将lapply()用于模拟研究列表列表中构造的数据

|| 关于lapply()在模拟研究中的应用,我碰壁了。这些数据旨在帮助我们了解标准化公式如何影响提案评级活动的结果。 评估者需要满足以下三个条件:无偏差,统一偏差(各个评估者之间的偏差增加)和双向偏差(各个评估者之间的偏差为正负平衡)。 假定提案的真实价值是已知的。 我们希望在每个偏差条件下生成一组重复的数据集,以便这些数据集可以模拟一个提案评估期(一个小组)。然后,我们想复制面板以模拟具有许多投标评估期。 这是数据结构的示意图:
 The data structure looks like this:

 p = number of proposals
 r = number of raters

 n.panels = number of replicate panels

 t.reps = list of several replicate panels

 three bias conditions:     n.bias - no bias
                            u.bias - uniform bias (raters higher than previous rater)
                            b.bias - bidirectional bias (balanced up and down bias)


 -|
 t     1        |..| --> 10*(n.bias(p*r)) + 10*(u.bias(p*r)) + 10*(b.bias(p*r)  {panel replication 1}
 .     2        |..| --> 10*(n.bias(p*r)) + 10*(u.bias(p*r)) + 10*(b.bias(p*r)  {panel replication 2}
 r     :                    :                         :               :                  :
 e     :                    :                         :               :                  :
 p     n.panels |..| --> 10*(n.bias(p*r)) + 10*(u.bias(p*r)) + 10*(b.bias(p*r)  {n. panels replications}
 s      
 _|
以下R代码正确生成数据:
##########  start of simulation parameters

set.seed(271828)

means <- matrix(c(rep(50,3), rep(60,3), rep(70,4) ), ncol = 1)      #  matrix of true proposal values
bias.u <- matrix(c(0,2,4,6,8), nrow=1)                              #  unidirectional bias
bias.b <- matrix(c(0,3,-3, 5, -5), nrow=1)                          #  bidirectional bias   


ones.u <- matrix(rep(1,ncol(bias.u)), nrow = 1)                 #  number of raters is the number of columns  (r)
ones.b <- matrix(rep(1,ncol(bias.b)), nrow = 1)
ones.2 <- matrix(rep(1,nrow(means)),  ncol = 1)                 #  number of proposals is the number of rows  (p)

true.ratings <- means%*%ones.u                                  #  gives matrix of true proposal value for each rater (p*r)
uni.bias    <- ones.2%*%bias.u
bid.bias    <- ones.2%*%bias.b                                  #  gives matrix of true rater bias for each proposal  (p*r)

n.val <- nrow(means)*ncol(ones.u)

#   true.ratings
#   uni.bias
#   bid.bias



library(MASS)



#####
#####  generating replicate data...
#####

##########--------------------  analyzing mse of adjusted scores across replications

##########--------------------  developing random replicates of panel data

##########-----  This means that there are (reps) replications in each of the bias conditions
##########-----  to represent a plausible set of ratings in a particular collection 
##########-----  of panels. So for one proposal cycle (panel) , there are 3 * (reps) * nrow(means) 
##########-----  number of proposal ratings.
##########-----
##########-----  There are (n.panels) replications of the total number of proposal ratings placed in a list
##########-----  (t.reps).



n.panels <- 2    #  put in the number of replicate panels that should be produced
reps     <- 10   #  put in the number of times each bias condition should be included in a panel

t.reps <- list()

n.bias <- list()
u.bias <- list()
b.bias <- list()




for (i in 1:n.panels)

    {
        {
            for(j in 1:reps) 
                n.bias[[j]] <- true.ratings + matrix(round(rnorm(n.val,4,2), digits=0), nrow = nrow(means)) 
            for(j in 1:reps)    
                u.bias[[j]] <- true.ratings + uni.bias + matrix(round(rnorm(n.val,4,2), digits=0), nrow = nrow(means))
            for(j in 1:reps)
                b.bias[[j]] <- true.ratings + bid.bias + matrix(round(rnorm(n.val,4,2), digits=0), nrow = nrow(means))
        }

    t.reps[[i]] <- list(n.bias, u.bias, b.bias)

