Last updated: 2021-08-26

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File	Version	Author	Date	Message
Rmd	1a785f3	wolfemd	2021-08-26	Typo fixes plus save outputs for future sim inputs
html	ceae21a	wolfemd	2021-08-26	Build site.
Rmd	c2c7dae	wolfemd	2021-08-26	Update site with new version of inputs for simulations including 2 approaches now.
Rmd	8db43ac	wolfemd	2021-08-26	Revised empirical analysis for sim inputs. Two approaches: direct estimate with mixed model + indirect with SI_GETGV on SI_TrialBLUP.

Estimate selection error

Approach 1: direct estimation with multivar mixed model

Try a multivariate model with the proper error and other heterogeneous variances.

This will be for DIRECT calculation, if I can get the models to converge, of the variance components of interest.

Goal is to get estimate of errorCov matrix per stage.

Then compute SI errorVar per stage.

Things not modeled, which could be input to sims:

GxL, GxYr, GxYrxL variance
genCor among locs

screen;
cd ~/IITA_2021GS/;
salloc -n 8 --mem=60G --time=06:00:00;
export PATH=/programs/R-4.0.5clean-p/bin:$PATH
export OMP_NUM_THREADS=8
R;

library(genomicMateSelectR); 
library(tidyverse)

# CLEANED PLOT-LEVEL TRIAL DATA
dbdata<-readRDS(here::here("output","IITA_ExptDesignsDetected_2021Aug08.rds"))
# SELECTION INDEX WEIGHTS
SIwts<-c(logFYLD=20,
         HI=10,
         DM=15,
         MCMDS=-10,
         logRTNO=12,
         logDYLD=20,
         logTOPYLD=15,
         PLTHT=10) 
# FILTER TRIALS TO-BE-CONSIDERED
### Restrict consideration to >2012 
### to measure the selection error during the current "era" at IITA.
### Only trials with >=50% genotyped and key TrialTypes
### Keep only trials with full plotWidth and plotLength meta-data
### Calc plotArea=plotWidth*plotLength (in meters-squared)
trialdata<-dbdata %>% 
  filter(studyYear>=2013,
         !is.na(MaxNOHAV),
         !is.na(plotWidth),
         !is.na(plotLength),
         !is.na(PropNOHAV)) %>% 
  nest(TrialData=-c(studyName,TrialType,plotWidth,plotLength,CompleteBlocks,IncompleteBlocks,MaxNOHAV)) %>% 
  mutate(propGenotyped=map_dbl(TrialData,
                              ~length(which(!is.na(unique(.$FullSampleName))))/length(unique(.$GID))),
         plotArea=plotWidth*plotLength,
         IncompleteBlocks=ifelse(IncompleteBlocks==TRUE,"Yes","No"),
         CompleteBlocks=ifelse(CompleteBlocks==TRUE,"Yes","No")) %>% 
  filter(propGenotyped>=0.5,
         TrialType %in% c("GeneticGain","CET","ExpCET","PYT","AYT","UYT")) %>%
  unnest(TrialData) %>% 
  select(yearInLoc,studyName,studyYear,locationName,TrialType,
         plotArea,plotWidth,plotLength,
         CompleteBlocks,IncompleteBlocks,observationUnitDbId,
         GID,trialInLocYr,repInTrial,blockInRep,PropNOHAV,MaxNOHAV,
         all_of(names(SIwts)))
trialdata %>% nrow(.) %>% paste0(.," plots");

[1] "108254 plots"

# [1] "108254 plots"
trialdata %>% distinct(studyName) %>% nrow(.) %>% paste0(.," trials");

[1] "382 trials"

# [1] "382 trials"

Filters applied to the data-to-be-considered:

studyYear>=2013
propGenotyped>=0.5
TrialType %in% c("GeneticGain","CET","ExpCET","PYT","AYT","UYT")
Must have plotLength, plotWidth and MaxNOHAV meta-data.

It turns out, most IITA trials at least already have this.

trialdata %>% 
  distinct(studyYear,locationName,studyName,TrialType,CompleteBlocks,IncompleteBlocks,plotArea,MaxNOHAV) %>% 
  mutate(TrialType=factor(TrialType,levels=c("CrossingBlock","GeneticGain","CET","ExpCET","PYT","AYT","UYT","NCRP"))) %>% 
  ggplot(.,aes(x=TrialType,y=plotArea,fill=TrialType)) + 
  geom_boxplot(notch = T) + 
  theme_bw() + theme(axis.text.x = element_text(angle=45,vjust=.5)) +
  labs(title = "Plot Area (m-squared) by TrialType",
       subtitle="plotArea = plotWidth*plotLength. studyYear>=2013")

Version	Author	Date
ceae21a	wolfemd	2021-08-26

trialdata %>% 
  distinct(studyYear,locationName,studyName,TrialType,CompleteBlocks,IncompleteBlocks,plotArea,MaxNOHAV) %>% 
  mutate(TrialType=factor(TrialType,levels=c("CrossingBlock","GeneticGain","CET","ExpCET","PYT","AYT","UYT","NCRP"))) %>% 
  ggplot(.,aes(x=TrialType,y=MaxNOHAV,fill=TrialType)) + 
  geom_boxplot(notch = T) + 
  theme_bw() + theme(axis.text.x = element_text(angle=45,vjust=.5)) +
  labs(title = "Max number harvested as a proxy for planned plot size",
       subtitle="MaxNOHAV = The maximum number stands harvested per trial. studyYear>=2013")

Version	Author	Date
ceae21a	wolfemd	2021-08-26

Much less clear difference between trials using MaxNOHAV.

