bug spotted but not fixed, knitting broken, do not trust data

CODE/SM.Rmd

@@ -314,11 +314,9 @@ fig2 = ggarrange(bad, good,
           font.label = list(size = 20))  + labs(color= "Corpus")  +  theme(text = element_text(size = 20))
 fig2 
 
-<<<<<<< HEAD
+
 ggsave("../output/fig2.png", plot = fig2, width = 6, height = 4.5, units = "in")
-=======
-ggsave("fig1.png", plot = fig2, width = 6, height = 4.5, units = "in")
->>>>>>> origin/master
+
 ```
 
 
@@ -339,6 +337,7 @@ rval_tab$fin<-paste0(rval_tab$m," ","[",rval_tab$m-2*rval_tab$sd,",",rval_tab$m+
 #2024-04-19, this chunk stopped working because the line below was picking up on repeated rows, 
 #dim(all_rs) #375, 5 repetitions of our 75 metrics
 #all I did to fix this was re-run the lines that create all ICCs and create all r's. Probably the former wasn't necessary. Strange that I needed to do this... To be on the safe side, I re-did the simulation too. It's a bit annoying that this changes all the numbers in tab 
+#2024-04-26 the problem returned and it was not fixed when I reran things. To be checked! pushing but this doesn't knit at present
 
 mytab=rbind(cbind(rval_tab[rval_tab$data_set=="aclew" & rval_tab$metric== "wc_adu_ph","fin"],rval_tab[rval_tab$data_set=="lena" & rval_tab$metric== "wc_adu_ph","fin"]),
             cbind(rval_tab[rval_tab$metric== "can_voc_chi_ph","fin"],rval_tab[rval_tab$metric== "lena_CVC_ph","fin"]),
@@ -669,7 +668,6 @@ f_labels$age_bin<-factor(f_labels$age_bin,levels=age_levels)
 
 fig6 <- ggplot(df.icc.age, aes(y = icc_child_id, x = toupper(data_set))) +
   geom_violin(alpha = 0.5) +
-<<<<<<< HEAD
   stat_summary(fun = mean, geom = "point", aes(x = as.numeric(factor(toupper(data_set))) - 0.5), shape = 23, size = 3, fill = "white", color = "black", position = position_dodge(width = 0.75)) +
   geom_quasirandom(aes(colour = Type, shape = Type)) +  
   scale_color_manual(values = type_colors) +  # Using color-blind-friendly palette for metric type
@@ -683,23 +681,6 @@ fig6 <- ggplot(df.icc.age, aes(y = icc_child_id, x = toupper(data_set))) +
         legend.key = element_blank(),
         axis.line = element_line(colour = "black"))
 
-=======
-#    stat_summary(fun = mean, geom = "point", aes(x = as.numeric(factor(toupper(data_set))) - 0.5), shape = 23, size = 3, fill = "white", color = "black", position = position_dodge(width = 0.75)) +
-  geom_quasirandom(aes(colour = Type,shape = Type)) +  
-  theme(legend.position="none") +labs( y = "r",x="Pipeline") + facet_wrap(~age_bin, ncol = 3) +
-  geom_text(x=1.5,y=max(df.icc.age$icc_child_id,na.rm=T),aes(label=facet_labels_chi),data=f_labels,size=3) +
-  geom_text(x=1.5,y=max(df.icc.age$icc_child_id,na.rm=T)*.95,aes(label=facet_labels_cor),data=f_labels,size=3) + 
-    stat_summary(fun = mean, geom = "point", aes(group = Type,x = as.numeric(factor(toupper(data_set))) + 0.5), shape = 1, size = 3, fill = "white", color = "black") +
-  stat_summary(
-    aes(group = Type, x = as.numeric(factor(toupper(data_set))) + 0.5, y = icc_child_id,color = Type, shape = Type), 
-    fun = mean, 
-    geom = "point", 
-    show.legend = FALSE,
-    inherit.aes = FALSE
-  ) +
-  theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
-panel.background = element_blank(), legend.key=element_blank(), axis.line = element_line(colour = "black")) 
->>>>>>> origin/master
 
 fig6
 
@@ -816,7 +797,7 @@ fig8 <- ggplot(df.icc.corpus, aes(y = icc_child_id, x = toupper(data_set))) +
 #    stat_summary(fun = mean, geom = "point", aes(x = as.numeric(factor(toupper(data_set))) - 0.5), shape = 23, size = 3, fill = "white", color = "black", position = position_dodge(width = 0.75)) +
   geom_quasirandom(aes(colour = Type,shape = Type)) +  
