Last updated: 2021-03-24
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Knit directory: PredictOutbredCrossVar/
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Modified: analysis/NGCleadersCall.Rmd
Modified: code/fitDirectionalDomMtBRR.R
Modified: code/fitmtBRR.R
Modified: code/getDirectionalDomGenomicBLUPs.R
Modified: code/getDirectionalDomMtCrossMeanPreds.R
Modified: code/getDirectionalDomMtCrossVarBVpreds.R
Modified: code/getDirectionalDomMtCrossVarTGVpreds.R
Modified: code/getDirectionalDomVarComps.R
Modified: code/getGenomicBLUPs.R
Modified: code/getMtCrossMeanPreds.R
Modified: code/getMtCrossVarPreds.R
Modified: code/getUntestedMtCrossVarPreds.R
Modified: code/getVarComps.R
Modified: data/blups_forawcdata.rds
Modified: data/genmap_awc_May2020.rds
Modified: data/parentwise_crossVal_folds.rds
Modified: data/ped_awc.rds
Modified: data/selection_index_weights_4traits.rds
Modified: output/CrossesToPredict_top100stdSI_and_209originalParents.rds
Modified: output/accuraciesMeans.rds
Modified: output/accuraciesUC.rds
Modified: output/accuraciesVars.rds
Modified: output/crossRealizations/realizedCrossMeans.rds
Modified: output/crossRealizations/realizedCrossMeans_BLUPs.rds
Modified: output/crossRealizations/realizedCrossMetrics.rds
Modified: output/crossRealizations/realizedCrossVars.rds
Modified: output/crossRealizations/realizedCrossVars_BLUPs.rds
Modified: output/crossRealizations/realized_cross_means_and_covs_traits.rds
Modified: output/crossRealizations/realized_cross_means_and_vars_selindices.rds
Modified: output/ddEffects.rds
Modified: output/gebvs_ModelA_GroupAll_stdSI.rds
Modified: output/obsVSpredMeans.rds
Modified: output/obsVSpredUC.rds
Modified: output/obsVSpredVars.rds
Modified: output/pmv_DirectionalDom_varcomps_geneticgroups.rds
Modified: output/pmv_varcomps_geneticgroups.rds
Modified: output/pmv_varcomps_geneticgroups_tidy_includingSIvars.rds
Modified: output/propHomozygous.rds
Modified: output/top100stdSI.rds
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Format predicted and observed values so prediction accuracy can be computed.
library(tidyverse); library(magrittr); library(predCrossVar)
predmeans<-readRDS(here::here("output/crossPredictions","predictedCrossMeans_tidy_withSelIndices.rds"))
predmeans_dd<-readRDS(here::here("output/crossPredictions","predictedCrossMeans_DirectionalDom_tidy_withSelIndices.rds"))
#predmeans %>% count(Model,predOf)
#predmeans_dd %>% count(predOf)
predmeans %<>%
bind_rows(predmeans_dd %>%
mutate(Model=ifelse(predOf=="MeanBV","DirDomBV","DirDomAD"))) %>%
#rename(VarComp=predOf) %>%
mutate(predOf=gsub("MeanGV","MeanTGV",predOf))
rm(predmeans_dd)
#predmeans %>% count(Model,VarComp)
obsMeans<-readRDS(here::here("output/crossRealizations","realizedCrossMeans.rds")) %>%
rename(predOf=obsOf) %>%
mutate(Model=ifelse(Model=="DirDom",
ifelse(predOf=="MeanBV","DirDomBV","DirDomAD"),
Model))
#obsMeans %>% count(Model,predOf)
obsMeanBLUPs<-readRDS(here::here("output/crossRealizations","realizedCrossMeans_BLUPs.rds"))