I decided to take a narrow view of plot configurations and analyze only trials confi=orming to the common (median) plotArea for each TrialType. Does not exclude too many.

Below, I work carefully up to a multivariate model with 7 of the 8 SELIND traits. Starting with homogenous variances and one trait, then 2 traits, 2 traits + heterogenous error by TrialType, 4 + heterog. error, and finally 7 traits skipping PLTHT b/c of >50% missingness.

trialdata %<>% 
  semi_join(trialdata %>% 
              distinct(TrialType,studyName,plotArea,plotWidth,plotLength) %>% 
              group_by(TrialType) %>% 
              summarize(plotArea=median(plotArea)) %>% ungroup())

trialdata %>% nrow(.) %>% paste0(.," plots");

[1] "70301 plots"

# [1] "70301 plots"
trialdata %>% distinct(studyName) %>% nrow(.) %>% paste0(.," trials");

[1] "240 trials"

# [1] "240 trials"

trialdata %>% 
  distinct(TrialType,plotArea) %>% 
  arrange(plotArea)

# A tibble: 6 × 2
  TrialType   plotArea
  <chr>          <dbl>
1 CET              2.5
2 PYT              8  
3 GeneticGain     10  
4 ExpCET          16  
5 AYT             22  
6 UYT             33

Work up to the full analysis

MultiTrialTraitData<-trialdata %>%
  filter(!is.na(DM)) %>% 
  mutate(across(c(GID,yearInLoc,
                  CompleteBlocks,
                  IncompleteBlocks,
                  trialInLocYr,
                  repInTrial,
                  blockInRep),as.factor)) %>% 
  droplevels

fixedFormula="DM ~ yearInLoc"
randFormula=paste0("~idv(GID) + idv(trialInLocYr) + at(CompleteBlocks,'Yes'):repInTrial ",
                   "+ at(IncompleteBlocks,'Yes'):blockInRep")

require(asreml); 
fixedFormula<-as.formula(fixedFormula)
randFormula<-as.formula(randFormula)
# fit asreml 
out<-asreml(fixed = fixedFormula,
            random = randFormula,
            data = MultiTrialTraitData, 
            maxiter = 40, workspace=1000e6, 
            na.method.X="omit")

MultiTrialTraitData<-trialdata %>%
  filter(!is.na(DM),
         !is.na(logFYLD)) %>% 
  mutate(across(c(GID,yearInLoc,
                  CompleteBlocks,
                  IncompleteBlocks,
                  trialInLocYr,
                  repInTrial,
                  blockInRep,
                  TrialType),as.factor)) %>% 
  droplevels

fixedFormula="cbind(DM,logFYLD) ~ yearInLoc*trait + PropNOHAV*trait"
randFormula=paste0("~us(trait,init=c(0,0,0)):GID + idv(trialInLocYr) + at(CompleteBlocks,'Yes'):repInTrial ",
                   "+ at(IncompleteBlocks,'Yes'):blockInRep")
errFormula=paste0("~units:us(trait,init=c(0,0,0))")
require(asreml); 
fixedFormula<-as.formula(fixedFormula)
randFormula<-as.formula(randFormula)
errFormula<-as.formula(errFormula)
# fit asreml 
out<-asreml(fixed = fixedFormula,
            random = randFormula,
            rcov = errFormula,
            data = MultiTrialTraitData, 
            maxiter = 40, workspace=1000e6)

fixedFormula="cbind(DM,logFYLD) ~ yearInLoc*trait + PropNOHAV*trait"
randFormula=paste0("~us(trait,init=c(0,0,0)):GID + idv(trialInLocYr) + at(CompleteBlocks,'Yes'):repInTrial ",
                   "+ at(IncompleteBlocks,'Yes'):blockInRep")
errFormula=paste0("~units:at(TrialType):us(trait,init=c(0,0,0))")
require(asreml); 
fixedFormula<-as.formula(fixedFormula)
randFormula<-as.formula(randFormula)
errFormula<-as.formula(errFormula)
# fit asreml 
out<-asreml(fixed = fixedFormula,
            random = randFormula,
            rcov = errFormula,
            data = MultiTrialTraitData %>% arrange(TrialType), 
            maxiter = 40, workspace=1000e6)