    }


# t.reps
列表(t.reps)中的每个元素都是一组审阅者的随机复制  整套建议。 我想将以下功能应用于“调整”面板中的分数  使用整个提案分数集的特征(在所有评分者和提案中)  调整评估者中的值。这个想法是纠正一种或另一种偏见  (例如,对建议进行评级时过于苛刻或过于容易)。 该调整应应用于每个(重复)数据集。 因此,对于一个面板,将有30个重复数据集(每个偏差条件10个)  并且每个重复数据集将有5个评分者对10个提案进行评分,结果  共有300项提案。 因此,其想法是进行随机复制,以了解调整后的分数与未调整后的分数之间的比较。 我试图在(t.reps)列表中的整个列表中使用lapply()函数,但此方法不起作用。
adj.scores <- function(x, tot.dat)
    {
    t.sd <- sd(array(tot.dat))
    t.mn <- mean(array(tot.dat))

    ones.t.mn <- diag(1,ncol(x))

    p <- nrow(x)
    r <- ncol(x)

    ones.total <- matrix(1,p,r)

    r.sd <- diag(apply(x,2, sd))
    r.mn <- diag(apply(x,2, mean))


    den.r.sd <- ginv(r.sd)
    b.shift <- x%*%den.r.sd

    a <- t.mn*ones.t.mn - den.r.sd%*%r.mn
    a.shift <- ones.total%*%a


    l.x <- b.shift + a.shift

    return(l.x)

    }

##########  I would like to do something like this...

##########  apply the function to each element in the list t.reps


dat.1 <- matrix(unlist(t.reps[[1]]), ncol=5)
adj.rep.1 <- lapply(t.reps[[1]], adj.scores, tot.dat = dat.1)
我对其他方法/解决方法持开放态度,这些方法/解决方法将允许使用整个评分组中的统计信息在一组提案评分中调整评分者。可能有些R功能我不知道或没有遇到过。 另外,如果有人可以推荐一本书(R,Perl或Python)中的数据结构编程书籍,将不胜感激。到目前为止,我发现的文本并未详细解决这些问题。 非常感谢。 -乔恩     
已邀请:
        我不能说我完全理解了整个问题(我不是统计学家!),但您失败的行失败的原因是,当3期望矩阵时,3会通过4的列表。 由于您具有列表列表(列表!),所以
rapply
似乎更合适。以下内容似乎会产生合理的结果:
adj.rep.1 <- rapply(t.reps[[1]], adj.scores, how=\'replace\', tot.dat = dat.1)

# comparing the structures
str(t.reps[[1]])
str(adj.rep.1)
希望这可以帮助!     
        我发布对我有用的解决方案很晚。我确信可以进行改进,因此请随时发表评论! 这项练习的目的是了解提案等级对提案的选择进行线性转换的程度。这个想法是试图将“提案质量”与“评估者偏好”和“面板偏好”区分开。 一种方法是,将所有等级基本上以面板平均值为中心,然后使用总体平均值和所有等级的sd对面板为中心的等级进行均值/标准差转换。该过程在功能ѭ3中进行。 这是不平凡的,因为提案是由人们进行评估的,并且成功进行提案评估(赠款,合同等)可能会有大量的财务激励措施。 欢迎对改进或竞争策略提出任何想法。
####################
##########  proposal ratings project
##########  17 June 2011
##########  original code by:  jjb with help from es