obsVSpredMeans<-bind_rows(left_join(predmeans,obsMeans) %>% mutate(ValidationData="GBLUPs"),
left_join(predmeans,obsMeanBLUPs) %>% mutate(ValidationData="iidBLUPs"))
# obsVSpredMeans %>% count(Model,ValidationData,VarComp) %>% spread(ValidationData,n)# Variances
predvars<-readRDS(here::here("output/crossPredictions","predictedCrossVars_tidy_withSelIndices.rds")) %>%
bind_rows(readRDS(here::here("output/crossPredictions","predictedCrossVars_DirectionalDom_tidy_withSelIndices.rds"))) %>%
select(-Nsegsnps,-totcomputetime) %>%
pivot_longer(cols=c(VPM,PMV),names_to = "VarMethod",values_to = "predVar") %>%
group_by(Repeat,Fold,Model,sireID,damID,Trait1,Trait2,VarMethod) %>%
# sum over VarComps (ModelA = VarA, ModelAD = VarA+VarD)
summarize(predVar=sum(predVar),.groups="drop") %>%
mutate(predOf=ifelse(Model %in% c("A","DirDomBV"),"VarBV",
ifelse(Model %in% c("AD","DirDomAD"),"VarTGV",NA)))
predvars %>%
count(Model,predOf)# A tibble: 4 x 3
Model predOf n
<chr> <chr> <int>
1 A VarBV 99648
2 AD VarTGV 99648
3 DirDomAD VarTGV 99648
4 DirDomBV VarBV 99648obsVars<-readRDS(here::here("output/crossRealizations","realizedCrossVars.rds")) %>%
rename(predOf=obsOf) %>%
mutate(Model=ifelse(Model=="DirDom",
ifelse(predOf=="VarBV","DirDomBV","DirDomAD"),
Model))
obsVars %>% count(Model,predOf)# A tibble: 4 x 3
Model predOf n
<chr> <chr> <int>
1 A VarBV 40374
2 AD VarTGV 40374
3 DirDomAD VarTGV 40374
4 DirDomBV VarBV 40374obsVarBLUPs<-readRDS(here::here("output/crossRealizations","realizedCrossVars_BLUPs.rds"))
obsVSpredVars<-bind_rows(left_join(predvars,obsVars) %>% mutate(ValidationData="GBLUPs"),
left_join(predvars,obsVarBLUPs) %>% mutate(ValidationData="iidBLUPs"))
obsVSpredVars %>% count(Model,ValidationData,predOf)# A tibble: 8 x 4
Model ValidationData predOf n
<chr> <chr> <chr> <int>
1 A GBLUPs VarBV 99648
2 A iidBLUPs VarBV 99648
3 AD GBLUPs VarTGV 99648
4 AD iidBLUPs VarTGV 99648
5 DirDomAD GBLUPs VarTGV 99648
6 DirDomAD iidBLUPs VarTGV 99648
7 DirDomBV GBLUPs VarBV 99648
8 DirDomBV iidBLUPs VarBV 99648For ValidationData==“GBLUPs”, weight by the observed “FamSize”.
# add Family Sizes, for weighted correlations
obsVSpredVars %<>%
left_join(readRDS(file=here::here("output/crossRealizations","realizedCrossMetrics.rds")) %>%
distinct(Repeat,Fold,sireID,damID,FamSize) %>% ungroup())
obsVSpredVars %>% head# A tibble: 6 x 13
Repeat Fold Model sireID damID Trait1 Trait2 VarMethod predVar predOf
<chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <dbl> <chr>
1 Repeat1 Fold1 A IITA-TMS… IITA-TM… biofo… biofo… PMV 55.4 VarBV
2 Repeat1 Fold1 A IITA-TMS… IITA-TM… biofo… biofo… VPM 5.86 VarBV
3 Repeat1 Fold1 A IITA-TMS… IITA-TM… DM DM PMV 4.35 VarBV
4 Repeat1 Fold1 A IITA-TMS… IITA-TM… DM DM VPM 0.355 VarBV
5 Repeat1 Fold1 A IITA-TMS… IITA-TM… DM logFY… PMV -0.0762 VarBV
6 Repeat1 Fold1 A IITA-TMS… IITA-TM… DM logFY… VPM -0.00459 VarBV
# … with 3 more variables: obsVar <dbl>, ValidationData <chr>, FamSize <dbl>For ValidationData==“iidBLUPs”, weight by the number of observed non-missing BLUPs per family per trait.