   theme(legend.position = "top", axis.title.y=element_blank() ,axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1)) +labs( y = "Child ICC",x="Pipeline") +   
-  facet_wrap(~corpus,nrow=1) +
+  facet_wrap(~corpus,nrow=2) +
   geom_text(x=1.5,y=max(df.icc.corpus$icc_child_id,na.rm=T),aes(label=facet_labels_chi),data=f_labels,size=3)+ 
   theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
 panel.background = element_blank(), legend.key=element_blank(), axis.line = element_line(colour = "black")) +

OUTPUT/df.icc.simu.csv

@@ -1,376 +1,376 @@
 "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","avg_can_voc_dur_chi","1.3065050872509","0.166593607434845","0.166593607434845","0.0843418913090521","0.0822517161257935","0.0844227299253617","0.0823305513856804","0.834205182093738","0.290555898108026","0.286933008532794","0.913348335572873","382","191","8","full","0.151626765934109","0.1"
-"aclew","avg_cry_voc_dur_chi","1.55482323228047","0.254058589337241","0.254058589337241","0.0520024624942501","0.202056126842991","0.0642317408784383","0.249573119421314","0.921362433663307","0.253439817073873","0.499572937038541","0.95987625955813","382","191","8","full","0.197878964679982","0.1"
-"aclew","avg_non_can_voc_dur_chi","1.2092319327045","0.153077764872925","0.153077764872925","0.0874035079878478","0.0656742568850774","0.0815322570078615","0.0612626485415085","0.790031005959782","0.285538538568547","0.247512926008943","0.888836883775523","382","191","8","full","0.131821705564685","0.1"
-"aclew","avg_voc_dur_chi","1.13824413742393","0.157630999791308","0.157630999791308","0.093526342937458","0.0641046568538505","0.0817964177673188","0.0560647527547889","0.736720420057318","0.286000730361513","0.236779966962556","0.858324192864979","382","191","8","full","0.473791659034432","0.1"
-"aclew","avg_voc_dur_fem","1.30825758070143","0.165462155476618","0.165462155476618","0.102874609859744","0.0625875456168743","0.115867936541067","0.0704925129114374","0.939942111490737","0.340393796272886","0.265504261569259","0.969506117304443","382","191","8","full","0.0105566587205713","0.1"
-"aclew","avg_voc_dur_mal","1.29192606884568","0.213743186845319","0.213743186845319","0.0795436681650443","0.134199518680275","0.0889446169655243","0.150060024403303","0.879181369125108","0.298235841181982","0.387375818041476","0.93764671871932","382","191","8","full","0.014956169975715","0.1"
-"aclew","avg_voc_dur_och","1.42466473674755","0.246349541615658","0.246349541615658","0.0910626607718412","0.155286880843816","0.110680721005292","0.188741068938447","0.916012945513908","0.332687121790568","0.434443401306139","0.957085652130418","382","191","8","full","0.435577879676294","0.1"
-"aclew","can_voc_chi_ph","0.960076807075558","0.433965467361628","0.433965467361628","0.0551650727174992","0.378800394644131","0.0438968168030207","0.301424990659546","0.450413875291207","0.209515671974725","0.549021848981938","0.671128806780939","382","191","8","full","3.84315865363709e-06","0.1"
-"aclew","can_voc_dur_chi_ph","0.932154777011447","0.569877065129267","0.569877065129267","0.0412082525022844","0.528668812626986","0.0373055063435987","0.47859971111431","0.389386904345384","0.193146334015427","0.691809013467091","0.624008737395066","382","191","8","full","8.47220462451459e-05","0.1"
-"aclew","cp_dur","1.29810051249101","0.31808529438017","0.31808529438017","0.0722883971495897","0.245796897230582","0.0819667456794912","0.278705470843622","0.77321301141843","0.286298350815179","0.527925630030994","0.879325316034078","382","191","8","full","0.0600663198306449","0.1"