##########------  functions to be read in and called when desired

##########  applying  this function to a single matrix will give detailed output 
##########  calculating generalizability theory components
##########  not a very robust formulation, but a good place to start
##########  for future, put panel facet on this design

    g.pxr.long = function(x)
     {
      m.raters <<- colMeans(x)
      n.raters <<- length(m.raters)

      m.props <<-  rowMeans(x)
      n.props <<-  length(m.props)

      m.total <<-  mean(x)
      n.total <<-  nrow(x)*ncol(x)

      m.raters.2 <<- m.raters^2
      m.props.2 <<- m.props^2

      sum.m.raters.2 <<- sum(m.raters.2)
      sum.m.props.2  <<- sum(m.props.2)

      ss.props <<- n.raters*(sum.m.props.2) - n.total*(m.total^2)
      ss.raters <<- n.props*(sum.m.raters.2) - n.total*(m.total^2)
      ss.pr  <<-  sum(x^2) - n.raters*(sum.m.props.2) - n.props*(sum.m.raters.2) +  n.total*(m.total^2)

      df.props <- n.props - 1
      df.raters <- n.raters - 1
      df.pr  <-  df.props*df.raters

      ms.props <- ss.props / df.props
      ms.raters <- ss.raters / df.raters
      ms.pr <- ss.pr / df.pr

      var.p <- (ms.props - ms.pr) / n.raters
      var.r <- (ms.raters - ms.pr) / n.props
      var.pr <- ms.pr


      out.1 <- as.data.frame( matrix(c( df.props, df.raters, df.pr, 
                                        ss.props, ss.raters, ss.pr, 
                                        ms.props, ms.raters, ms.pr,  
                                        var.p, var.r, var.pr), ncol = 4))

      out.2 <- as.data.frame(matrix(c(\"p\", \"r\", \"pr\" ), ncol = 1))
      g.out.1 <- as.data.frame(cbind(out.2, out.1))
      colnames(g.out.1) <- c(\"   source\", \"   df  \", \"   ss  \", \"   ms  \", \"   variance\")



     var.abs <- (var.r / n.raters) + (var.pr / n.raters)
     var.rel <- (var.pr / n.raters)
     var.xbar <- (var.p / n.props) + (var.r / n.raters) + (var.pr / (n.raters*n.props) )

     gen.coef <- var.p / (var.p + var.rel)
     dep.coef <- var.p / (var.p + var.abs)

     out.3 <- as.data.frame(matrix(c(var.rel, var.abs, var.xbar, gen.coef, dep.coef), ncol=1))
     out.3 <- round(out.3, digits = 4)
     out.4 <- as.data.frame(matrix(c(\"relative error variance\", \"absolute error variance\", \"xbar error variance\", \"E(rho^2)\", \"Phi\"), ncol=1))

     g.out.2 <- as.data.frame(cbind(out.4,out.3))
     colnames(g.out.2) <- c(\"   estimate \", \"   value\")

    outs <- list(g.out.1, g.out.2)
    names(outs) <- c(\"generalizability theory: G-study components\", \"G-study Indices\")
    return(outs)

     }

##########-----  calculating confidence intervals using Chebychev, Cramer, and Normal   

##########-----  use this to find alpha for desired k

factor.choose = function(k)

    {
    alpha <- 1 / k^2
    return(alpha)   
    }




conf.intervals = function(dat, alpha)
    {   



    k <- sqrt( 1 / alpha )  # specifying what the k factor is...

    x.bar <- mean(dat)
    x.sd  <- sd(dat)

    n.obs <- length(dat)

    sem <- x.sd / sqrt(n.obs)

    ub.cheb <- x.bar + k*sem
    lb.cheb <- x.bar - k*sem

    ub.crem <- x.bar + (4/9)*k*sem
    lb.crem <- x.bar - (4/9)*k*sem

    ub.norm <- x.bar + qnorm(1-alpha/2)*sem
    lb.norm <- x.bar - qnorm(1-alpha/2)*sem

    out.lb <- matrix(c(lb.cheb,  lb.crem,  lb.norm), ncol=1)
    out.ub <- matrix(c(ub.cheb,  ub.crem, ub.norm), ncol=1)