parentfolds<-readRDS(file = here::here("data","parentwise_crossVal_folds.rds")) %>%
rename(Repeat=id,Fold=id2) %>%
select(Repeat,Fold,testparents)
ped<-readRDS(here::here("data","ped_awc.rds")) %>%
nest(FamilyMembers=FullSampleName)
parentfolds %<>%
mutate(CrossesToPredict=map(testparents,~filter(ped,sireID %in% . | damID %in% .))) %>%
select(-testparents)
indices<-readRDS(file=here::here("data","selection_index_weights_4traits.rds"))
blups<-readRDS(here::here("data","blups_forawcdata.rds")) %>%
select(Trait,blups) %>%
unnest(blups) %>%
select(Trait,germplasmName,BLUP) %>%
spread(Trait,BLUP) %>%
select(germplasmName,all_of(c("DM","logFYLD","MCMDS","TCHART"))) # precaution to ensure consistent column order
crossblups<-parentfolds %>%
unnest(CrossesToPredict) %>%
distinct(sireID,damID,FamilyMembers) %>%
unnest(FamilyMembers) %>%
rename(germplasmName=FullSampleName) %>%
left_join(blups) %>%
select(sireID,damID,germplasmName,all_of(indices$Trait)) %>%
nest(famblups=c(germplasmName,all_of(indices$Trait))) %>%
mutate(stdSI=map(famblups,~as.data.frame(.) %>%
column_to_rownames(var = "germplasmName") %>%
as.matrix(.)%*%indices$stdSI),
biofortSI=map(famblups,~as.data.frame(.) %>%
column_to_rownames(var = "germplasmName") %>%
as.matrix(.)%*%indices$biofortSI))
nObs<-bind_rows(crossblups %>%
select(-famblups) %>%
mutate(stdSI=map_dbl(stdSI,~length(which(!is.na(.)))),
biofortSI=map_dbl(biofortSI,~length(which(!is.na(.))))) %>%
pivot_longer(cols = c(stdSI,biofortSI), names_to = "Trait1", values_to = "Nobs",values_drop_na = TRUE) %>%
mutate(Trait2=Trait1),
crossblups %>%
select(sireID,damID,famblups) %>%
mutate(famblups=map(famblups,function(famblups){
NobsMat<-psych::pairwiseCount(famblups %>% select(-germplasmName),diagonal=TRUE)
NobsMat[lower.tri(NobsMat, diag = F)]<-NA
NobsMat %<>%
as.data.frame %>%
rownames_to_column(var = "Trait1") %>%
pivot_longer(cols = -Trait1, names_to = "Trait2", values_to = "Nobs",values_drop_na = TRUE)
return(NobsMat) })) %>%
unnest(famblups))
rm(parentfolds,ped,indices,blups,crossblups)
# add N obs, for weighted correlations
obsVSpredVars %<>%
left_join(nObs) %>%
mutate(CorrWeight=ifelse(ValidationData=="GBLUPs",FamSize,Nobs))# Usefulness
realizedcrossmetrics<-readRDS(file=here::here("output/crossRealizations","realizedCrossMetrics.rds"))
# previously only calculated UC accuracy
# for sel. indices
# Now include component traits
predUsefulness<-left_join(predvars %>% # Variances
filter(#Trait1 %in% c("stdSI","biofortSI"),
Trait1==Trait2) %>%
rename(Trait=Trait1) %>%
select(-Trait2) %>%
mutate(predOf=gsub("Var","",predOf)),
predmeans %>% # Means
#filter(Trait %in% c("stdSI","biofortSI")) %>%
mutate(predOf=gsub("Mean","",predOf))) %>%
mutate(predSD=sqrt(predVar)) %>%
select(-predVar)## Add the realized selection intensities
## Create a variable "Stage" for which there are several applying to "Usefulness" for TGV
predBVs<-predUsefulness %>%
filter(predOf=="BV") %>%
left_join(realizedcrossmetrics %>%
select(Repeat,Fold,Model,sireID,damID,Trait,FamSize,realIntensityParent) %>%
rename(realIntensity=realIntensityParent) %>%
mutate(Stage="Parent",
Model=ifelse(Model=="ClassicAD","A","DirDomBV")))
predTGVs<-predUsefulness %>%
filter(predOf=="TGV") %>%
left_join(realizedcrossmetrics %>%
select(Repeat,Fold,Model,sireID,damID,Trait,FamSize,
contains("realIntensity"),-realIntensityParent) %>%
