sims updated

CODE/SM.Rmd

@@ -70,9 +70,7 @@ if(RECALC) source("create-sib-subdataset.R") #This code may not be reproducible
 
 if(RECALC) source("create-all-icc.R") 
 
-if(RECALC) source("simulate-r-for-icc.R") #when ran on Aug 2 2023, it gave an error chol(): decomposition failed -- perhaps one of our newly added datasets (lyon, quechua) is too small? -- happened again on Aug 15, need to double check how this affects simulation; I suspect this is bc overlap bet function names across this & previous code
-#aug 18, now it runs for ever...
-#nov 27 it still runs for ever
+if(RECALC) source("simulate-r-for-icc.R") # note, this takes several minutes to run
 
 if(RECALC) source("create-all-rs.R")
 ```

CODE/simulate-r-for-icc.R

@@ -1,5 +1,7 @@
 library(simstudy)
 
+## Functions ###----------
+
 check_small_var<-function(x,y,i) round(x[i],3)==round(y[i],3) & round(y[i],3) == 0
 
 fit_child_model<-function(dataframe, metric){
@@ -89,14 +91,15 @@ new_fit_models_sim<-function(dataframe, data_set, metric,  fit_full = TRUE){ #ag
   return (icc.row)
 }
 
-
+## Main loop ###----------
 
 #create matrix to hold info in
 df.vars.cols = c("data_set","experiment","n","metric", "mean","sd")
 df.vars = data.frame(matrix(ncol=length(df.vars.cols),nrow=0, dimnames=list(NULL, df.vars.cols)), stringsAsFactors=FALSE)
 
+### Pull out the mean and SD for first day ###----------
 for (data_set in data_sets){   # data_set = "aclew"
-  mydat <- read.csv(paste0('../data_output/', data_set,'_metrics_scaled.csv')) # TO DISCUSS: scaled or unscaled?
+  mydat <- read.csv(paste0('../data_output/', data_set,'_metrics_scaled.csv')) 
   
   metrics = colnames(mydat)[!is.element(colnames(mydat), no.scale.columns)]
   
@@ -117,6 +120,7 @@ for (data_set in data_sets){   # data_set = "aclew"
 }
 colnames(df.vars)<-df.vars.cols
 
+### Generate second day with varying levels of association ###----------
 alldays=NULL
 
 for(i in 1:nrow(df.vars)) for(myr in c(.1,.3,.5, .7, .9)){#i=2;myr=.5
@@ -139,6 +143,8 @@ for(i in 1:nrow(df.vars)) for(myr in c(.1,.3,.5, .7, .9)){#i=2;myr=.5
 
 write.csv(alldays,"../output/simulated_correlated_2day.csv",row.names=F)
 
+### Estimate ICCs for paired observations for the whole dataset ###----------
+
 read.csv("../output/simulated_correlated_2day.csv")->alldays
 
 df.icc.mixed.cols = c("data_set", "metric", "iqr", # removed "age_bin",
@@ -164,3 +170,31 @@ for(myr in levels(factor(alldays$myr)))for(data_set in levels(factor(alldays$dat
 }
 write.csv(df.icc.mixed,"../output/df.icc.simu.csv",row.names=F)
 
+### Estimate ICCs for paired observations halving the dataset, to see if obs N affects results ###----------
+
+df.icc.mixed.cols = c("data_set", "metric", "iqr", # removed "age_bin",
+                      #"age_b","age_se","age_t", # beta, standard error, T #removed age
+                      "icc_adjusted", "icc_conditional", 
+                      "icc_child_id", "icc_corpus",
+                      "child_id_var","corpus_var","residual_var",
+                      "child_id_sd","corpus_sd","residual_sd",
+                      "nobs","nchi", "ncor",
+                      "formula","sw","myr")
+
+df.icc.mixed = data.frame(matrix(ncol=length(df.icc.mixed.cols),nrow=0, dimnames=list(NULL, df.icc.mixed.cols)),
+                          stringsAsFactors = FALSE)
+
+for(myr in levels(factor(alldays$myr)))for(data_set in levels(factor(alldays$data_set))) for(metric in levels(factor(alldays$metric[alldays$data_set==data_set]))) {   # myr=.5 ; data_set = "aclew"; metric="wc_adu_ph"