    dat <- as.data.frame(dat)

    mean.raters <- as.matrix(rowMeans(dat))

    dat$z.values <- matrix((mean.raters - x.bar) / x.sd)

    select.cheb <- dat[ which(abs(dat$z.values) >= k ) , ]

    select.crem <- dat[ which(abs(dat$z.values) >= (4/9)*k ) , ]

    select.norm <- dat[ which(abs(dat$z.values) >=  qnorm(1-alpha/2)) , ]

    count.cheb <- nrow(select.cheb)
    count.crem <- nrow(select.crem)
    count.norm <- nrow(select.norm)

    out.dat <- list()

    out.dat <- list(select.cheb, select.crem, select.norm)
    names(out.dat) <- c(\"Selected cases: Chebychev\", \"Selected cases: Cramer\'s\", \"Selected cases: Normal\")



    out.sum <- matrix(c(x.bar, x.sd, n.obs), ncol=3)
    colnames(out.sum) <- c(\"mean\", \"sd\", \"n\")

    out.crit <- matrix(c(alpha, k, (4/9)*k, qnorm(1-alpha/2)) ,ncol=4 )
    colnames(out.crit) <- c(\"alpha\", \"k\", \"(4/9)*k\", \"z\" )

    out.count <- matrix(c(count.cheb, count.crem, count.norm) ,ncol=3 )
    colnames(out.count) <- c(\"Chebychev\", \"Cramer\" , \"Normal\")
    rownames(out.count) <- c(\"count\")


    outs <- list(out.sum, out.crit, out.count, out.dat)
    names(outs) <- c(\"Summary of data\", \"Critical values\", \"Count of Selected Cases\", \"Selected Cases\")

    return(outs)




    }


rm(list = ls())


set.seed(271828)

means <- matrix(c( rep(50,19), rep(70,1) ), ncol = 1)      #  matrix of true proposal values
bias.u <- matrix(c(0,2,4), nrow=1)                                  #  unidirectional bias
bias.b <- matrix(c(0,5, -5), nrow=1)                                #  bidirectional bias   


ones.u <- matrix(rep(1,ncol(bias.u)), nrow = 1)                 #  number of raters is the number of columns  (r)
ones.b <- matrix(rep(1,ncol(bias.b)), nrow = 1)
ones.2 <- matrix(rep(1,nrow(means)),  ncol = 1)                 #  number of proposals is the number of rows  (p)

true.ratings <- means%*%ones.u                                  #  gives matrix of true proposal value for each rater (p*r)
uni.bias    <- ones.2%*%bias.u
bid.bias    <- ones.2%*%bias.b                                  #  gives matrix of true rater bias for each proposal  (p*r)


pan.bias.pos <- matrix(20,nrow=nrow(true.ratings), ncol=ncol(true.ratings))  #  gives a matrix of bias for every member in a panel (p*r)



n.val <- nrow(true.ratings)*ncol(true.ratings)

#   true.ratings
#   uni.bias
#   bid.bias
#   pan.bias.pos



library(MASS)



#####
#####  generating replicate data...
#####




n.panels <- 10      #  put in the number of replicate panels that should be produced
reps     <- 2        #  put in the number of times each bias condition should be included in a panel 

t.reps <- list()

n.bias <- list()
u.bias <- list()
b.bias <- list()
pan.bias <- list()

n.bias.out <- list()
u.bias.out <- list()
b.bias.out <- list()
pan.bias.out <- list()


for (i in 1:n.panels)

    {
        {
            for(j in 1:reps) 
                n.bias[[j]] <- true.ratings + matrix(round(rnorm(n.val,4,2), digits=0), nrow = nrow(means)) 
            for(j in 1:reps)    
                u.bias[[j]] <- true.ratings + uni.bias + matrix(round(rnorm(n.val,4,2), digits=0), nrow = nrow(means))
            for(j in 1:reps)
                b.bias[[j]] <- true.ratings + bid.bias + matrix(round(rnorm(n.val,4,2), digits=0), nrow = nrow(means))