# Check the proportion missing for each trait
trialdata %>% 
  summarize(across(any_of(names(SIwts)),~length(which(is.na(.)))/length(.)))
#   logFYLD     HI    DM   MCMDS logRTNO logDYLD logTOPYLD PLTHT
#     <dbl>  <dbl> <dbl>   <dbl>   <dbl>   <dbl>     <dbl> <dbl>
# 1  0.0166 0.0327 0.101 0.00613  0.0104   0.109    0.0186 0.544
MultiTrialTraitData<-trialdata %>%
  # filter(!is.na(DM),
  #        !is.na(logFYLD)) %>% 
  mutate(across(c(GID,yearInLoc,
                  CompleteBlocks,
                  IncompleteBlocks,
                  trialInLocYr,
                  repInTrial,
                  blockInRep,
                  TrialType),as.factor)) %>% 
  droplevels

fixedFormula="cbind(DM,logFYLD,MCMDS,logTOPYLD) ~ yearInLoc*trait + PropNOHAV*trait"
randFormula=paste0("~us(trait):GID + ",
                   "idv(trialInLocYr) + at(CompleteBlocks,'Yes'):repInTrial ",
                   "+ at(IncompleteBlocks,'Yes'):blockInRep")
errFormula=paste0("~units:at(TrialType):us(trait)")
require(asreml); 
fixedFormula<-as.formula(fixedFormula)
randFormula<-as.formula(randFormula)
errFormula<-as.formula(errFormula)
# fit asreml 
out<-asreml(fixed = fixedFormula,
            random = randFormula,
            rcov = errFormula,
            data = MultiTrialTraitData %>% arrange(TrialType), 
            maxiter = 40, workspace=1000e6)
names(SIwts)

Full multi-trait model

7 traits. Heterogeneous error by TrialType. Skip PLTHT b/c >50% missing data.

# Check the proportion missing for each trait
trialdata %>% 
  summarize(across(any_of(names(SIwts)),~length(which(is.na(.)))/length(.)))
#   logFYLD     HI    DM   MCMDS logRTNO logDYLD logTOPYLD PLTHT
#     <dbl>  <dbl> <dbl>   <dbl>   <dbl>   <dbl>     <dbl> <dbl>
# 1  0.0166 0.0327 0.101 0.00613  0.0104   0.109    0.0186 0.544

# SKIP ONLY PLTHT B/C AMOUNT MISSING...
MultiTrialTraitData<-trialdata %>%
  mutate(across(c(GID,yearInLoc,
                  CompleteBlocks,
                  IncompleteBlocks,
                  trialInLocYr,
                  repInTrial,
                  blockInRep,
                  TrialType),as.factor)) %>% 
  droplevels

fixedFormula="cbind(logFYLD,HI,DM,MCMDS,logRTNO,logDYLD,logTOPYLD) ~ yearInLoc*trait + PropNOHAV*trait"
randFormula=paste0("~us(trait):GID + ",
                   "idv(trialInLocYr) + at(CompleteBlocks,'Yes'):repInTrial ",
                   "+ at(IncompleteBlocks,'Yes'):blockInRep")
errFormula=paste0("~units:at(TrialType):us(trait)")
require(asreml); 
fixedFormula<-as.formula(fixedFormula)
randFormula<-as.formula(randFormula)
errFormula<-as.formula(errFormula)
# fit asreml 
out<-asreml(fixed = fixedFormula,
            random = randFormula,
            rcov = errFormula,
            data = MultiTrialTraitData %>% arrange(TrialType), 
            maxiter = 60, workspace=1000e6)
saveRDS(out,file=here::here("output","estimateErrorCov_byTrialType_asreml_2021Aug25.rds"))
as_summary<-summary(out)
saveRDS(as_summary,file=here::here("output","estimateErrorCov_byTrialType_asreml_summary_2021Aug25.rds"))
# 
# ASReml: Wed Aug 25 16:48:25 2021
# 
#  US matrix updates modified 7 times to remain positive definite.
#      LogLik         S2      DF      wall     cpu
# -552132.9648      1.0000471133  16:50:44   107.3 (199 restrained)
#  Notice: NonPosDef US matrix modified
# -172985.8107      1.0000471133  16:52:02    77.5 (199 restrained)
#  -11758.3924      1.0000471133  16:53:15    73.2 (199 restrained)
#   86902.0709      1.0000471133  16:54:31    76.4 (199 restrained)
#  171214.2253      1.0000471133  16:55:47    75.0 (199 restrained)
#  225677.4607      1.0000471133  16:56:57    70.1 (155 restrained)
#  260884.6336      1.0000471133  16:58:06    68.7 (148 restrained)
#  280487.3333      1.0000471133  16:59:13    67.2 (87 restrained)
#  295260.2919      1.0000471133  17:00:20    66.5 (32 restrained)
#  302995.2011      1.0000471133  17:01:30    70.4 (5 restrained)
#  311088.9518      1.0000471133  17:02:46    75.9 (4 restrained)
#  Notice: NonPosDef US matrix modified
#  316645.9289      1.0000471133  17:03:59    72.2 (5 restrained)
#  324430.0701      1.0000471133  17:05:06    67.1 (2 restrained)
#  331602.8926      1.0000471133  17:06:14    67.9
#  335069.2210      1.0000471133  17:07:27    72.8
#  337425.1130      1.0000471133  17:08:50    77.6
#  339834.7415      1.0000471133  17:10:49    98.5
#  340877.5399      1.0000471133  17:13:12   114.1
#  341423.1058      1.0000471133  17:14:50    84.5
#  341734.7595      1.0000471133  17:16:00    70.2
#  341939.2189      1.0000471133  17:17:12    71.2
#  342091.3023      1.0000471133  17:18:27    75.2
#  342215.4180      1.0000471133  17:19:49    81.6
#  342322.6216      1.0000471133  17:21:38    94.1
#  342418.1298      1.0000471133  17:23:04    84.4
#  342504.5682      1.0000471133  17:24:26    79.1
#  342583.3893      1.0000471133  17:25:54    83.8
#  342655.5189      1.0000471133  17:27:22    84.5
#  342721.6172      1.0000471133  17:28:59    85.1
#  342782.2099      1.0000471133  17:30:46    90.1
#  342837.7490      1.0000471133  17:32:17    76.1
#  342888.6246      1.0000471133  17:33:23    65.9
#  342935.2019      1.0000471133  17:34:25    62.7
#  342977.8038      1.0000471133  17:35:29    63.7
#  343016.7322      1.0000471133  17:36:35    65.5
#  343052.2701      1.0000471133  17:37:34    59.8
#  343084.6751      1.0000471133  17:38:37    63.0
#  343114.1894      1.0000471133  17:39:42    64.2
#  343141.0370      1.0000471133  17:40:46    64.7
#  343165.4329      1.0000471133  17:41:46    59.9
#  343187.5770      1.0000471133  17:42:51    64.7
#  343207.6489      1.0000471133  17:43:54    63.5
#  343225.8251      1.0000471133  17:44:58    63.8
#  343242.2660      1.0000471133  17:46:06    67.9
#  343257.1194      1.0000471133  17:47:25    77.2
#  343270.5287      1.0000471133  17:48:49    76.7
#  343282.6168      1.0000471133  17:50:12    81.2
#  343293.5105      1.0000471133  17:51:18    66.5
#  343303.3166      1.0000471133  17:52:25    66.2
#  343312.1366      1.0000471133  17:53:44    75.7
#  343320.0631      1.0000471133  17:55:06    80.0
#  343327.1802      1.0000471133  17:56:25    74.7
#  343333.5731      1.0000471133  17:57:53    79.7
#  343339.3063      1.0000471133  17:59:17    78.3
#  343344.4459      1.0000471133  18:01:01    76.5
#  343349.0523      1.0000471133  18:02:05    64.3
#  343353.1798      1.0000471133  18:03:08    63.0
#  343356.8724      1.0000471133  18:04:13    64.6
#  343360.1798      1.0000471133  18:05:19    66.5
#  343363.1377      1.0000471133  18:06:29    70.0
# US variance structures were modified in 51 instances to make them positive definite
# 
# Finished on: Wed Aug 25 18:06:31 2021
# 
# LogLikelihood not converged