pivot_longer(cols = contains("realIntensity"),
names_to = "Stage",
values_to = "realIntensity",
names_prefix = "realIntensity") %>%
mutate(Model=ifelse(Model=="ClassicAD","AD","DirDomAD")))
predUsefulness<-bind_rows(predBVs,
predTGVs) %>%
# include a "stage" (=="ConstIntensity")
# where intensity for predicted UC is set to 2.67
bind_rows(predUsefulness %>%
left_join(realizedcrossmetrics %>%
distinct(Repeat,Fold,sireID,damID,Trait,FamSize)) %>%
mutate(Stage="ConstIntensity",
realIntensity=2.67))
## Compute predicted UCs
predUsefulness %<>%
dplyr::mutate(predUC=predMean+(realIntensity*predSD))
# predUsefulness %>% count(Model,predOf,Stage)
# predUsefulness %>% filter(!is.na(predUC)) %>% count(Model,predOf,Stage)
## Format observed UCs
obsUCgca<-realizedcrossmetrics %>%
select(Repeat,Fold,Model,sireID,damID,Trait,realizedUCparent) %>%
rename(obsUC=realizedUCparent) %>%
mutate(predOf="BV",
Stage="Parent")
#obsUCgca %>% count(VarComp,Stage,Model,Trait)
obsUCtgv<-realizedcrossmetrics %>%
select(Repeat,Fold,Model,sireID,damID,Trait,contains("realizedUCat")) %>%
pivot_longer(cols = contains("realizedUCat"),
names_to = "Stage",
values_to = "obsUC",
names_prefix = "realizedUCat",
values_drop_na = T) %>%
mutate(predOf="TGV")
#obsUCtgv %>% count(VarComp,Stage,Model)
obsUsefulness<-bind_rows(obsUCgca,obsUCtgv)
obsUsefulness %<>%
bind_rows(realizedcrossmetrics %>%
select(Repeat,Fold,Model,sireID,damID,Trait,meanTop1pctGEBV) %>%
rename(obsUC=meanTop1pctGEBV) %>%
mutate(predOf="BV",
Stage="ConstIntensity")) %>%
bind_rows(realizedcrossmetrics %>%
select(Repeat,Fold,Model,sireID,damID,Trait,meanTop1pctGETGV) %>%
rename(obsUC=meanTop1pctGETGV) %>%
mutate(predOf="TGV",
Stage="ConstIntensity"))
obsUsefulness %<>%
mutate(Model=ifelse(Model=="ClassicAD",
ifelse(predOf=="BV","A","AD"),
ifelse(predOf=="BV","DirDomBV","DirDomAD")))
#obsUsefulness %>% count(Trait,Stage,predOf,Model) %>% spread(Trait,n)
# predUsefulness %>% count(Model,predOf,Stage)
# obsUsefulness %>% count(Model,predOf,Stage)
# obsUsefulness %>% filter(!is.na(obsUC))
# predUsefulness %>% filter(!is.na(predUC)) %>% count(Model,predOf,Stage)
#predUsefulness %>% filter(is.na(FamSize)) %>% count(Model,predOf,VarMethod,Stage)obsVSpredUC<-left_join(predUsefulness,obsUsefulness) %>% ungroup()
obsVSpredUC %<>% drop_na(.) %>% ungroup()
obsVSpredUC %>% strtibble [391,848 × 15] (S3: tbl_df/tbl/data.frame)
$ Repeat : chr [1:391848] "Repeat1" "Repeat1" "Repeat1" "Repeat1" ...
$ Fold : chr [1:391848] "Fold1" "Fold1" "Fold1" "Fold1" ...
$ Model : chr [1:391848] "A" "A" "A" "A" ...
$ sireID : chr [1:391848] "IITA-TMS-IBA030075" "IITA-TMS-IBA030075" "IITA-TMS-IBA030075" "IITA-TMS-IBA030075" ...
$ damID : chr [1:391848] "IITA-TMS-IBA940006" "IITA-TMS-IBA940006" "IITA-TMS-IBA940006" "IITA-TMS-IBA940006" ...
$ Trait : chr [1:391848] "biofortSI" "biofortSI" "DM" "DM" ...
$ VarMethod : chr [1:391848] "PMV" "VPM" "PMV" "VPM" ...
$ predOf : chr [1:391848] "BV" "BV" "BV" "BV" ...
$ predMean : num [1:391848] 4.49 4.49 1.4605 1.4605 0.0746 ...
$ predSD : num [1:391848] 7.263 2.294 2.055 0.626 0.186 ...
$ FamSize : num [1:391848] 38 38 38 38 38 38 38 38 38 38 ...
$ realIntensity: num [1:391848] 2.32 2.32 2.32 2.32 2.32 ...
$ Stage : chr [1:391848] "Parent" "Parent" "Parent" "Parent" ...
$ predUC : num [1:391848] 21.327 9.807 6.225 2.913 0.505 ...
