那些遇到过的问题

不同电脑的回归输出不同

com*_*ues 6 statistics regression r numeric glm

我们正在 Fedora 33 上使用 R 将广义线性模型拟合到一组数据。我们 3 个人拥有完全相同的数据集、完全相同的操作系统 (Fedora 33)、完全相同的 R 版本和软件包版本。sessionInfo() 输出看起来也一样。这是当前的函数调用：

probitModel <- glm(Y ~ a + b + c +
                     d + e + f + g,
                   control=glm.control(maxit=100), 
                   start=startingval,
                   family = binomial(link = "probit"),
                   data = thisData)
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需要注意的是，正常的“lm”拟合在比较时会产生完全相同的结果。关于“glm”的一些东西在不同的计算机上会产生不同的结果。最后，结果是一致的，因为我们在同一台计算机上使用相同的数据得到相同的结果。只有当我们比较结果时才会出现问题。

我们已经检查过：

  • 相同的操作系统版本。
  • 相同的R版本。
  • 相同的包版本。
  • 一样的种子。
  • 所有计算机都是 64 位，R 安装是 64 位。
  • 相同的 sessionInfo()
  • 相同的 g++ 版本。

数据文件可以在这里找到。我们只是使用 load() 来设置数据，调用上面的函数，当输出应该相同时，我们得到的输出略有不同。

我的 sprintf("%.20f", probitModel$coefficients) 结果：

"-2.87521118137333120401" "-0.29134882504319664642" "0.11641651353472137753"  "-0.00811350544106945529" "0.00939647781971938295"  "0.00000000889056301580"  "-0.00000000003021053820" "0.04553200818707187070"
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另一台电脑的结果：

"-2.87521124006409856122" "-0.29134881939721285482" "0.11641651896472486605"  "-0.00811350937056383621" "0.00939647799201156347" "0.00000000889056417264"  "-0.00000000003021022404" "0.04553201421062236243"
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我的跟踪输出：

    Deviance = 67234.8 Iterations - 1
    Deviance = 67079.56 Iterations - 2
    Deviance = 67102.68 Iterations - 3
    Deviance = 67088.05 Iterations - 4
    Deviance = 67078.07 Iterations - 5
    Deviance = 67073.77 Iterations - 6
    Deviance = 67076.34 Iterations - 7
    Deviance = 67074.41 Iterations - 8
    Deviance = 67075.74 Iterations - 9
    Deviance = 67074.77 Iterations - 10
    Deviance = 67075.45 Iterations - 11
    Deviance = 67074.96 Iterations - 12
    Deviance = 67075.31 Iterations - 13
    Deviance = 67075.06 Iterations - 14
    Deviance = 67075.23 Iterations - 15
    Deviance = 67075.11 Iterations - 16
    Deviance = 67075.2 Iterations - 17
    Deviance = 67075.13 Iterations - 18
    Deviance = 67075.18 Iterations - 19
    Deviance = 67075.15 Iterations - 20
    Deviance = 67075.17 Iterations - 21
    Deviance = 67075.15 Iterations - 22
    Deviance = 67075.16 Iterations - 23
    Deviance = 67075.16 Iterations - 24
    Deviance = 67075.16 Iterations - 25
    Deviance = 67075.16 Iterations - 26
    Deviance = 67075.16 Iterations - 27
    Deviance = 67075.16 Iterations - 28
    Deviance = 67075.16 Iterations - 29
    Deviance = 67075.16 Iterations - 30
    Deviance = 67075.16 Iterations - 31
    Deviance = 67075.16 Iterations - 32
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其他电脑的trace输出：