Independent but heterogeneous error covariances were fit by TrialType. After 40 iterations (~30 minutes), likelihood wasn’t converged… but looks on the way.

Result

asfit<-readRDS(file=here::here("output","estimateErrorCov_byTrialType_asreml_2021Aug25.rds"))
as_summary<-readRDS(file=here::here("output","estimateErrorCov_byTrialType_asreml_summary_2021Aug25.rds"))
varcomps<-as_summary$varcomp %>% 
  rownames_to_column(var = "VarComp") %>% 
  select(VarComp,component)

# SELECTION INDEX WEIGHTS
SIwts<-c(logFYLD=20,
         HI=10,
         DM=15,
         MCMDS=-10,
         logRTNO=12,
         logDYLD=20,
         logTOPYLD=15)
#         PLTHT=10) 
adjSIwts<-trialdata %>% 
  summarize(across(all_of(names(SIwts)),~sqrt(var(.,na.rm=T)))) %>% 
  magrittr::divide_by(SIwts,.) %>% 
  as.numeric() %>% 
  `names<-`(.,names(SIwts))

SIwts, specified by breeder as relative importances, essentially.

Try adjusting weights by dividing by Trait Std. Devs.

Trait Standard Deviations:

trialdata %>%
  summarize(across(all_of(names(SIwts)),~sqrt(var(.,na.rm=T)),.names = paste0("sd_","{.col}")));

# A tibble: 1 × 7
  sd_logFYLD sd_HI sd_DM sd_MCMDS sd_logRTNO sd_logDYLD sd_logTOPYLD
       <dbl> <dbl> <dbl>    <dbl>      <dbl>      <dbl>        <dbl>
1      0.892 0.142  5.80    0.787      0.879      0.866        0.798