+  #select data
+  mydat=alldays[alldays$myr==myr & alldays$data_set==data_set & alldays$metric==metric,] 
+  mydat$child_id=factor(mydat$child_id)
+  mydat=mydat[mydat$child_id %in% sample(levels(mydat$child_id),size=round(length(levels(mydat$child_id))/2)),] #sample half of the kids
+  #reshape mydat so that it fits expectation from the following function
+  colnames(mydat)[4]<-metric
+  icc.row <- new_fit_models_sim(mydat, data_set, metric,  TRUE) #removed age NA,
+  df.icc.mixed[nrow(df.icc.mixed) + 1,] <- cbind(icc.row,myr)
+  
+}
+write.csv(df.icc.mixed,"../output/df.icc.simu_halved.csv",row.names=F)
+read.csv("../output/df.icc.simu.csv")->full
+plot(full$icc_child_id~df.icc.mixed$icc_child_id)

OUTPUT/df.icc.simu.csv

@@ -1,51 +1,341 @@
 "data_set","metric","iqr","icc_adjusted","icc_conditional","icc_child_id","icc_corpus","child_id_var","corpus_var","residual_var","child_id_sd","corpus_sd","residual_sd","nobs","nchi","ncor","formula","sw","myr"
-"aclew","can_voc_dur_chi_ph","0.826205334208741","0.585241324428531","0.585241324428531","0.0209628738271698","0.564278450601363","0.0208879068655726","0.562260490598116","0.413275424851171","0.144526491916093","0.749840310064827","0.642865012931308","350","175","4","full","1.81495338034977e-11","0.1"
-"aclew","pc_adu_ph","1.36758555047642","0.27079046486146","0.27079046486146","0.0849138372806438","0.185876627580815","0.0815129730198998","0.178432126191036","0.700004134392722","0.285504768821643","0.422412270407757","0.836662497302659","540","270","8","full","0.731467963125115","0.1"
-"aclew","pc_fem_ph","1.49400267301766","0.2595222313354","0.2595222313354","0.0692019665682204","0.190320264767182","0.0787120724187892","0.216475097544367","0.842238199895283","0.280556718719743","0.465268844373194","0.917735364849412","540","270","8","full","0.745980405137587","0.1"
-"aclew","pc_mal_ph","1.32667831674253","0.327030893611514","0.327030893611514","0.0774897462678257","0.249541147343688","0.0892940388378789","0.28755465046358","0.775484917899349","0.298821081649001","0.536241224136657","0.880616214874192","540","270","8","full","0.000926281265285847","0.1"
-"aclew","sc_adu_ph","1.24048738634418","0.233464134474717","0.233464134474717","0.0693673264365746","0.164096808038143","0.0627940386696935","0.148546900087638","0.693898485845672","0.250587387291726","0.385417825337177","0.833005693765458","540","270","8","full","0.0503529313282223","0.1"
-"aclew","sc_fem_ph","1.43363221021318","0.226730880435486","0.226730880435486","0.0885106565020421","0.138220223933445","0.0907823747945957","0.141767790108183","0.793115877835266","0.301301136397783","0.376520637028281","0.890570535014081","540","270","8","full","0.404293319572876","0.1"
-"aclew","sc_mal_ph","1.25646555636552","0.34867392652953","0.34867392652953","0.070687319053063","0.277986607476469","0.0759786298199436","0.298795340201","0.700081192655529","0.275642213421572","0.546621752403799","0.836708547019528","540","270","8","full","0.194337694871232","0.1"
-"aclew","wc_adu_ph","1.37198539676104","0.273941694077992","0.273941694077992","0.0801835794159381","0.193758114662055","0.0861000774745424","0.208054926024021","0.779631900275258","0.293428147038662","0.456130382702162","0.882967666608046","540","270","8","full","5.10059006031894e-05","0.1"