        }   

        pan.bias[[i]]  <- true.ratings + pan.bias.pos + matrix(round(rnorm(n.val,4,2), digits=0), nrow = nrow(means))

        n.bias.out[[i]] <- n.bias
        u.bias.out[[i]] <- u.bias
        b.bias.out[[i]] <- b.bias

        t.reps[[i]] <- c(n.bias, u.bias, b.bias, pan.bias[i])

    }

#  t.reps


#  rm(list = ls())



##########-----  this is the standardization formula to be applied to proposal ratings **WITHIN** a panel

adj.scores <- function(x, tot.dat)

    {
    t.sd <- sd(array(tot.dat))
    t.mn <- mean(array(tot.dat))

    ones.t.mn <- diag(1,ncol(x))

    p <- nrow(x)
    r <- ncol(x)

    ones.total <- matrix(1,p,r)

    r.sd <- diag(apply(x,2, sd))
    r.mn <- diag(apply(x,2, mean))


    den.r.sd <- ginv(r.sd)
    b.shift <- x%*%den.r.sd

    a <- t.mn*ones.t.mn - den.r.sd%*%r.mn
    a.shift <- ones.total%*%a


    l.x <- b.shift + a.shift

    return(l.x)
    }



##########-----  applying standardization formula and getting 
##########-----  proposal means for adjusted and unadjusted ratings

adj.rep <- list()
m.adj <- list()
m.reg <- list()

for (i in 1:n.panels)

    {

    panel.data <- array(unlist(t.reps[[i]]))

    adj.rep[[i]] <- lapply(t.reps[[i]], adj.scores, tot.dat = panel.data)

    m.adj[[i]] <- lapply(adj.rep[[i]], rowMeans)
    m.reg[[i]] <- lapply(t.reps[[i]], rowMeans)

    }









##########----- 
##########-----  This function extracts the replicate proposal means for each set of reviews    
##########-----  across panels.  So, if there are 8 sets of reviewers that are simulated 10 times, 
##########-----  this extracts the first set of means across the 10 replications and puts them together,
##########-----  and then extracts the second set of means across replications and puts them together, etc..
##########-----  The result will be 8 matrices made up of 10 columns with rows .
##########-----  



##########-----  first for unadjusted means 





means.reg <- matrix(unlist(m.reg), nrow=nrow(means))
sets <- length(m.reg[[1]])
counter <- n.panels*length(m.reg[[1]])


m.reg.panels.set <- list()

        for (j in 1:sets)

            {
                m.reg.panels.set[[j]] <- means.reg[ , c(seq( j, counter, sets))]

            }






##########-----  now for adjusted means


means.adj <- matrix(unlist(m.adj), nrow=nrow(means))
sets <- length(m.adj[[1]])
counter <- n.panels*length(m.adj[[1]])


m.adj.panels.set <- list()

        for (j in 1:sets)

            {
                m.adj.panels.set[[j]] <- means.adj[ , c(seq( j, counter, sets))]

            }    



##########   calculating msd as bias^2 and error^2




msd.calc <- function(x)
        {

            true.means  <- means
            calc.means  <- as.matrix(rowMeans(x))


            t.means.mat <- matrix(rep(true.means, n.panels), ncol=ncol(x))
            c.means.mat <- matrix(rep(calc.means, n.panels), ncol=ncol(x))

            msd <- matrix( rowSums( (x - t.means.mat )^2) / ncol(c.means.mat) )
            bias.2 <- (calc.means - true.means)^2
            e.var <-  matrix( rowSums( (x - c.means.mat )^2) / ncol(c.means.mat ) )

            msd <- matrix(c(msd, bias.2, e.var), ncol = 3)
            colnames(msd) <- c(\"msd\", \"bias^2\", \"e.var\")

            return(msd)

        }


##########  checking work...