Adjusted Weights:

adjSIwts

   logFYLD         HI         DM      MCMDS    logRTNO    logDYLD  logTOPYLD 
 22.422466  70.381762   2.584201 -12.706449  13.656355  23.096896  18.790244

errorVars<-varcomps %>% 
  filter(grepl("TrialType",VarComp),
         grepl("!trait.",VarComp)) %>% 
  separate(VarComp,c("TrialType","VarParam"),"!trait.",remove = T) %>% 
  separate(VarParam,c("Trait1","Trait2"),":",remove = T) %>% 
  mutate(TrialType=gsub("TrialType_","",TrialType)) %>% 
  nest(VarEsts=c(Trait1,Trait2,component))
errorVars %<>% 
  mutate(siErrorVarEst=map_dbl(VarEsts,
                           function(VarEsts,SIwts){
                             covMat<-VarEsts %>% 
                               spread(Trait2,component) %>% 
                               column_to_rownames("Trait1") %>% 
                               as.matrix() %>% 
                               .[names(SIwts),names(SIwts)]
                             covMat[upper.tri(covMat)]<-t(covMat)[upper.tri(covMat)]
                             siError<-SIwts%*%covMat%*%SIwts
                             return(siError) },SIwts=SIwts))

errorVars %>% 
  left_join(trialdata %>% 
              distinct(TrialType,plotArea)) %>% 
  arrange(plotArea) %>% 
  ggplot(.,aes(x=plotArea,y=siErrorVarEst)) + geom_line() + theme_bw() + 
  geom_label(aes(label=TrialType,color=TrialType),size=4) + 
  labs(title = "Unadjusted SIwts - siError vs. plotArea")

Version	Author	Date
ceae21a	wolfemd	2021-08-26

adjErrorVars<-varcomps %>% 
  filter(grepl("TrialType",VarComp),
         grepl("!trait.",VarComp)) %>% 
  separate(VarComp,c("TrialType","VarParam"),"!trait.",remove = T) %>% 
  separate(VarParam,c("Trait1","Trait2"),":",remove = T) %>% 
  mutate(TrialType=gsub("TrialType_","",TrialType)) %>% 
  nest(VarEsts=c(Trait1,Trait2,component))
adjErrorVars %<>% 
  mutate(siErrorVarEst=map_dbl(VarEsts,
                           function(VarEsts,SIwts){
                             covMat<-VarEsts %>% 
                               spread(Trait2,component) %>% 
                               column_to_rownames("Trait1") %>% 
                               as.matrix() %>% 
                               .[names(SIwts),names(SIwts)]
                             covMat[upper.tri(covMat)]<-t(covMat)[upper.tri(covMat)]
                             siError<-SIwts%*%covMat%*%SIwts
                             return(siError) },SIwts=adjSIwts))
saveRDS(adjErrorVars,file=here::here("output","siErrorVarEst_byTrialType_directApproach_2021Aug25.rds"))

adjErrorVars %>% 
  left_join(trialdata %>% 
              distinct(TrialType,plotArea)) %>% 
  arrange(plotArea) %>% 
  ggplot(.,aes(x=plotArea,y=siErrorVarEst)) + geom_line() + theme_bw() + 
  geom_label(aes(label=TrialType,color=TrialType),size=4) + 
  labs(title = "Adjusted SIwts - siError vs. plotArea")

Version	Author	Date
ceae21a	wolfemd	2021-08-26

Convergence check

asfit$monitor["loglik",] %>% 
  as.numeric %>% plot(.,ylab='loglik',xlab='iter')

Version	Author	Date
ceae21a	wolfemd	2021-08-26

asfit$monitor %>% 
  as.data.frame %>% 
  rownames_to_column("param") %>% 
  select(-constraint) %>% 
  pivot_longer(cols=-c("param"),names_to="iter",values_to="value") %>% 
  mutate(iter=as.numeric(iter)) %>% 
  filter(grepl("!trait",param)) %>% 
  mutate(Component=ifelse(grepl("GID!trait",param),"genVar","errorVar")) %>% 
  ggplot(.,aes(x=iter,y=value,group=param,color=Component)) + geom_line(alpha=0.7) + 
  labs(title="ErrorVarCovars")#geom_label(aes(label=param))

Version	Author	Date
ceae21a	wolfemd	2021-08-26

asfit$monitor %>% 
  as.data.frame %>% 
  rownames_to_column("param") %>% 
  select(-constraint) %>% 
  pivot_longer(cols=-c("param"),names_to="iter",values_to="value") %>% 
  mutate(iter=as.numeric(iter)) %>% 
  filter(!grepl("!trait|!variance|loglik|S2|df",param)) %>% 
  ggplot(.,aes(x=iter,y=value,group=param,color=param)) + geom_line()

Version	Author	Date
ceae21a	wolfemd	2021-08-26

asfit$monitor %>% 
  as.data.frame %>% 
  rownames_to_column("param") %>% 
  select(-constraint) %>% 
  pivot_longer(cols=-c("param"),names_to="iter",values_to="value") %>% 
  mutate(iter=as.numeric(iter)) %>% 
  filter(grepl("!trait",param)) %>% 
  mutate(Component=ifelse(grepl("GID!trait",param),"genVar","errorVar")) %>% 
  filter(Component=="genVar") %>% 
  ggplot(.,aes(x=iter,y=value,group=param,color=param)) + geom_line(alpha=0.7) + 
  labs(title="Genetic VarCovars") + theme(legend.position = 'bottom')

Version	Author	Date
ceae21a	wolfemd	2021-08-26

Approach 2: indirect - regress SI GETGV on Trial-specific SI BLUP

This will be a revised version of the original version of this approach, which is documented here.

