.198733964039536,0.41185829802507,-1.20613149869099,0.349425404892837,0.42213841295849,1.56247896703638,-0.381214958911687,-0.561994541033535,-0.561994541033535),"`scaled:center`" = 1.67953928571429,"`scaled:scale`" = 0.398828225808178,SNC = structure(c(0.248739188017824,0.248739188017824,-0.156470857543067,0.00417693903715141,2.88764474556734,-0.308032697947342,0.692282191545496,0.0974639176599148,-1.05547480711491,-0.426908696004394,-0.83090503313362,-1.21694859971112,-1.10457942741272,-0.848183521223307,-0.31204467859646,-0.885285913696871,-0.448637448343523,-0.496696930825182,-0.458937112951132,-0.593203608204169,4.07313445619698,-0.554988649668245,-0.717507580080615,0.0712680440097931,-0.0862443391219557,-0.825139918083207,-0.448283450050954,1.28526304572203,0.340829315270473,-0.26578890170075,0.241389509181626,-0.280488259373148,1.74291540976782,0.544833474159644,-0.179025605898191,1.64495902509545,-0.530107626819095,0.225392157769807,0.579339879154367,-0.440006632829455,-0.135416387665974,-0.762600219729313,-0.0303126088960203,-0.4224078605703,-0.4224078605703),"`scaled:center`" = 16.3174214285714,"`scaled:scale`" = 5.93223200247334,Latitude = c(41.05686278,41.05686278,41.11095806,41.04523861,40.95670806,40.99668806,41.04156694,41.09246028,40.99216861,41.03523028,41.02716667,41.01156083,41.06100694,40.94746417,40.900705,40.87212056,40.90833583,40.82387833,40.99983361,41.17633167,40.80911056,40.80239444,40.82870833,41.02167088,40.98107699,40.98334098,40.99086151,41.16152528,41.16686889,41.07348806,41.03278333,40.97858194,41.03570917,41.021529,41.016319,41.045005,41.083288,41.129119,41.172374,40.998956,40.970129,40.886755,40.85327,40.829648,40.829648),Longitude = c(80.34026694,80.34026694,80.46016028,80.48630833,80.50068278,80.56087556,80.54815722,80.53416472,80.29715028,80.242545,80.205635,80.32743694,80.21906472,80.34813583,80.3566375,80.42242306,80.41108333,80.46019611,80.3918025,80.41081194,80.56281944,80.46875,80.41125278,80.35851237,80.39885327,80.33922402,80.26167842,80.47888889,80.52739444,80.53371111,80.557725,80.57384333,80.48125,80.349776,80.551031,80.520748,80.507795,80.484277,80.406286,80.327168,80.373821,80.387362,80.434011,80.497346,80.497346)),row.names = c(NA,-143L),class = "data.frame")
解决方法
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