$ obsUC : num [1:391848] -0.886 -0.886 1.805 1.805 0.121 ...obsVSpredUC %>% count(Trait)# A tibble: 6 x 2
Trait n
<chr> <int>
1 biofortSI 65308
2 DM 65308
3 logFYLD 65308
4 MCMDS 65308
5 stdSI 65308
6 TCHART 65308#obsVSpredUC %>% count(Model,predOf,Stage)saveRDS(obsVSpredMeans,here::here("output","obsVSpredMeans.rds"))
saveRDS(obsVSpredVars,here::here("output","obsVSpredVars.rds"))
saveRDS(obsVSpredUC,here::here("output","obsVSpredUC.rds"))rm(list=ls())
library(tidyverse); library(magrittr);
obsVSpredMeans<-readRDS(here::here("output","obsVSpredMeans.rds"))
obsVSpredVars<-readRDS(here::here("output","obsVSpredVars.rds"))
obsVSpredUC<-readRDS(here::here("output","obsVSpredUC.rds"))
# Means
obsVSpredMeans %<>%
drop_na(.) %>%
nest(predVSobs=c(sireID,damID,predMean,obsMean)) %>%
mutate(Accuracy=map_dbl(predVSobs,~cor(.$predMean,.$obsMean,use = 'complete.obs'))) %>%
select(-predVSobs)
# Variances
obsVSpredVars %<>%
drop_na(.) %>%
select(-FamSize,-Nobs) %>%
nest(predVSobs=c(sireID,damID,predVar,obsVar,CorrWeight)) %>%
mutate(AccuracyWtCor=map_dbl(predVSobs,~psych::cor.wt(.[,3:4],w = .$CorrWeight) %$% r[1,2]),
AccuracyCor=map_dbl(predVSobs,~cor(.$predVar,.$obsVar,use = 'complete.obs'))) %>%
select(-predVSobs)
# Usefulness
obsVSpredUC %<>%
select(-predMean,-predSD,-realIntensity) %>%
nest(predVSobs=c(sireID,damID,predUC,obsUC,FamSize)) %>%
mutate(AccuracyWtCor=map_dbl(predVSobs,~psych::cor.wt(.[,3:4],w = .$FamSize) %$% r[1,2]),
AccuracyCor=map_dbl(predVSobs,~cor(.$predUC,.$obsUC,use = 'complete.obs'))) %>%
select(-predVSobs)
obsVSpredUC %>% count(Model,predOf,Stage)# A tibble: 14 x 4
Model predOf Stage n
<chr> <chr> <chr> <int>
1 A BV ConstIntensity 300
2 A BV Parent 300
3 AD TGV AYT 300
4 AD TGV CET 300
5 AD TGV ConstIntensity 300
6 AD TGV PYT 300
7 AD TGV UYT 300
8 DirDomAD TGV AYT 300
9 DirDomAD TGV CET 300
10 DirDomAD TGV ConstIntensity 300
11 DirDomAD TGV PYT 300
12 DirDomAD TGV UYT 300
13 DirDomBV BV ConstIntensity 300
14 DirDomBV BV Parent 300saveRDS(obsVSpredMeans,here::here("output","accuraciesMeans.rds"))
saveRDS(obsVSpredVars,here::here("output","accuraciesVars.rds"))
saveRDS(obsVSpredUC,here::here("output","accuraciesUC.rds"))
sessionInfo()R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] predCrossVar_0.1.0 magrittr_2.0.1 forcats_0.5.1 stringr_1.4.0
[5] dplyr_1.0.5 purrr_0.3.4 readr_1.4.0 tidyr_1.1.3
[9] tibble_3.1.0 ggplot2_3.3.3 tidyverse_1.3.0 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 lattice_0.20-41 lubridate_1.7.10 here_1.0.1
[5] assertthat_0.2.1 rprojroot_2.0.2 digest_0.6.27 psych_2.0.12
[9] utf8_1.2.1 R6_2.5.0 cellranger_1.1.0 backports_1.2.1
[13] reprex_1.0.0 evaluate_0.14 httr_1.4.2 pillar_1.5.1
[17] rlang_0.4.10 readxl_1.3.1 rstudioapi_0.13 whisker_0.4
[21] jquerylib_0.1.3 rmarkdown_2.7 munsell_0.5.0 broom_0.7.5
[25] compiler_4.0.3 httpuv_1.5.5 modelr_0.1.8 xfun_0.22
[29] pkgconfig_2.0.3 mnormt_2.0.2 tmvnsim_1.0-2 htmltools_0.5.1.1
[33] tidyselect_1.1.0 fansi_0.4.2 crayon_1.4.1 dbplyr_2.1.0
[37] withr_2.4.1 later_1.1.0.1 grid_4.0.3 nlme_3.1-152
[41] jsonlite_1.7.2 gtable_0.3.0 lifecycle_1.0.0 DBI_1.1.1
[45] git2r_0.28.0 scales_1.1.1 cli_2.3.1 stringi_1.5.3
[49] fs_1.5.0 promises_1.2.0.1 xml2_1.3.2 bslib_0.2.4
[53] ellipsis_0.3.1 generics_0.1.0 vctrs_0.3.6 tools_4.0.3
[57] glue_1.4.2 hms_1.0.0 parallel_4.0.3 yaml_2.2.1
[61] colorspace_2.0-0 rvest_1.0.0 knitr_1.31 haven_2.3.1
[65] sass_0.3.1