Last updated: 2020-03-30

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options(stringsAsFactors = FALSE)

mse <- function(Y, Yhat) {
    msee <- rep(NA, ncol(Y))
    
    for(i in 1:ncol(Y)){
        msee[i] <- mean((Y[, i] - Yhat[, i])^2)
    }
    
    return(msee)
}

accuracy <- function(Y, Yhat) {
  bias <- rep(NA, ncol(Y))
  r2 <- rep(NA, ncol(Y))
  
  for(i in 1:ncol(Y)){
    fit  <- lm(Y[, i] ~ Yhat[, i])
    bias[i] <- coef(fit)[2] 
    r2[i] <- summary(fit)$r.squared
  }
  
  return(list(bias=bias, r2=r2))
}

Simulation 1 – Shared effects, independent variables

dat1 <- readRDS("output/fit_mr_mash_n600_p1000_p_caus50_r5_pve0.5_sigmaoffdiag1_sigmascale0.8_gammaoffdiag0_gammascale0.8_Voffdiag0.2_Vscale0_updatew0TRUE_updatew0TRUE_updatew0methodmixsqp_updateVTRUE.rds")
n1 <- dat1$params$n
p1 <- dat1$params$p
p_causal1 <- dat1$params$p_causal
r1 <- dat1$params$r
pve1 <- dat1$params$pve
prop_testset1 <- dat1$params$prop_testset
B1 <- dat1$inputs$B
V1 <- dat1$inputs$V
Sigma1 <- dat1$inputs$Sigma
Gamma1 <- dat1$inputs$Gamma
Ytrain1 <- dat1$Ytrain
Ytest1 <- dat1$Ytest
mu11 <- dat1$fit$mu1
fitted1 <- dat1$fit$fitted
Yhat_test1 <- dat1$Yhat_test

The simulation below is based on 600 samples, 1000 variables of which 50 were causal, 5 responses with a per-response proportion of variance explained (PVE) of 0.5. Variables, X, were drawn from MVN(0, Gamma), causal effects, B, were drawn from MVN(0, Sigma). The responses, Y, were drawn from MN(XB, I, V).

cat("Gamma (First 5 elements)")

Gamma (First 5 elements)

Gamma1[1:5, 1:5]

     [,1] [,2] [,3] [,4] [,5]
[1,]  0.8  0.0  0.0  0.0  0.0
[2,]  0.0  0.8  0.0  0.0  0.0
[3,]  0.0  0.0  0.8  0.0  0.0
[4,]  0.0  0.0  0.0  0.8  0.0
[5,]  0.0  0.0  0.0  0.0  0.8

cat("Sigma")

Sigma

Sigma1

     [,1] [,2] [,3] [,4] [,5]
[1,]  0.8  0.8  0.8  0.8  0.8
[2,]  0.8  0.8  0.8  0.8  0.8
[3,]  0.8  0.8  0.8  0.8  0.8
[4,]  0.8  0.8  0.8  0.8  0.8
[5,]  0.8  0.8  0.8  0.8  0.8

cat("V")

V1

         [,1]     [,2]     [,3]     [,4]     [,5]
[1,] 25.55836  0.00000  0.00000  0.00000  0.00000
[2,]  0.00000 25.55836  0.00000  0.00000  0.00000
[3,]  0.00000  0.00000 25.55836  0.00000  0.00000
[4,]  0.00000  0.00000  0.00000 25.55836  0.00000
[5,]  0.00000  0.00000  0.00000  0.00000 25.55836

mr.mash was fitted to the training data (80% of the data) updating V and updating the prior weights using mixSQP. Then, responses were predicted on the test data (20% of the data).

In the plots below, each color/symbol defines a diffrent response.