-"aclew","wc_fem_ph","1.41648595334425","0.277922696150407","0.277922696150407","0.0799535259762819","0.197969170174121","0.0922779376418145","0.228485067009409","0.833381687719045","0.303772838880988","0.478001116117326","0.9128974135789","540","270","8","full","0.127040396055236","0.1"
-"aclew","wc_mal_ph","1.24349753094456","0.20223484731913","0.20223484731913","0.0699085972601712","0.132326250058961","0.0640902685806864","0.121313046448232","0.731369029038705","0.253160558896299","0.348300224588259","0.855201162907713","540","270","8","full","0.0116213777111453","0.1"
-"aclew","can_voc_dur_chi_ph","0.766147075785522","0.75765321040987","0.75765321040987","0.105885813313302","0.651767397096573","0.113996105717095","0.701689327186226","0.260909269918642","0.337633093338161","0.837668984257043","0.510792785695571","350","175","4","full","3.60684672003298e-07","0.3"
-"aclew","pc_adu_ph","1.28605742623422","0.39502774033393","0.39502774033393","0.259541072232785","0.135486668101146","0.232568799119563","0.121406494262814","0.542101759543449","0.482253874136396","0.348434347134168","0.736275600263549","540","270","8","full","0.132281679717163","0.3"
-"aclew","pc_fem_ph","1.52284035209469","0.425306040191767","0.425306040191767","0.236621651365577","0.188684388826189","0.267352142355284","0.213189178972223","0.64933052603877","0.517061062501601","0.461724137307357","0.805810477741987","540","270","8","full","0.866712651840399","0.3"
-"aclew","pc_mal_ph","1.30929161432624","0.416584519066889","0.416584519066889","0.236043480293526","0.180541038773363","0.241650899211535","0.184829948744678","0.597275024949221","0.491580002859692","0.42991853733548","0.772835703723127","540","270","8","full","0.753323949567742","0.3"
-"aclew","sc_adu_ph","1.39370319836432","0.463041971503339","0.463041971503339","0.232458653364168","0.230583318139168","0.235968142612931","0.234064494960259","0.545064624662361","0.485765522256295","0.483802123765759","0.738284921058504","540","270","8","full","0.146813406551544","0.3"
-"aclew","sc_fem_ph","1.57233418467772","0.448452596227054","0.448452596227054","0.229929869548574","0.218522726678482","0.289973056880306","0.275587087389673","0.695576816532967","0.538491464073764","0.524963891510334","0.834012479842459","540","270","8","full","0.838183350612249","0.3"
-"aclew","sc_mal_ph","1.15032188318673","0.497183653729087","0.497183653729087","0.208994313599303","0.288189340129781","0.217124660572533","0.29940055104212","0.522377028514316","0.46596637279157","0.547175064346064","0.722756548579337","540","270","8","full","0.0393514204572388","0.3"
-"aclew","wc_adu_ph","1.42385012286715","0.419969091086854","0.419969091086854","0.231922775429876","0.188046315656983","0.232570120201153","0.188571192090411","0.581649895989203","0.482255243829606","0.434247846385461","0.762659751127069","540","270","8","full","0.646570478983806","0.3"
-"aclew","wc_fem_ph","1.48649009414202","0.419626768674112","0.419626768674112","0.261894098614876","0.157732670059234","0.280189129584402","0.168751337905901","0.620916131288689","0.529328942704253","0.410793546572851","0.787982316609128","540","270","8","full","0.483827938514011","0.3"
-"aclew","wc_mal_ph","1.17794560556157","0.435287175010546","0.435287175010546","0.244866848951358","0.190420326059186","0.254276964999788","0.197738088238389","0.586414469127667","0.504258827389058","0.444677510380713","0.765777036171539","540","270","8","full","0.159255841525871","0.3"