Deviance = 67234.8 Iterations - 1
Deviance = 67079.56 Iterations - 2
Deviance = 67102.68 Iterations - 3
Deviance = 67088.05 Iterations - 4
Deviance = 67078.07 Iterations - 5
Deviance = 67073.77 Iterations - 6
Deviance = 67076.34 Iterations - 7
Deviance = 67074.41 Iterations - 8
Deviance = 67075.74 Iterations - 9
Deviance = 67074.77 Iterations - 10
Deviance = 67075.45 Iterations - 11
Deviance = 67074.96 Iterations - 12
Deviance = 67075.31 Iterations - 13
Deviance = 67075.06 Iterations - 14
Deviance = 67075.23 Iterations - 15
Deviance = 67075.11 Iterations - 16
Deviance = 67075.2 Iterations - 17
Deviance = 67075.13 Iterations - 18
Deviance = 67075.18 Iterations - 19
Deviance = 67075.15 Iterations - 20
Deviance = 67075.17 Iterations - 21
Deviance = 67075.15 Iterations - 22
Deviance = 67075.16 Iterations - 23
Deviance = 67075.16 Iterations - 24
Deviance = 67075.16 Iterations - 25
Deviance = 67075.16 Iterations - 26
Deviance = 67075.16 Iterations - 27
Deviance = 67075.16 Iterations - 28
Deviance = 67075.16 Iterations - 29
Deviance = 67075.16 Iterations - 30
Deviance = 67075.16 Iterations - 31
Deviance = 67075.16 Iterations - 32
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我的 options() 输出：

$askpass
function (prompt) 
{
    .rs.askForPassword(prompt)
}
<environment: 0x5557fac219c8>

$asksecret
function (name, title = name, prompt = paste(name, ":", sep = "")) 
{
    .rs.askForSecret(name, title, prompt)
}
<environment: 0x5557fac219c8>

$bitmapType
[1] "cairo"
   
$CBoundsCheck
[1] FALSE

$check.bounds
[1] FALSE

$citation.bibtex.max
[1] 1


$continue
[1] "+ "

$contrasts
        unordered           ordered 
"contr.treatment"      "contr.poly" 

$defaultPackages
[1] "datasets"  "utils"     "grDevices" "graphics"  "stats"     "methods"  

$demo.ask
[1] "default"

$deparse.cutoff
[1] 60

$device
[1] "RStudioGD"

$device.ask.default
[1] FALSE

$digits
[1] 7

$download.file.method
[1] "libcurl"

$dvipscmd
[1] "dvips"

$echo
[1] TRUE

$editor
[1] "/usr/bin/nano"

$encoding
[1] "native.enc"

$example.ask
[1] "default"

$expressions
[1] 5000

$ggvis.renderer
[1] "svg"

$help_type
[1] "html"

$help.search.types
[1] "vignette" "demo"     "help"    

$help.try.all.packages
[1] FALSE

$HTTPUserAgent
[1] "RStudio Desktop (1.4.1106); R (4.0.4 x86_64-redhat-linux-gnu x86_64 linux-gnu)"

$internet.info
[1] 2

$keep.parse.data
[1] TRUE

$keep.parse.data.pkgs
[1] FALSE

$keep.source
[1] TRUE

$keep.source.pkgs
[1] FALSE

$locatorBell
[1] TRUE

$mailer
[1] "mailto"

$matprod
[1] "default"

$max.print
[1] 1000

$menu.graphics
[1] FALSE

$na.action
[1] "na.omit"

$nwarnings
[1] 50

$OutDec
[1] "."

$papersize
[1] "letter"

$PCRE_limit_recursion
[1] NA

$PCRE_study
[1] FALSE

$PCRE_use_JIT
[1] TRUE

$pdfviewer
[1] "/usr/bin/xdg-open"

$pkgType
[1] "source"

$profvis.keep_output
[1] TRUE

$profvis.print
function (x) 
{
    .rs.profilePrint(x)
}
<environment: 0x5557f91aadb0>

$profvis.prof_extension
[1] ".Rprof"


$prompt
[1] "> "

$repos
                       CRAN 
"https://cran.rstudio.com/" 
attr(,"RStudio")
[1] TRUE

$restart
function (afterRestartCommand = "") 
{
    .rs.restartR(afterRestartCommand)
}
<environment: 0x5557fac219c8>

