自定义列名作为稳定性 R 包函数中的参数

Question

我开发了 stability R 包，可以从 CRAN 安装。

install.packages("stability")

但是，我很难让它将自定义列名作为函数参数。这是 add_anova 函数

的示例

library(stability)
data(ge_data)

YieldANOVA <-
  add_anova(
      .data = ge_data
    , .y    = Yield
    , .rep  = Rep
    , .gen  = Gen
    , .env  = Env
  )
YieldANOVA

以上代码运行良好。但是，当我更改 data.frame 的列名时，它不起作用，如下所示：

df1 <- ge_data
names(df1) <- c("G", "Institute", "R", "Block", "E", "Y")

fm1 <-
  add_anova(
      .data = df1
    , .y    = Y
    , .rep  = Rep
    , .gen  = G
    , .env  = E
  )

Error in model.frame.default(formula = terms(.data$Y ~ .data$E + .data$Rep:.data$E +  : 
  invalid type (NULL) for variable '.data$Rep'

类似的另一个函数stab_reg

fm1Reg <-
  stab_reg(
      .data = df1
    , .y    = Y
    , .gen  = G
    , .env  = E
  )

Error in eval(predvars, data, env) : object 'Gen' not found

这些函数的代码可以通过

访问

getAnywhere(add_anova.default)

function (.data, .y, .rep, .gen, .env) 
{
    Y <- enquo(.y)
    Rep <- enquo(.rep)
    G <- enquo(.gen)
    E <- enquo(.env)
    fm1 <- lm(formula = terms(.data$Y ~ .data$E + .data$Rep:.data$E + 
        .data$G + .data$G:.data$E, keep.order = TRUE), data = .data)
    fm1ANOVA <- anova(fm1)
    rownames(fm1ANOVA) <- c("Env", "Rep(Env)", "Gen", "Gen:Env", 
        "Residuals")
    fm1ANOVA[1, 4] <- fm1ANOVA[1, 3]/fm1ANOVA[2, 3]
    fm1ANOVA[2, 4] <- NA
    fm1ANOVA[1, 5] <- 1 - pf(as.numeric(fm1ANOVA[1, 4]), fm1ANOVA[1, 
        1], fm1ANOVA[2, 1])
    fm1ANOVA[2, 5] <- 1 - pf(as.numeric(fm1ANOVA[2, 4]), fm1ANOVA[2, 
        1], fm1ANOVA[5, 1])
    class(fm1ANOVA) <- c("anova", "data.frame")
    return(list(anova = fm1ANOVA))
}
<bytecode: 0xc327c28>
<environment: namespace:stability>

和

   getAnywhere(stab_reg.default)

function (.data, .y, .rep, .gen, .env) 
{
    Y <- enquo(.y)
    Rep <- enquo(.rep)
    G <- enquo(.gen)
    E <- enquo(.env)
    g <- length(levels(.data$G))
    e <- length(levels(.data$E))
    r <- length(levels(.data$Rep))
    g_means <- .data %>% dplyr::group_by(!!G) %>% dplyr::summarize(Mean = mean(!!Y))
    names(g_means) <- c("G", "Mean")
    DataNew <- .data %>% dplyr::group_by(!!G, !!E) %>% dplyr::summarize(GEMean = mean(!!Y)) %>% 
        dplyr::group_by(!!E) %>% dplyr::mutate(EnvMean = mean(GEMean))
    IndvReg <- lme4::lmList(GEMean ~ EnvMean | Gen, data = DataNew)
    IndvRegFit <- summary(IndvReg)
    StabIndvReg <- tibble::as_tibble(data.frame(g_means, Slope = coef(IndvRegFit)[, 
        , 2][, 1], LCI = confint(IndvReg)[, , 2][, 1], UCI = confint(IndvReg)[, 
        , 2][, 2], R.Sqr = IndvRegFit$r.squared, RMSE = IndvRegFit$sigma, 
        SSE = IndvRegFit$sigma^2 * IndvRegFit$df[, 2], Delta = IndvRegFit$sigma^2 * 
            IndvRegFit$df[, 2]/r))
    MeanSlopePlot <- ggplot(data = StabIndvReg, mapping = aes(x = Slope, 
        y = Mean)) + geom_point() + geom_text(aes(label = G), 
        size = 2.5, vjust = 1.25, colour = "black") + geom_vline(xintercept = 1, 
        linetype = "dotdash") + geom_hline(yintercept = mean(StabIndvReg$Mean), 
        linetype = "dotdash") + labs(x = "Slope", y = "Mean") + 
        scale_x_continuous(sec.axis = dup_axis(), labels = scales::comma) + 
        scale_y_continuous(sec.axis = dup_axis(), labels = scales::comma) + 
        theme_bw()
    return(list(StabIndvReg = StabIndvReg, MeanSlopePlot = MeanSlopePlot))
}
<bytecode: 0xe431010>
<environment: namespace:stability>

Answer 1

数据 'df1' 中的一个问题是列名是 'R' 而不是传递给函数的 "Rep" 。其次，传递到公式中的项是 quosures。我们可以用 quo_names 将其更改为字符串，然后用 paste

构造公式

add_anova1 <- function (.data, .y, .rep, .gen, .env) {
    y1 <- quo_name(enquo(.y))
    r1 <- quo_name(enquo(.rep))
    g1 <- quo_name(enquo(.gen))
    e1 <- quo_name(enquo(.env))

    fm <- formula(paste0(y1, "~", paste(e1, paste(r1, e1, sep=":"), 
                  g1, paste(g1, e1, sep=":"), sep="+")))

    fm1 <- lm(terms(fm, keep.order = TRUE), data = .data)
    fm1ANOVA <- anova(fm1)
    rownames(fm1ANOVA) <- c("Env", "Rep(Env)", "Gen", "Gen:Env", 
        "Residuals")
    fm1ANOVA[1, 4] <- fm1ANOVA[1, 3]/fm1ANOVA[2, 3]
    fm1ANOVA[2, 4] <- NA
    fm1ANOVA[1, 5] <- 1 - pf(as.numeric(fm1ANOVA[1, 4]), fm1ANOVA[1, 
        1], fm1ANOVA[2, 1])
    fm1ANOVA[2, 5] <- 1 - pf(as.numeric(fm1ANOVA[2, 4]), fm1ANOVA[2, 
        1], fm1ANOVA[5, 1])
    class(fm1ANOVA) <- c("anova", "data.frame")
    return(list(anova = fm1ANOVA))

 }

YieldANOVA2 <- add_anova1(
      .data = df1
    , .y    = Y
    , .rep  = R
    , .gen  = G
    , .env  = E
  )

-检查使用 'ge_data' 生成的输出，而不更改列名

all.equal(YieldANOVA, YieldANOVA2, check.attributes = FALSE)
#[1] TRUE

同样stab_reg可以改变

自定义列名作为稳定性 R 包函数中的参数

Custom column names as arguments in the functions of stability R package

r

function

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stability