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Merge pull request #49 from DidierMurilloF/fix-random-square-lattice
Fix random square lattice
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,86 @@ | ||
| #' Function to estimate the efficiencies of a IBD design | ||
| #' This function is sourced from the `blocksdesign` package. | ||
| #' @param TF Treatment factor levels | ||
| #' @param BF Block factor levels | ||
| #' @author Rodney Edmondson <rodney.edmondson at gmail.com> | ||
| #' @return List containing design and A efficiencies | ||
| #' @noRd | ||
| blockEstEffics = function(TF, BF) { | ||
| TM = qr.Q(qr(scale(stats::model.matrix(~TF))[, -1])) | ||
| BM = qr.Q(qr(scale(stats::model.matrix(~BF))[, -1])) | ||
| if (nlevels(TF) <= nlevels(BF)) | ||
| E = eigen(diag(ncol(TM)) - tcrossprod(crossprod(TM, | ||
| BM)), symmetric = TRUE, only.values = TRUE) | ||
| else E = eigen(diag(ncol(BM)) - tcrossprod(crossprod(BM, | ||
| TM)), symmetric = TRUE, only.values = TRUE) | ||
| Deff = exp(sum(log(E$values))/ncol(TM)) | ||
| if (nlevels(TF) <= nlevels(BF)) | ||
| Aeff = ncol(TM)/sum(1/E$values) | ||
| else Aeff = ncol(TM)/(ncol(TM) - ncol(BM) + sum(1/E$values)) | ||
| return(list(Deffic = round(Deff, 7), Aeffic = round(Aeff, | ||
| 7))) | ||
| } | ||
|
|
||
| #' Function to estimate the A bound and report the efficiencies of a IBD design | ||
| #' This function is sourced from the `blocksdesign` package. | ||
| #' @param Design The IBD design matrix | ||
| #' @return Data frame of efficiencies and bounds | ||
| #' @author Rodney Edmondson <rodney.edmondson at gmail.com> | ||
| #' @noRd | ||
| BlockEfficiencies = function(Design) { | ||
| TF = Design[, ncol(Design)] | ||
| regreps = table(TF) | ||
| regReps = isTRUE(max(regreps) == min(regreps)) | ||
| sizes = lapply(1:(ncol(Design) - 2), function(i) { | ||
| table(Design[, i]) | ||
| }) | ||
| regBlocks = sapply(1:length(sizes), function(i) { | ||
| max(sizes[[i]]) == min(sizes[[i]]) | ||
| }) | ||
| bounds = sapply(1:(ncol(Design) - 2), function(i) { | ||
| if (regBlocks[i] & regReps) | ||
| blocksdesign::A_bound(length(TF), nlevels(TF), nlevels(Design[, | ||
| i])) | ||
| else 1 | ||
| }) | ||
| blocklevs = unlist(lapply(1:(ncol(Design) - 2), function(j) { | ||
| nlevels(Design[, j]) | ||
| })) | ||
| Effics = t(sapply(1:(ncol(Design) - 2), function(i) { | ||
| if (nlevels(Design[, i]) > 1) | ||
| blockEstEffics(TF, Design[, i]) | ||
| else list(Deffic = 1, Aeffic = 1) | ||
| })) | ||
| efficiencies = data.frame(1:(ncol(Design) - 2), blocklevs, | ||
| as.numeric(Effics[, 1]), as.numeric(Effics[, 2]), | ||
| round(bounds, 7)) | ||
| colnames(efficiencies) = c("Level", "Blocks", "D-Efficiency", | ||
| "A-Efficiency", "A-Bound") | ||
| return(efficiencies) | ||
| } | ||
|
|
||
| #' Function to re-randomize IBD design | ||
| #' | ||
| #' @param ibd_design Input design from the `blocksdesign` package | ||
| #' @return Modified IBD design with re-randomized treatments | ||
| #' @author Didier Murillo | ||
| #' @noRd | ||
| rerandomize_ibd <- function(ibd_design) { | ||
| mydes <- ibd_design | ||
| tretments <- sort(unique(mydes$Design$treatments)) | ||
| new_order <- data.frame( | ||
| treatments = tretments, | ||
| new_order_treatments = sample(tretments, replace = FALSE) | ||
| ) | ||
|
|
||
| newDesign <- mydes$Design |> | ||
| dplyr::left_join(new_order, by = "treatments") | ||
|
|
||
| mydes$Design_new <- newDesign |> | ||
| dplyr::select(-treatments) |> | ||
| dplyr::rename(treatments = new_order_treatments) | ||
|
|
||
| mydes$Blocks_model_new <- BlockEfficiencies(mydes$Design_new) | ||
|
|
||
| return(mydes) | ||
| } |
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