#       msd.calc <- bias.2 + e.var
#       all.equal(msd, msd.calc)


##########-----  applying function to each set across panels        

msd.reg.panels <- lapply(m.reg.panels.set, msd.calc)        

msd.adj.panels <- lapply(m.adj.panels.set, msd.calc)

msd.reg.panels
msd.adj.panels        

##########  for the unadjusted scores, the msd is very large (as is expected)
##########  for the adjusted scores, the msd is in line with the other panels






##########-----  trying to evaluate impact of adjusting scores on proposal awards



reg.panel.1 <- matrix(unlist(m.reg[[1]]), nrow=nrow(means))
adj.panel.1 <- matrix(unlist(m.adj[[1]]), nrow=nrow(means))


reg <- matrix(array(reg.panel.1), ncol=1)
adj <- matrix(array(adj.panel.1), ncol=1)

panels.1 <- cbind(reg,adj)

colnames(panels.1) <- c(\"unadjusted\", \"adjusted\")

cor(panels.1, method=\"spearman\")

plot(panels.1)
########   identify(panels.1)


plot(panels.1, xlim = c(25,95), ylim = c(25,95) )
abline(0,1, col=\"red\")


##########  the adjustment greatly reduces variances of ratings 
##########  compare the projection of the panel means onto the respective margins



##########-----  examining the selection of the top 10% of the proposals


pro.names <- matrix(seq(1,nrow(reg),1))

df.reg <- as.data.frame(cbind(pro.names, reg))
colnames(df.reg) <- c(\"pro\", \"rating\")
df.reg$q.pro <- ecdf(df.reg$rating)(df.reg$rating) 


df.adj <- as.data.frame(cbind(pro.names, adj))
colnames(df.adj) <- c(\"pro\", \"rating\")
df.adj$q.pro <- ecdf(df.adj$rating)(df.adj$rating)


awards.reg <- df.reg[ which(df.reg$q.pro >= .90) , ]
awards.adj <- df.adj[ which(df.adj$q.pro >= .90) , ]


awards.reg[order(-awards.reg$q.pro) , ]
awards.adj[order(-awards.adj$q.pro) , ]


awards.reg[order(-awards.reg$pro) , ]
awards.adj[order(-awards.adj$pro) , ]


#####  using unadjusted scores, the top 10% of proposals come mostly from one (biased) panel, and the rest are made up of the 
#####  highest scoring proposal (from the biased rater) from the remaining panels.

#####  using the adjusted scores, the top 10% of proposals are made up of the highest scoring proposal (the biased rater) from the 
#####  several panels, and a few proposals from other panels.  Doesn\'t seem to be a systematic explanation as to why...




#########-----  treating rating data in an ANOVA model


ratings <- do.call(\"rbind\", t.reps[[1]] )
panels <- factor(gl(7,20))



fit <- manova(ratings ~ panels)
summary(fit, test=\"Wilks\")




adj.ratings <- do.call(\"rbind\", adj.rep[[1]] )
adj.fit <- manova(adj.ratings ~ panels)
summary(adj.fit, test=\"Wilks\")


##########-----  thinking... extra ideas for later

##########-----  calculating Mahalanobis distance to identify biased panels

mah.dist = function(dat)
        {md.dat <- as.matrix(mahalanobis(dat, center = colMeans(dat) , cov = cov(dat) ))
         md.pv <- as.matrix(pchisq(md.dat, df = ncol(dat), lower.tail = FALSE))

        out <- cbind(md.dat, md.pv)

        out.2 <- as.data.frame(out)
        colnames(out.2) <- c(\"MD\", \"pMD\")


        return(out.2)
        }



mah.dist(ratings)

mah.dist(adj.ratings)
    

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