$reticulate.initialized
function () 
{
    options(reticulate.initialized = NULL)
    .rs.reticulate.onPythonInitialized()
    .rs.reticulate.enqueueClientEvent(.rs.reticulateEvents$PYTHON_INITIALIZED, 
        list())
    .Call("rs_reticulateInitialized", PACKAGE = "(embedding)")
}
<environment: 0x5557f8bbf4d0>

$reticulate.repl.hook
function (buffer, contents, trimmed) 
{
    .rs.reticulate.replHook(buffer, contents, trimmed)
}
<environment: 0x5557f8bbf4d0>

$reticulate.repl.initialize
function () 
{
    .rs.reticulate.replInitialize()
}
<environment: 0x5557f8bbf4d0>

$reticulate.repl.teardown
function () 
{
    .rs.reticulate.replTeardown()
}
<environment: 0x5557f8bbf4d0>

$rl_word_breaks
[1] " \t\n\"\\'`><=%;,|&{()}"

$rsconnect.check.certificate
[1] TRUE

$rstudio.notebook.executing
[1] FALSE

$RStudioGD.antialias
[1] "default"

$RStudioGD.backend
[1] "default"

$scipen
[1] 0

$shiny.launch.browser
function (url) 
{
    invisible(.Call("rs_shinyviewer", url, getwd(), "window", 
        NULL, PACKAGE = "(embedding)"))
}
<environment: base>
attr(,"shinyViewerType")
[1] "window"

$shinygadgets.showdialog
function (caption, url, width = NULL, height = NULL) 
{
    if (!is.character(caption) || (length(caption) != 1)) 
        stop("caption must be a single element character vector.", 
            call. = FALSE)
    if (!is.character(url) || (length(url) != 1)) 
        stop("url must be a single element character vector.", 
            call. = FALSE)
    if (is.null(width)) 
        width <- 600
    if (is.null(height)) 
        height <- 600
    if (!is.numeric(width) || (length(width) != 1)) 
        stop("width must be a single element numeric vector.", 
            call. = FALSE)
    if (!is.numeric(height) || (length(height) != 1)) 
        stop("height must be a single element numeric vector.", 
            call. = FALSE)
    invisible(.Call("rs_showShinyGadgetDialog", caption, url, 
        width, height, PACKAGE = "(embedding)"))
}
<environment: 0x5557fac219c8>

$show.coef.Pvalues
[1] TRUE

$show.error.messages
[1] TRUE

$show.signif.stars
[1] TRUE

$str
$str$strict.width
[1] "no"

$str$digits.d
[1] 3

$str$vec.len
[1] 4

$str$list.len
[1] 99

$str$deparse.lines
NULL

$str$drop.deparse.attr
[1] TRUE

$str$formatNum
function (x, ...) 
format(x, trim = TRUE, drop0trailing = TRUE, ...)
<environment: 0x5557f9ae0330>


$str.dendrogram.last
[1] "`"

$stringsAsFactors
[1] FALSE

$terminal.manager
$terminal.manager$terminalActivate
function (id = NULL, show = TRUE) 
{
    if (!is.null(id) && (!is.character(id) || (length(id) != 
        1))) 
        stop("'id' must be NULL or a character vector of length one")
    if (!is.logical(show)) 
        stop("'show' must be TRUE or FALSE")
    .Call("rs_terminalActivate", id, show)
    invisible(NULL)
}

$terminal.manager$terminalCreate
function (caption = NULL, show = TRUE, shellType = NULL) 
{
    if (!is.null(caption) && (!is.character(caption) || (length(caption) != 
        1))) 
        stop("'caption' must be NULL or a character vector of length one")
    if (is.null(show) || !is.logical(show)) 
        stop("'show' must be a logical vector")
    if (!is.null(shellType) && (!is.character(shellType) || (length(shellType) != 
        1))) 
        stop("'shellType' must be NULL or a character vector of length one")
    validShellType = TRUE
    if (!is.null(shellType)) {
        validShellType <- tolower(shellType) %in% c("default", 
            "win-cmd", "win-ps", "win-git-bash", "win-wsl-bash", 
            "ps-core", "custom")
    }
    if (!validShellType) 
        stop("'shellType' must be NULL, or one of 'default', 'win-cmd', 'win-ps', 'win-git-bash', 'win-wsl-bash', 'ps-core', 'bash', 'zsh', or 'custom'.")
    .Call("rs_terminalCreate", caption, show, shellType)
}