Changes:

Analyze the same subset of trials chosen in Approach 1 above, which is more restrictively chosen than the previous analysis
Adopt a SI weighting scheme for computing the Trial-specific SI with BLUPs, which is invariant to which traits are observed
Categorize trials according to plotArea and/or TrialType

Procedure:

Use the SELECTION INDEX GETGV from genomic prediction using all entire available training population and all of the latest available data as a best estimate of “true” net merit
- The predictions documented here is the most up-to-date. See the summary of genomic prediction results here.
- Alternative best estimate of “true” net merit: actual national performance trial data (e.g. from NCRPs in Nigeria?)
For each trial, analyze the cleaned plot-basis data:
1. Fit a univariate mixed-model to each trait scored
2. Extract trial-specific BLUPs for whatever clones were present
3. Compute the SELIND for the current trial using BLUPs for whatever component traits were scored (\(SI_{TrialBLUP}\)).
  - Scale weights so their sum always equals the sum of the full set of weights, even when only subsets of traits are present.
4. Regress \(SI_{GETGV}\) on the \(SI_{TrialBLUP}\)
5. Extract the \(\hat{\sigma}^2_e\) of the regression as the trial-specific estimate of the selection error
Use mean (or median) \(\hat{\sigma}^2_e\) for each TrialType / plotArea as potential simulation input. Consider a weighted mean/median according to number of clones available to measure \(\hat{\sigma}^2_e\) for each trial.

screen;
cd ~/IITA_2021GS/;
salloc -n 20 --mem=60G --time=06:00:00;
#export PATH=/programs/R-4.0.5clean-p/bin:$PATH
#export OMP_NUM_THREADS=8
R;

library(genomicMateSelectR); 
library(tidyverse)

# CLEANED PLOT-LEVEL TRIAL DATA
dbdata<-readRDS(here::here("output","IITA_ExptDesignsDetected_2021Aug08.rds"))
# SELECTION INDEX WEIGHTS
SIwts<-c(logFYLD=20,
         HI=10,
         DM=15,
         MCMDS=-10,
         logRTNO=12,
         logDYLD=20,
         logTOPYLD=15) # ,PLTHT=10) 

# FILTER TRIALS TO-BE-CONSIDERED
### Restrict consideration to >2012 
### to measure the selection error during the current "era" at IITA.
### Only trials with >=50% genotyped and key TrialTypes
### Keep only trials with full plotWidth and plotLength meta-data
### Calc plotArea=plotWidth*plotLength (in meters-squared)
trialdata<-dbdata %>% 
  filter(studyYear>=2013,
         !is.na(MaxNOHAV),
         !is.na(plotWidth),
         !is.na(plotLength),
         !is.na(PropNOHAV)) %>% 
  nest(TrialData=-c(studyName,TrialType,plotWidth,plotLength,CompleteBlocks,IncompleteBlocks,MaxNOHAV)) %>% 
  mutate(propGenotyped=map_dbl(TrialData,
                              ~length(which(!is.na(unique(.$FullSampleName))))/length(unique(.$GID))),
         plotArea=plotWidth*plotLength,
         IncompleteBlocks=ifelse(IncompleteBlocks==TRUE,"Yes","No"),
         CompleteBlocks=ifelse(CompleteBlocks==TRUE,"Yes","No")) %>% 
  filter(propGenotyped>=0.5,
         TrialType %in% c("GeneticGain","CET","ExpCET","PYT","AYT","UYT")) %>%
  unnest(TrialData) %>% 
  select(yearInLoc,studyName,studyYear,locationName,TrialType,
         plotArea,plotWidth,plotLength,
         CompleteBlocks,IncompleteBlocks,observationUnitDbId,
         GID,trialInLocYr,repInTrial,blockInRep,PropNOHAV,MaxNOHAV,
         all_of(names(SIwts)))
trialdata %<>% 
  semi_join(trialdata %>% 
              distinct(TrialType,studyName,plotArea,plotWidth,plotLength) %>% 
              group_by(TrialType) %>% 
              summarize(plotArea=median(plotArea)) %>% ungroup())

### ADJUSTED SELIND WEIGHTS
adjSIwts<-trialdata %>% 
  summarize(across(all_of(names(SIwts)),~sqrt(var(.,na.rm=T)))) %>% 
  magrittr::divide_by(SIwts,.) %>% 
  as.numeric() %>% 
  `names<-`(.,names(SIwts))

# SELIND GETGVS (for input to estimateSelectionError func below)
gpreds<-readRDS(file = here::here("output","genomicPredictions_full_set_2021Aug09.rds"))
getgvs<-gpreds$gblups[[1]] %>% 
  filter(predOf=="GETGV") %>% 
  select(GID,SELIND,all_of(names(SIwts)))
siadj_getgvs<-getgvs %>% 
  mutate(SELIND=as.numeric(getgvs %>% 
                             select(-SELIND,-GID) %>% 
                             as.matrix(.)%*%adjSIwts)) %>% 
  select(GID,SELIND)
si_getgvs<-getgvs %>% 
  select(GID,SELIND)

trialdata %<>% 
  nest(TrialData=-c(studyYear,locationName,studyName,TrialType,CompleteBlocks,IncompleteBlocks,MaxNOHAV,plotArea))