-"aclew","can_voc_dur_chi_ph","0.770154440465886","0.745261540691773","0.745261540691773","0.228601069989046","0.516660470702725","0.231185576988589","0.522501705842099","0.257618469148805","0.480817613018272","0.722842794694738","0.507561295952326","350","175","4","full","1.45873845053571e-13","0.5"
-"aclew","pc_adu_ph","1.4320836843377","0.587081806950756","0.587081806950756","0.404808936414466","0.182272870536284","0.436260515674059","0.196434538224065","0.444999819980324","0.660500201115835","0.443209361616003","0.667083068275852","540","270","8","full","0.40586439555631","0.5"
-"aclew","pc_fem_ph","1.39339593116368","0.591329326076123","0.591329326076123","0.394705933538436","0.196623392537681","0.396103912910593","0.197319798199453","0.410118113963679","0.629367867713782","0.444206931732782","0.640404648611859","540","270","8","full","0.728679427207443","0.5"
-"aclew","pc_mal_ph","1.11241082018536","0.613509432542783","0.613509432542783","0.38602200784712","0.227487424695663","0.375096080570846","0.221048643983772","0.375551378117848","0.612450880129049","0.470158105304771","0.612822468679019","540","270","8","full","0.0917028847037914","0.5"
-"aclew","sc_adu_ph","1.40431745424914","0.584064253319646","0.584064253319646","0.395196600394535","0.18886765292511","0.374370231988869","0.178914562954687","0.394016451107459","0.611858016200547","0.422982934590377","0.627707297318949","540","270","8","full","0.879316171652019","0.5"
-"aclew","sc_fem_ph","1.4959626977556","0.591699760055764","0.591699760055764","0.401556712608194","0.190143047447567","0.457101703100302","0.216444422648137","0.464778023115443","0.676092969272941","0.465235878504804","0.681746304071715","540","270","8","full","0.514692672466483","0.5"
-"aclew","sc_mal_ph","1.28549708656848","0.631984217159476","0.631984217159476","0.359983140829463","0.272001076330017","0.405052040968948","0.306054863734349","0.414090347689247","0.636436989001227","0.553222255277523","0.643498521901369","540","270","8","full","0.0880137639042592","0.5"
-"aclew","wc_adu_ph","1.30776513217596","0.60087062468986","0.60087062468986","0.398390358988891","0.202480265700966","0.375174555683477","0.190680928905588","0.375870506561081","0.612514943232798","0.436670274813375","0.613082789320563","540","270","8","full","0.647156530610892","0.5"
-"aclew","wc_fem_ph","1.43588980175994","0.574370420020665","0.574370420020665","0.419342494781057","0.15502792523961","0.472640458456488","0.174731801738967","0.4797266251757","0.687488515145153","0.418009332119472","0.69262300364318","540","270","8","full","0.286152998334193","0.5"
-"aclew","wc_mal_ph","1.24394354729975","0.601816619108124","0.601816619108124","0.387384048441982","0.214432570666145","0.367202831884027","0.203261459818661","0.37743956071684","0.605972632949729","0.450845272592117","0.614361099612305","540","270","8","full","0.0553540591858858","0.5"
-"aclew","can_voc_dur_chi_ph","0.844495856965831","0.889978784306181","0.889978784306181","0.244454594001593","0.64552419030459","0.291628483343536","0.770094918236082","0.131252678639335","0.540026372822232","0.877550521757056","0.362288115509377","350","175","4","full","4.44344030305681e-07","0.7"
-"aclew","pc_adu_ph","1.3562066000421","0.756781594183231","0.756781594183231","0.561404994378128","0.195376599805104","0.550246174349415","0.191493178145377","0.238384051927228","0.741785800854543","0.437599335174742","0.488245892893354","540","270","8","full","0.0718138807554758","0.7"