$terminal.manager$terminalClear
function (id) 
{
    if (is.null(id) || !is.character(id) || length(id) != 1) 
        stop("'id' must be a character vector of length one")
    .Call("rs_terminalClear", id)
    invisible(NULL)
}

$terminal.manager$terminalList
function () 
{
    .Call("rs_terminalList")
}

$terminal.manager$terminalContext
function (id) 
{
    if (is.null(id) || !is.character(id) || (length(id) != 1)) 
        stop("'id' must be a single element character vector")
    .Call("rs_terminalContext", id)
}

$terminal.manager$terminalBuffer
function (id, stripAnsi = TRUE) 
{
    if (is.null(id) || !is.character(id) || (length(id) != 1)) 
        stop("'id' must be a single element character vector")
    if (is.null(stripAnsi) || !is.logical(stripAnsi)) 
        stop("'stripAnsi' must be a logical vector")
    .Call("rs_terminalBuffer", id, stripAnsi)
}

$terminal.manager$terminalVisible
function () 
{
    .Call("rs_terminalVisible")
}

$terminal.manager$terminalBusy
function (id) 
{
    if (is.null(id) || !is.character(id)) 
        stop("'id' must be a character vector")
    .Call("rs_terminalBusy", id)
}

$terminal.manager$terminalRunning
function (id) 
{
    if (is.null(id) || !is.character(id)) 
        stop("'id' must be a character vector")
    .Call("rs_terminalRunning", id)
}

$terminal.manager$terminalKill
function (id) 
{
    if (is.null(id) || !is.character(id)) 
        stop("'id' must be a character vector")
    .Call("rs_terminalKill", id)
    invisible(NULL)
}

$terminal.manager$terminalSend
function (id, text) 
{
    if (!is.character(text)) 
        stop("'text' should be a character vector", call. = FALSE)
    if (is.null(id) || !is.character(id) || length(id) != 1) 
        stop("'id' must be a character vector of length one")
    .Call("rs_terminalSend", id, text)
    invisible(NULL)
}

$terminal.manager$terminalExecute
function (command, workingDir = NULL, env = character(), show = TRUE) 
{
    if (is.null(command) || !is.character(command) || (length(command) != 
        1)) 
        stop("'command' must be a single element character vector")
    if (!is.null(workingDir) && (!is.character(workingDir) || 
        (length(workingDir) != 1))) 
        stop("'workingDir' must be a single element character vector")
    if (!is.null(env) && !is.character(env)) 
        stop("'env' must be a character vector")
    if (is.null(show) || !is.logical(show)) 
        stop("'show' must be a logical vector")
    .Call("rs_terminalExecute", command, workingDir, env, show, 
        PACKAGE = "(embedding)")
}


$texi2dvi
[1] "/usr/bin/texi2dvi"

$timeout
[1] 60

$ts.eps
[1] 1e-05

$ts.S.compat
[1] FALSE

$unzip
[1] "/usr/bin/unzip"

$useFancyQuotes
[1] TRUE

$verbose
[1] FALSE

$viewer
function (url, height = NULL) 
{
    if (!is.character(url) || (length(url) != 1)) 
        stop("url must be a single element character vector.", 
            call. = FALSE)
    if (identical(height, "maximize")) 
        height <- -1
    if (!is.null(height) && (!is.numeric(height) || (length(height) != 
        1))) 
        stop("height must be a single element numeric vector or 'maximize'.", 
            call. = FALSE)
    invisible(.Call("rs_viewer", url, height, PACKAGE = "(embedding)"))
}
<environment: 0x5557fac219c8>