# SOURCE FUNCTION estimateSelectionError() 
source(here::here("code","estimateSelectionError.R"))

###### unit test inputs for estimateSelectionError
# TrialData<-trialdata$TrialData[[1]]
# CompleteBlocks<-trialdata$CompleteBlocks[[1]]
# IncompleteBlocks<-trialdata$IncompleteBlocks[[1]]
# getgvs<-si_getgvs
# TrialData<-trialdata %>% filter(propGenotyped>0.75) %>% slice(4) %$% TrialData[[1]]
# CompleteBlocks<-trialdata %>% filter(propGenotyped>0.75) %>% slice(4) %$% CompleteBlocks[[1]]
# IncompleteBlocks<-trialdata %>% filter(propGenotyped>0.75) %>% slice(4) %$% IncompleteBlocks[[1]]
# ncores=4
# rm(TrialData,CompleteBlocks,IncompleteBlocks)

Run function estimateSelectionError() across trials to estimation selection errors.

Two runs: once with “original” SIwts, also with adjusted SIwts and SI_GETGVs.

# ORIGINAL SIwts
require(furrr); plan(multisession, workers = 20)
options(future.globals.maxSize=+Inf); options(future.rng.onMisuse="ignore")
trialdata %<>% 
  mutate(SelectionError=future_pmap(.,estimateSelectionError,
                                    SIwts=SIwts,getgvs=si_getgvs))
plan(sequential)
saveRDS(trialdata,here::here("output","estimateSelectionError_origSIwts_2021Aug24.rds"))

# ADJUSTED SIwts
require(furrr); plan(multisession, workers = 20)
options(future.globals.maxSize=+Inf); options(future.rng.onMisuse="ignore")
trialdata %<>% 
  mutate(SelectionError=future_pmap(.,estimateSelectionError,
                                    SIwts=adjSIwts,getgvs=siadj_getgvs))
plan(sequential)
saveRDS(trialdata,here::here("output","estimateSelectionError_adjSIwts_2021Aug24.rds"))

estSelError_adj<-readRDS(here::here("output","estimateSelectionError_adjSIwts_2021Aug24.rds"))
estSelError_adj %<>% 
  select(-TrialData) %>% 
  unnest(SelectionError) %>% 
  select(-SI_BLUPs,-BLUPs,-SelectionError) %>% 
  filter(!is.na(TrialMSE))

estSelError<-readRDS(here::here("output","estimateSelectionError_origSIwts_2021Aug24.rds"))
estSelError %<>% 
  select(-TrialData) %>% 
  unnest(SelectionError) %>% 
  select(-SI_BLUPs,-BLUPs,-SelectionError) %>% 
  filter(!is.na(TrialMSE))

Use mean (or median) \(\hat{\sigma}^2_e\) for each TrialType / plotArea as potential simulation input. Consider a weighted mean/median according to number of clones available to measure \(\hat{\sigma}^2_e\) for each trial.

estSelError_adj %>% 
  ggplot(.,aes(x=plotArea,y=TrialMSE, size=NcloneForReg, fill=TrialType)) + 
  geom_boxplot(notch = T) + theme_bw() + 
  labs(title="Distributions of TrialMSE by TrialType (sorted by plotArea)",
       subtitle="From regression of SI_GETGV on Trial-specific SI_BLUP.")

Version	Author	Date
ceae21a	wolfemd	2021-08-26

Compute per TrialType means:

meanTrialMSE: from regression of SI_GETGV on Trial-specific SI_BLUP
meanCor2si: correlation b/t SI_GETGV and Trial-specific SI_BLUP
weighted by NcloneForReg: the number of clones in a trial that had data to compute SELIND.

estSelError_adj_summarized<-estSelError_adj %>% 
  group_by(TrialType,plotArea) %>% 
  summarize(meanTrialMSE=weighted.mean(TrialMSE,w = NcloneForReg),
            meanCor2si=weighted.mean(cor2si,w = NcloneForReg,na.rm = T)) %>% 
  arrange(plotArea)
saveRDS(estSelError_adj_summarized,file=here::here("output","siErrorVarEst_byTrialType_indirectApproach_2021Aug25.rds"))

estSelError_adj_summarized

# A tibble: 6 × 4
# Groups:   TrialType [6]
  TrialType   plotArea meanTrialMSE meanCor2si
  <chr>          <dbl>        <dbl>      <dbl>
1 CET              2.5         204.      0.414
2 PYT              8           179.      0.384
3 GeneticGain     10           226.      0.399
4 ExpCET          16           222.      0.409
5 AYT             22           137.      0.188
6 UYT             33           149.      0.335

estSelError_adj_summarized %>% 
  ggplot(.,aes(x=plotArea,y=meanTrialMSE)) + geom_line() + theme_bw() + 
  geom_label(aes(label=TrialType,color=TrialType),size=4) + 
  labs(title = "Regress SELIND GETGV on Trial-specific SELIND BLUP",
       subtitle = "Per TrialType mean MSE. Adjusted SIwts. Order TrialType by plotArea.")