Here, we compare the estimated effects with the true effects.

plot(B1[, 1], mu11[, 1], xlab="True effects", ylab="Estimated effects", main="True vs Estimated Effects", pch=1, cex.lab=1.5)
points(B1[, 2], mu11[, 2], col="blue", pch=2)
points(B1[, 3], mu11[, 3], col="red", pch=3)
points(B1[, 4], mu11[, 4], col="green", pch=4)
points(B1[, 5], mu11[, 5], col="yellow", pch=8)

Version	Author	Date
4e9aad6	fmorgante	2020-03-30
7911e81	fmorgante	2020-03-30
e1707b2	fmorgante	2020-03-30

Then, we compare the predicted responses with the true responses in the training data (left panel) and test data (right panel).

par(mfrow=c(1,2))
plot(Ytrain1[, 1], fitted1[, 1], xlab="True responses", ylab="Fitted values", main="True vs Fitted values \nTraining data", pch=1, cex.lab=1.5)
points(Ytrain1[, 2], fitted1[, 2], col="blue", pch=2)
points(Ytrain1[, 3], fitted1[, 3], col="red", pch=3)
points(Ytrain1[, 4], fitted1[, 4], col="green", pch=4)
points(Ytrain1[, 5], fitted1[, 5], col="yellow", pch=8)
abline(0, 1)

plot(Ytrain1[, 1], fitted1[, 1], xlab="True responses", ylab="Predicted responses", main="True vs Predicted Responses \nTest data", pch=1, cex.lab=1.5)
points(Ytest1[, 2], Yhat_test1[, 2], col="blue", pch=2)
points(Ytest1[, 3], Yhat_test1[, 3], col="red", pch=3)
points(Ytest1[, 4], Yhat_test1[, 4], col="green", pch=4)
points(Ytest1[, 5], Yhat_test1[, 5], col="yellow", pch=8)
abline(0, 1)

Version	Author	Date
4e9aad6	fmorgante	2020-03-30
7911e81	fmorgante	2020-03-30

par(mfrow=c(1,1))

r2_train1 <- accuracy(Ytrain1, fitted1)$r2
r2_test1 <- accuracy(Ytest1, Yhat_test1)$r2
bias_train1 <- accuracy(Ytrain1, fitted1)$bias
bias_test1 <- accuracy(Ytest1, Yhat_test1)$bias
mse_train1 <- mse(Ytrain1, fitted1)
mse_test1 <- mse(Ytest1, Yhat_test1)

acc1 <- rbind(r2_train1, r2_test1, bias_train1, bias_test1, mse_train1, mse_test1)
colnames(acc1) <- paste0("Y", seq(1, r1))
part_metric1 <- c("Training data r2", "Test data r2", "Training data bias", "Test data bias" , "Training data MSE" , "Test data MSE")
res1 <- data.frame(part_metric1, acc1)
colnames(res1)[1] <- c("Partition_metric")
rownames(res1) <- NULL
print(res1)

    Partition_metric         Y1         Y2         Y3         Y4
1   Training data r2  0.5337638  0.5418288  0.4904039  0.5238892
2       Test data r2  0.4590632  0.4475933  0.4630462  0.4522742
3 Training data bias  1.0605741  1.0585743  0.9935321  1.0012798
4     Test data bias  0.9891530  1.0660257  1.0665580  1.0904600
5  Training data MSE 24.6985394 23.8540429 25.3912912 22.4603256
6      Test data MSE 24.5054076 29.4890004 27.1641594 29.6733910
          Y5
1  0.5620165
2  0.4236621
3  1.0970937
4  0.9659183
5 23.9105976
6 26.7496399

sessionInfo()

R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] workflowr_1.6.1 Rcpp_1.0.3      digest_0.6.23   later_0.7.5    
 [5] rprojroot_1.3-2 R6_2.4.1        backports_1.1.5 git2r_0.26.1   
 [9] magrittr_1.5    evaluate_0.12   stringi_1.4.3   fs_1.3.1       
[13] promises_1.0.1  whisker_0.3-2   rmarkdown_1.10  tools_3.5.1    
[17] stringr_1.4.0   glue_1.3.1      httpuv_1.4.5    yaml_2.2.0     
[21] compiler_3.5.1  htmltools_0.3.6 knitr_1.20

Prediction accuracy

Fabio Morgante

30 March, 2020

Simulation 1 – Shared effects, independent variables