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

Question

I developed the stability R package which can be installed from CRAN.
install.packages("stability")
However, I have difficulty in making it to take custom column names as function arguments. Here is an example of add_anova function
library(stability)
data(ge_data)
YieldANOVA <-
add_anova(
.data = ge_data
, .y = Yield
, .rep = Rep
, .gen = Gen
, .env = Env
)
YieldANOVA
The above code works fine. However, when I change the column names of the data.frame, it doesn't work as below:
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$Rep'
Similarly another function stab_reg
fm1Reg <-
stab_reg(
.data = df1
, .y = Y
, .gen = G
, .env = E
)
Error in eval(predvars, data, env) : object 'Gen' not found
The codes of these functions can be accessed by
getAnywhere(add_anova.default)
function (.data, .y, .rep, .gen, .env)
{
Y <- enquo(.y)
Rep <- enquo(.rep)
G <- enquo(.gen)
E <- enquo(.env)
fm1 <- lm(formula = terms(.data$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>
and
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

One of the problems in the data 'df1' is the column name is 'R' instead of "Rep" which was passed into the function. Second, the terms passed into the formula are quosures. we could change it to string with quo_names and then construct formula with paste
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
)
-checking with the output generated using 'ge_data' without changing the column names
all.equal(YieldANOVA, YieldANOVA2, check.attributes = FALSE)
#[1] TRUE
Similarly stab_reg could be changed