Version	Author	Date
ceae21a	wolfemd	2021-08-26

estSelError_adj_summarized %>% 
  ggplot(.,aes(x=plotArea,y=meanCor2si)) + geom_line() + theme_bw() + 
  geom_label(aes(label=TrialType,color=TrialType),size=4) + 
  labs(title = "Regress SELIND GETGV on Trial-specific SELIND BLUP",
       subtitle = "Per TrialType mean cor(SI_GETGV,SI_TrialBLUP). Adjusted SIwts. Order TrialType by plotArea.")

Version	Author	Date
ceae21a	wolfemd	2021-08-26

Conclusions

library(patchwork)
p1<-adjErrorVars %>% 
  left_join(trialdata %>% 
              distinct(TrialType,plotArea)) %>% 
  arrange(plotArea) %>% 
  ggplot(.,aes(x=plotArea,y=siErrorVarEst)) + geom_line() + theme_bw() + 
  geom_label(aes(label=TrialType,color=TrialType),size=4) + 
  labs(title = "Direct Estimate by Multivariate Mixed Model")
p2<-estSelError_adj_summarized %>% 
  ggplot(.,aes(x=plotArea,y=meanTrialMSE)) + geom_line() + theme_bw() + 
  geom_label(aes(label=TrialType,color=TrialType),size=4) + 
  labs(title = "Indirect Estimate by SELIND GETGV on Trial BLUP")
p1 + p2 + 
  plot_annotation(tag_levels = 'A') + 
  plot_layout(guides='collect') &
  theme(legend.position = "bottom")

Version	Author	Date
ceae21a	wolfemd	2021-08-26

Above is a side-by-side plot of the key result from two approaches I have tried above for empirically estimating measurement (or selection) error relative to the selection index. The first approach (A), was to fit a multivariate mixed-model with heterogenous error covariances among TrialType. The direct approach allowed calculating the SELIND error variance (y-axis) by \(b^T\boldsymbol{R}_{TrialType}b\), where \(\boldsymbol{R}_{TrialType}\) is the TrialType-specific estimate of the error covariance matrix and \(b\) are the SELIND weights. The second approach (B) was to fit univariate mixed-models to each trait in each trial, then compute trial-specific SELIND using the resulting BLUPs. The SELIND GETGV value for all clones based on using all phenotypic data and genomic information was then regressed on each trial’s SELIND BLUPs. The mean squared error (mean residual variance) from each regression was extracted and then the average TrialMSE by TrialType was computed (y-axis, B).

We need to choose one of these two options, or revise the approach further, for use input for VDP simulations. Note that in simulation, the error variances we input will be divided by the Nrep and Nloc for each stage specific, so even if UYT has worse error than AYT overall, at the clone-level, UYT would have lower error b/c of more reps and locs.

I prefer option A / approach #1 and only hesitate that it may be challenging to successfully fit these models for each breeding program’s data.

See the baseline simulations page for downstream usage / next steps.

sessionInfo()

R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/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] patchwork_1.1.1          forcats_0.5.1            stringr_1.4.0           
 [4] readr_2.0.1              ggplot2_3.3.5            tidyverse_1.3.1         
 [7] genomicMateSelectR_0.2.0 purrr_0.3.4              tidyr_1.1.3             
[10] dplyr_1.0.7              tibble_3.1.3             workflowr_1.6.2         

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.7        lubridate_1.7.10  here_1.0.1        assertthat_0.2.1 
 [5] rprojroot_2.0.2   digest_0.6.27     utf8_1.2.2        R6_2.5.0         
 [9] cellranger_1.1.0  backports_1.2.1   reprex_2.0.1      evaluate_0.14    
[13] highr_0.9         httr_1.4.2        pillar_1.6.2      rlang_0.4.11     
[17] readxl_1.3.1      rstudioapi_0.13   whisker_0.4       jquerylib_0.1.4  
[21] rmarkdown_2.10    labeling_0.4.2    munsell_0.5.0     broom_0.7.9      
[25] compiler_4.1.0    httpuv_1.6.1      modelr_0.1.8      xfun_0.25        
[29] pkgconfig_2.0.3   htmltools_0.5.1.1 tidyselect_1.1.1  fansi_0.5.0      
[33] crayon_1.4.1      tzdb_0.1.2        dbplyr_2.1.1      withr_2.4.2      
[37] later_1.2.0       grid_4.1.0        jsonlite_1.7.2    gtable_0.3.0     
[41] lifecycle_1.0.0   DBI_1.1.1         git2r_0.28.0      magrittr_2.0.1   
[45] scales_1.1.1      cli_3.0.1         stringi_1.7.3     farver_2.1.0     
[49] fs_1.5.0          promises_1.2.0.1  xml2_1.3.2        bslib_0.2.5.1    
[53] ellipsis_0.3.2    generics_0.1.0    vctrs_0.3.8       tools_4.1.0      
[57] glue_1.4.2        hms_1.1.0         yaml_2.2.1        colorspace_2.0-2 
[61] rvest_1.0.1       knitr_1.33        haven_2.4.3       sass_0.4.0

Empirical inputs for simulations - IITA

2021-Aug-13