插入符號 - 設置gafsControl（）裏面的種子

Question

我想設置的插入符的gafsControl()的seeds，但我得到這個錯誤：

Error in { : task 1 failed - "supplied seed is not a valid integer" 

我明白seeds爲trainControl()等於矢量重新採樣加一（在我的情況36，SVM與6西格瑪和6的成本值）中的每個（重採樣）項的數量，用模型的調整參數的組合數。但是，我無法弄清楚我應該使用什麼gafsControl()。我試過iters * popSize（100 * 10），iters（100），popSize（10），但沒有工作過。

在此先感謝。

這裏是我的代碼（使用模擬數據）：

library(caret) 
library(doMC) 
library(kernlab) 

registerDoMC(cores=32) 

set.seed(1234) 
train.set <- twoClassSim(300, noiseVars = 100, corrVar = 100, corrValue = 0.75) 

mylogGA <- caretGA 
mylogGA$fitness_extern <- mnLogLoss 

#Index for gafsControl 
set.seed(1045481) 
ga_index <- createFolds(train.set$Class, k=3) 

#Seed for the gafsControl() 
set.seed(1056) 
ga_seeds <- vector(mode = "list", length = 4) 
for(i in 1:3) ga_seeds[[i]] <- sample.int(1500, 1000) 

## For the last model: 
ga_seeds[[4]] <- sample.int(1000, 1) 

#Index for the trainControl() 
set.seed(1045481) 
tr_index <- createFolds(train.set$Class, k=5) 

#Seeds for the trainControl() 
set.seed(1056) 
tr_seeds <- vector(mode = "list", length = 6) 
for(i in 1:5) tr_seeds[[i]] <- sample.int(1000, 36)# 

## For the last model: 
tr_seeds[[6]] <- sample.int(1000, 1) 


gaCtrl <- gafsControl(functions = mylogGA, 
         method = "cv", 
         number = 3, 
         metric = c(internal = "logLoss", 
           external = "logLoss"), 
         verbose = TRUE, 
         maximize = c(internal = FALSE, 
            external = FALSE), 
         index = ga_index, 
         seeds = ga_seeds, 
         allowParallel = TRUE) 

tCtrl = trainControl(method = "cv", 
        number = 5, 
        classProbs = TRUE, 
        summaryFunction = mnLogLoss, 
        index = tr_index, 
        seeds = tr_seeds, 
        allowParallel = FALSE) 


svmGrid <- expand.grid(sigma= 2^c(-25, -20, -15,-10, -5, 0), C= 2^c(0:5)) 

t1 <- Sys.time() 
set.seed(1234235) 
svmFuser.gafs <- gafs(x = train.set[, names(train.set) != "Class"], 
         y = train.set$Class, 
         gafsControl = gaCtrl, 
         trControl = tCtrl, 
         popSize = 10, 
         iters = 100, 
         method = "svmRadial", 
         preProc = c("center", "scale"), 
         tuneGrid = svmGrid, 
         metric="logLoss", 
         maximize = FALSE) 

t2<- Sys.time() 
svmFuser.gafs.time<-difftime(t2,t1) 

save(svmFuser.gafs, file ="svmFuser.gafs.rda") 
save(svmFuser.gafs.time, file ="svmFuser.gafs.time.rda") 

會議信息：

> sessionInfo() 
R version 3.2.2 (2015-08-14) 
Platform: x86_64-pc-linux-gnu (64-bit) 
Running under: Ubuntu 14.04.3 LTS 

locale: 
[1] LC_CTYPE=en_CA.UTF-8  LC_NUMERIC=C    LC_TIME=en_CA.UTF-8  
[4] LC_COLLATE=en_CA.UTF-8  LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8 
[7] LC_PAPER=en_CA.UTF-8  LC_NAME=C     LC_ADDRESS=C    
[10] LC_TELEPHONE=C   LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C  

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

other attached packages: 
[1] kernlab_0.9-22 doMC_1.3.3  iterators_1.0.7 foreach_1.4.2 caret_6.0-52 ggplot2_1.0.1 lattice_0.20-33 

loaded via a namespace (and not attached): 
[1] Rcpp_0.12.0   magrittr_1.5  splines_3.2.2  MASS_7.3-43   munsell_0.4.2  
[6] colorspace_1.2-6 foreach_1.4.2  minqa_1.2.4   car_2.0-26   stringr_1.0.0  
[11] plyr_1.8.3   tools_3.2.2   parallel_3.2.2  pbkrtest_0.4-2  nnet_7.3-10   
[16] grid_3.2.2   gtable_0.1.2  nlme_3.1-122  mgcv_1.8-7   quantreg_5.18  
[21] MatrixModels_0.4-1 iterators_1.0.7  gtools_3.5.0  lme4_1.1-9   digest_0.6.8  
[26] Matrix_1.2-2  nloptr_1.0.4  reshape2_1.4.1  codetools_0.2-11 stringi_0.5-5  
[31] compiler_3.2.2  BradleyTerry2_1.0-6 scales_0.3.0  stats4_3.2.2  SparseM_1.7   
[36] brglm_0.5-9   proto_0.3-10  
> 

Answer 1

我能夠通過檢查gafs.default找出我的錯誤。內部gafsControl()的seeds需要vector與長度(n_repeats*nresampling)+1而不是list（如在trainControl$seeds）。這是?gafsControl是seeds is a vector or integers that can be used to set the seed during each search. The number of seeds must be equal to the number of resamples plus one.我理解了它艱難地在文檔中居然說，這是一個提醒仔細閱讀文檔：d。

if (!is.null(gafsControl$seeds)) { 
     if (length(gafsControl$seeds) < length(gafsControl$index) + 
      1) 
      stop(paste("There must be at least", length(gafsControl$index) + 
      1, "random number seeds passed to gafsControl")) 
    } 
    else { 
     gafsControl$seeds <- sample.int(1e+05, length(gafsControl$index) + 
     1) 
    } 

所以，正確的方式來設置我的ga_seeds是：

#Index for gafsControl 
set.seed(1045481) 
ga_index <- createFolds(train.set$Class, k=3) 

#Seed for the gafsControl() 
set.seed(1056) 
ga_seeds <- sample.int(1500, 4) 

Answer 2

我不太熟悉你所提到的gafsControl（）函數，但設置平行時，我遇到了一個非常類似的問題種子使用trainControl（）。在說明中，它描述瞭如何創建一個列表（長度=重採樣次數+ 1），其中每個項目是一個列表（長度=要測試的參數組合的數量）。我發現這樣做不起作用（有關信息，請參閱topepo/caret issue＃248）。但是，如果您然後將每個項目轉換爲矢量，例如

seeds <- lapply(seeds, as.vector) 

然後種子似乎工作（即模型和預測是完全可重現的）。我應該澄清，這是使用doMC作爲後端。其他並行後端可能會有所不同。

希望這有助於

Answer 3

如果這樣設置的種子就可以保證每個相同的特徵子集選擇運行？我問AMS GA因randominess