-"aclew","pc_fem_ph","1.39892150161154","0.742610823428803","0.742610823428803","0.565151544045828","0.177459279382977","0.601543025331095","0.18888631362291","0.273963091127222","0.775592048264482","0.434610530961814","0.523414836556265","540","270","8","full","0.796564014054579","0.7"
-"aclew","pc_mal_ph","1.29598254625882","0.773671716632511","0.773671716632511","0.508166387665084","0.265505328967435","0.620373750622443","0.324131112840014","0.276303449879425","0.787638083527227","0.569325138071396","0.525645745611458","540","270","8","full","0.326478762877869","0.7"
-"aclew","sc_adu_ph","1.38521180122398","0.740701934244866","0.740701934244866","0.567769381739105","0.172932552505763","0.545904755038733","0.166272972354929","0.249312575881589","0.738853676338376","0.407765830293478","0.499312102678865","540","270","8","full","0.0605693654553862","0.7"
-"aclew","sc_fem_ph","1.49948245477495","0.744589932057702","0.744589932057702","0.580972714465136","0.163617217592559","0.668295082763152","0.188209496332651","0.293799154838421","0.817493169857187","0.433831184140387","0.54203242969256","540","270","8","full","0.651425594215559","0.7"
-"aclew","sc_mal_ph","1.23416790167894","0.778313889755638","0.778313889755638","0.501524933243095","0.276788956512546","0.559493911277526","0.308781728709321","0.24730979593471","0.747993256171154","0.55568131938128","0.497302519533844","540","270","8","full","0.271620480495832","0.7"
-"aclew","wc_adu_ph","1.4091965680302","0.74776023835827","0.74776023835827","0.572622307559466","0.175137930798804","0.568826390323276","0.173976940244554","0.250567662517703","0.754205801040589","0.41710543061024","0.500567340642299","540","270","8","full","0.160754264168797","0.7"
-"aclew","wc_fem_ph","1.4768135789158","0.753749494698142","0.753749494698142","0.546011807636198","0.207737687061946","0.6600340356957","0.25111900885657","0.297674358930321","0.812424787716192","0.501117759470336","0.545595416889036","540","270","8","full","0.335846141542191","0.7"
-"aclew","wc_mal_ph","1.2871282279368","0.780423154057152","0.780423154057152","0.511788038568125","0.268635115489025","0.606624866681363","0.318414517024259","0.2602655100519","0.778861262794192","0.564282302597077","0.510162238951394","540","270","8","full","0.643630098656656","0.7"
-"aclew","can_voc_dur_chi_ph","0.862090119047868","0.947526663755028","0.947526663755028","0.455963636672611","0.491563027082414","0.34886170767086","0.376099108050054","0.0401478017483922","0.590645162234365","0.613269197049757","0.200369163666449","350","175","4","full","8.09978744588238e-10","0.9"
-"aclew","pc_adu_ph","1.30679204241526","0.913725468926537","0.913725468926537","0.761755396488505","0.15197007243804","0.686917680692385","0.137039960826018","0.0777985965849346","0.828804971445264","0.370189087934825","0.278923997864893","540","270","8","full","0.918603944090458","0.9"
-"aclew","pc_fem_ph","1.4559916171689","0.916911563142918","0.916911563142918","0.766581445093673","0.150330118049251","0.754455147248699","0.147952095729245","0.0817740884088497","0.868593775736793","0.384645415583294","0.285961690456693","540","270","8","full","0.254243312448354","0.9"
-"aclew","pc_mal_ph","1.32758132131629","0.923793818699554","0.923793818699554","0.679190176155017","0.244603642544541","0.686796423988658","0.247342957675301","0.0770596139939341","0.828731816686591","0.49733586003354","0.277596134688389","540","270","8","full","0.0789827575607083","0.9"
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OUTPUT/df.icc.simu_halved.csv

@@ -0,0 +1,341 @@
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