-"aclew","cp_n","1.18294607223716","0.470032854582036","0.470032854582036","0.0547534843947374","0.415279370187299","0.063940253983342","0.48495668718337","0.618887259056491","0.252864101808347","0.69638831637483","0.786693878873155","382","191","8","full","0.000332236331552382","0.1"
-"aclew","cry_voc_chi_ph","1.33305794965673","0.27449920533652","0.27449920533652","0.0821941049427901","0.19230510039373","0.0771167051012649","0.18042578268666","0.68068422755791","0.277698946885408","0.424765562029998","0.825035894708776","382","191","8","full","0.190294555383563","0.1"
-"aclew","cry_voc_dur_chi_ph","1.19231779678025","0.210437336994615","0.210437336994615","0.0646570627527033","0.145780274241912","0.0710589764038599","0.160214470414853","0.867739922774682","0.266568896167313","0.400267998239745","0.931525588899565","382","191","8","full","0.0897249169243435","0.1"
-"aclew","lp_dur","1.32035225005894","0.108910308334407","0.108910308334407","0.101160029449819","0.00775027888458782","0.100040322654058","0.0076644936195645","0.881226515578976","0.316291515305197","0.0875470937242608","0.938736659334755","382","191","8","full","0.158053054848148","0.1"
-"aclew","lp_n","1.23760308310167","0.101615174110225","0.101615174110225","0.0843895551372861","0.0172256189729391","0.0692029225697061","0.0141257193980973","0.736712682543576","0.263064483672171","0.118851669732054","0.858319685515587","382","191","8","full","0.34632986384349","0.1"
-"aclew","non_can_voc_chi_ph","1.25307976100016","0.295268540091223","0.295268540091223","0.0698157890961491","0.225452750995076","0.070299682426481","0.227015364322575","0.709615954627519","0.265140872794975","0.476461293624755","0.842387057490509","382","191","8","full","0.874168095316139","0.1"
-"aclew","non_can_voc_dur_chi_ph","1.30229665611891","0.290538686622286","0.290538686622286","0.0728904989414423","0.217648187680844","0.0707517511431745","0.211261970149622","0.688644350344414","0.265992013307119","0.459632429392903","0.829845979892904","382","191","8","full","0.698675315300884","0.1"
-"aclew","pc_adu_ph","1.28648017686217","0.272842233702243","0.272842233702243","0.0800249455755367","0.192817288126706","0.0808597035297217","0.194828608019654","0.734742910217556","0.284358406820902","0.441393937452311","0.857171459054462","382","191","8","full","0.512326271711078","0.1"
-"aclew","pc_fem_ph","1.3480375128645","0.222590797687046","0.222590797687046","0.0826390832200751","0.13995171446697","0.0906896256440523","0.153585544498992","0.853142929263235","0.301147182693201","0.391899916431469","0.923657365727809","382","191","8","full","0.0036507119829797","0.1"
-"aclew","pc_mal_ph","1.20166138410323","0.157799999188032","0.157799999188032","0.0961021977231382","0.0616978014648932","0.0885562068991737","0.0568532603956646","0.776070051355673","0.297583949330561","0.23843921740281","0.88094838177709","382","191","8","full","0.352490731771365","0.1"
-"aclew","peak_simple_CTC","1.22525920072431","0.359743264885607","0.359743264885607","0.0729023750964117","0.286840889789197","0.0638535914659899","0.251237644426786","0.560786832298352","0.252692681860773","0.501236116442925","0.748857017259204","382","191","8","full","0.471483872095468","0.1"
-"aclew","peak_voc_chi","1.13267512093386","0.324933216171141","0.324933216171141","0.0734099161068785","0.251523300064264","0.0565145179212715","0.193634849390153","0.51969918882902","0.237727823195501","0.440039599797738","0.720901649900331","382","191","8","full","0.296941952820391","0.1"