$warn
[1] 0

$warning.length
[1] 1000

$width
[1] 121
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第二台计算机的 options() 输出：

$add.smooth
[1] TRUE

$askpass
function (prompt) 
{
    .Call("rs_askForPassword", prompt)
}
<environment: 0x55ca5c0b0978>

$asksecret
function (name, title = name, prompt = paste(name, ":", sep = "")) 
{
    result <- .Call("rs_askForSecret", name, title, prompt, .rs.isPackageInstalled("keyring"), 
        .rs.hasSecret(name))
    if (is.null(result)) 
        stop("Ask for secret operation was cancelled.")
    result
}
<environment: 0x55ca5c0b0978>

$bitmapType
[1] "cairo"

$browser
function (url) 
{
    .Call("rs_browseURL", url)
}
<environment: 0x55ca5ca2c200>

$browserNLdisabled
[1] FALSE

$buildtools.check
function (action) 
{
    if (identical(.Platform$pkgType, "mac.binary.mavericks")) {
        .Call("rs_canBuildCpp")
    }
    else {
        if (!.Call("rs_canBuildCpp")) {
            .rs.installBuildTools(action)
            FALSE
        }
        else {
            TRUE
        }
    }
}
<environment: 0x55ca5c0b0978>

$buildtools.with
function (code) 
{
    .rs.addRToolsToPath()
    on.exit(.rs.restorePreviousPath(), add = TRUE)
    force(code)
}
<environment: 0x55ca5c0b0978>

$CBoundsCheck
[1] FALSE

$check.bounds
[1] FALSE

$citation.bibtex.max
[1] 1

$connectionObserver
$connectionObserver$connectionOpened
function (type, host, displayName, icon = NULL, connectCode, 
    disconnect, listObjectTypes, listObjects, listColumns, previewObject, 
    connectionObject, actions = NULL) 
{
    if (!inherits(listObjectTypes, "function")) {
        stop("listObjectTypes must be a function returning a list of object types", 
            call. = FALSE)
    }
    promote <- function(name, l) {
        if (length(l) == 0) 
            return(list())
        if (is.null(l$contains)) {
            return(list(list(name = name, icon = l$icon, contains = "data")))
        }
        else {
            return(unlist(append(list(list(list(name = name, 
                icon = l$icon, contains = names(l$contains)))), 
                lapply(names(l$contains), function(name) {
                  promote(name, l$contains[[name]])
                })), recursive = FALSE))
        }
        return(list())
    }
    objectTree <- listObjectTypes()
    objectTypes <- lapply(names(objectTree), function(name) {
        promote(name, objectTree[[name]])
    })[[1]]
    connection <- list(type = type, host = host, displayName = displayName, 
        icon = icon, connectCode = connectCode, disconnect = disconnect, 
        objectTypes = objectTypes, listObjects = listObjects, 
        listColumns = listColumns, previewObject = previewObject, 
        actions = actions, connectionObject = connectionObject)
    class(connection) <- "rstudioConnection"
    .rs.validateConnection(connection)
    cacheKey <- paste(connection$type, connection$host, .Call("rs_generateShortUuid"), 
        sep = "_")
    assign(cacheKey, value = connection, envir = .rs.activeConnections)
    invisible(.Call("rs_connectionOpened", connection))
}
<environment: 0x55ca5d0039e0>

$connectionObserver$connectionClosed
function (type, host, ...) 
{
    .rs.validateCharacterParams(list(type = type, host = host))
    name <- .rs.findConnectionName(type, host)
    if (!is.null(name)) 
        rm(list = name, envir = .rs.activeConnections)
    invisible(.Call("rs_connectionClosed", type, host))
}
<environment: 0x55ca5d0039e0>

$connectionObserver$connectionUpdated
function (type, host, hint, ...) 
{
    .rs.validateCharacterParams(list(type = type, host = host, 
        hint = hint))
    invisible(.Call("rs_connectionUpdated", type, host, hint))
}
<environment: 0x55ca5d0039e0>