-"aclew","peak_voc_fem","1.19169168488586","0.257679525504253","0.257679525504253","0.0905140207195327","0.167165504784721","0.0832888831475574","0.153821784554893","0.68306592466921","0.288598134345247","0.39220120417318","0.826478024311119","382","191","8","full","0.0721406608245538","0.1"
-"aclew","peak_voc_mal","1.32341888817472","0.10879760279418","0.10879760279418","0.0765763967330246","0.0322212060611543","0.0776969705633256","0.0326927121888028","0.904243727516674","0.278741763220594","0.180811261233372","0.950917308453618","382","191","8","full","0.154127425156672","0.1"
-"aclew","peak_voc_och","1.29760046707861","0.354580097257096","0.354580097257096","0.0813020797412685","0.273278017515828","0.0814019402540607","0.273613675386461","0.646212649529447","0.285310252626962","0.523080945348291","0.803873528317389","382","191","8","full","0.723147625769089","0.1"
-"aclew","peak_wc_adu","1.36789518818982","0.180751275723651","0.180751275723651","0.0832569752689177","0.0974943004547325","0.0944580434158876","0.110610802703431","0.929467246631957","0.307340273013296","0.332582024023295","0.964088816775694","382","191","8","full","0.0110513845976562","0.1"
-"aclew","peak_wc_fem","1.4348938915587","0.15674712606609","0.15674712606609","0.0911284789539527","0.0656186471121362","0.10389832053444","0.0748137937662496","0.961417971563465","0.322332624061605","0.273521102963281","0.980519235692735","382","191","8","full","0.38702235405045","0.1"
-"aclew","peak_wc_mal","1.33467562633464","0.191373501298832","0.191373501298832","0.0994264443160348","0.0919470569827973","0.104099958466004","0.0962690044768784","0.846635776913988","0.322645251733236","0.310272468125805","0.920128130704625","382","191","8","full","0.413357880106691","0.1"
-"aclew","sc_adu_ph","1.2621826358092","0.234717692953818","0.234717692953818","0.0673338163880761","0.16738387656574","0.0635959928637687","0.158092090877977","0.722800083945576","0.252182459468871","0.39760796128596","0.850176501642792","382","191","8","full","0.0155129900174402","0.1"
-"aclew","sc_fem_ph","1.41389559120194","0.227297387633927","0.227297387633927","0.0753025328010319","0.151994854832897","0.0843239485551925","0.170204186271508","0.865274153603592","0.290385861493277","0.412558100479809","0.930201136101","382","191","8","full","0.970821788992518","0.1"
-"aclew","sc_mal_ph","1.18603433602649","0.159943054319834","0.159943054319834","0.0946325273179356","0.0653105270018985","0.0933419613712779","0.0644198444375014","0.828600537211799","0.305519166945836","0.25381064681668","0.910274978900222","382","191","8","full","0.51826802172097","0.1"
-"aclew","simple_CTC_ph","1.19214564652502","0.487216794001105","0.487216794001105","0.0489348198995744","0.43828197410153","0.0520650221000257","0.466317454819886","0.545584289625366","0.228177610864926","0.682874406329514","0.73863677787216","382","191","8","full","8.33016345740898e-05","0.1"
-"aclew","voc_chi_ph","1.26170355281061","0.431667359213289","0.431667359213289","0.0630611389052286","0.368606220308061","0.0708876029669303","0.414353623324303","0.638867919175736","0.266247259078719","0.643703055239218","0.799292136315463","382","191","8","full","0.583202162909989","0.1"
-"aclew","voc_dur_chi_ph","1.23682807303495","0.404128989233471","0.404128989233471","0.0807924863936785","0.32333650283979","0.0835926673829993","0.334542999493373","0.616523261376883","0.289123965424866","0.578396922098807","0.785189952417173","382","191","8","full","8.67761124969302e-05","0.1"