$continue
[1] "+ "

$contrasts
        unordered           ordered 
"contr.treatment"      "contr.poly" 

$defaultPackages
[1] "datasets"  "utils"     "grDevices" "graphics"  "stats"     "methods"  

$demo.ask
[1] "default"

$deparse.cutoff
[1] 60

$device
[1] "RStudioGD"

$device.ask.default
[1] FALSE

$digits
[1] 7

$download.file.method
[1] "libcurl"

$dvipscmd
[1] "dvips"

$echo
[1] TRUE

$editor
[1] "vi"

$encoding
[1] "native.enc"

$error
(function () 
{
    .rs.recordTraceback(TRUE, 5, .rs.enqueueError)
})()

$example.ask
[1] "default"

$expressions
[1] 5000

$ggvis.renderer
[1] "svg"

$help_type
[1] "html"

$help.search.types
[1] "vignette" "demo"     "help"    

$help.try.all.packages
[1] FALSE

$HTTPUserAgent
[1] "RStudio Desktop (1.3.1093); R (4.0.4 x86_64-redhat-linux-gnu x86_64 linux-gnu)"

$internet.info
[1] 2

$keep.parse.data
[1] TRUE

$keep.parse.data.pkgs
[1] FALSE

$keep.source
[1] TRUE

$keep.source.pkgs
[1] FALSE

$locatorBell
[1] TRUE

$mailer
[1] "mailto"

$matprod
[1] "default"

$max.print
[1] 1000

$menu.graphics
[1] FALSE

$na.action
[1] "na.omit"

$nwarnings
[1] 50

$OutDec
[1] "."

$page_viewer
function (url, title = "RStudio Viewer", self_contained = FALSE) 
{
    if (!is.character(url) || (length(url) != 1)) 
        stop("url must be a single element character vector.", 
            call. = FALSE)
    if (!is.character(title) || (length(title) != 1)) 
        stop("title must be a single element character vector.", 
            call. = FALSE)
    if (!is.logical(self_contained) || (length(self_contained) != 
        1)) 
        stop("self_contained must be a single element logical vector.", 
            call. = FALSE)
    invisible(.Call("rs_showPageViewer", url, title, self_contained))
}
<environment: 0x55ca5ca2c200>

$pager
function (files, header, title, delete.file) 
{
    for (i in 1:length(files)) {
        if ((i > length(header)) || !nzchar(header[[i]])) 
            fileTitle <- title
        else fileTitle <- header[[i]]
        .Call("rs_showFile", fileTitle, files[[i]], delete.file)
    }
}
<environment: 0x55ca5c0b0978>

$papersize
[1] "letter"

$PCRE_limit_recursion
[1] NA

$PCRE_study
[1] FALSE

$PCRE_use_JIT
[1] TRUE

$pdfviewer
[1] "/usr/bin/xdg-open"

$pkgType
[1] "source"

$plumber.swagger.url
function (url) 
{
    invisible(.Call("rs_plumberviewer", url, getwd(), "window", 
        PACKAGE = "(embedding)"))
}
<environment: 0x55ca5c0b0978>
attr(,"plumberViewerType")
[1] "window"

$printcmd
[1] "lpr"

$profvis.keep_output
[1] TRUE

$profvis.print
function (x) 
{
    envir <- as.environment(which(search() == "tools:rstudio"))
    eval(substitute(.rs.profilePrint(x), list(x = x)), envir = envir)
}
<environment: 0x55ca5c99fb80>

$prompt
[1] "> "

$repos
                       CRAN 
"https://cran.rstudio.com/" 
attr(,"RStudio")
[1] TRUE

$restart
function (afterRestartCommand = "") 
{
    afterRestartCommand <- paste(as.character(afterRestartCommand), 
        collapse = "\n")
    .Call("rs_restartR", afterRestartCommand, PACKAGE

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