-"aclew","voc_dur_fem_ph","1.40190523808009","0.263576198605761","0.263576198605761","0.0886059175454481","0.174970281060312","0.0920918457782655","0.181853950453379","0.765396138589237","0.303466383275422","0.426443373091174","0.874869212276462","382","191","8","full","0.766840975288563","0.1"
-"aclew","voc_dur_mal_ph","1.4499473124543","0.13897552935252","0.13897552935252","0.0920825120852328","0.0468930172672871","0.0949118506175519","0.0483338578530461","0.887480413876067","0.308077669780774","0.21984962554675","0.942061788778245","382","191","8","full","0.331456976968416","0.1"
-"aclew","voc_dur_och_ph","1.3276162579669","0.360121167652723","0.360121167652723","0.0692099241585417","0.290911243494184","0.0816712195287026","0.34329001685301","0.755089464752067","0.285781769062868","0.585909563715263","0.868958839503959","382","191","8","full","0.6781069725967","0.1"
-"aclew","voc_fem_ph","1.26670410728368","0.376750321985721","0.376750321985721","0.0654583718029726","0.311291950182749","0.0636687766416114","0.302781402907077","0.606210381475535","0.252326725975691","0.550255761357459","0.77859513322107","382","191","8","full","0.38170143209761","0.1"
-"aclew","voc_mal_ph","1.2019894937711","0.168999557323443","0.168999557323443","0.0409663136596145","0.128033243663829","0.0352260609195582","0.110093060325241","0.714559588180913","0.187686070126577","0.331802743094811","0.845316265181803","382","191","8","full","0.812336815369415","0.1"
-"aclew","voc_och_ph","1.16690756578807","0.407966428110843","0.407966428110843","0.0542087730591901","0.353757655051653","0.0669618583440791","0.436982219830679","0.731314618253661","0.258769894586057","0.661046306873186","0.855169350628085","382","191","8","full","0.00496309453579591","0.1"
-"aclew","wc_adu_ph","1.25043520672776","0.221884339160337","0.221884339160337","0.0987189989637817","0.123165340196556","0.102509895530429","0.127894997812435","0.807995988011675","0.320171665720795","0.357624101274558","0.898885970527783","382","191","8","full","0.0326073068119411","0.1"
-"aclew","wc_fem_ph","1.40399221906616","0.229877017513126","0.229877017513126","0.0844102434374821","0.145466774075644","0.0965691730884379","0.166420632286552","0.881055859650976","0.310755809420255","0.407946849830406","0.938645758340694","382","191","8","full","0.492681689030903","0.1"
-"aclew","wc_mal_ph","1.31189095744973","0.149005233189322","0.149005233189322","0.0897255840764217","0.059279649112901","0.0898623902114594","0.0593700338093619","0.852292293109147","0.299770562616578","0.243659667998957","0.923196779191277","382","191","8","full","0.0308887139195247","0.1"
-"lena","avg_cry_voc_dur_chi","1.64140154332237","0.28144830836272","0.28144830836272","0.080381551249796","0.201066757112925","0.118397000413477","0.296158764727695","1.05838172577068","0.344088651968467","0.544204708476226","1.02877681047479","382","191","8","full","0.46103968091443","0.1"
-"lena","avg_voc_dur_chi","1.40417413049134","0.362725599239405","0.362725599239405","0.0626757274413527","0.300049871798054","0.0779641847076054","0.373240879385825","0.792724410527483","0.279220673854221","0.610934431331076","0.890350723326198","382","191","8","full","0.891326600634945","0.1"
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OUTPUT/df.icc.simu_halved.csv

@@ -1,376 +1,376 @@
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data_output/all_rs.csv

@@ -1,154 +1,376 @@
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-=======
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->>>>>>> origin/master
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