如何修改R语言Biodiversity包中accumcomp函数的绘图形状？

It looks like the error you're seeing happens because the accumcomp function internally specifies the pch parameter when calling its underlying plotting function (accumplot), and your custom pch=c() passed via the ... argument conflicts with this pre-set value—hence the "multiple actual arguments" error.

Here are two practical solutions to fix this and match your manuscript's plot style:

Solution 1: Calculate First, Plot Manually (Most Straightforward) #

First, run accumcomp without generating the plot, then use the resulting data to build your plot with full control over point shapes:

# Step 1: Compute the accumulation curve data, skip plotting
accum_data <- accumcomp(fungi, y=fungi.env, factor='Stand.Composition', 
                        method='exact', legend=TRUE, conditioned=TRUE, 
                        ylim=c(0,50), xlim=c(0,110), xlab="Seedlings",
                        ylab="Species richness", rainbow=FALSE, labelit=FALSE,
                        plotit=FALSE)

# Step 2: Plot using accumplot with custom pch values
accumplot(accum_data, xlab="Seedlings", ylab="Species richness",
          xlim=c(0,110), ylim=c(0,50), rainbow=FALSE, labelit=FALSE,
          pch=c(16, 17)) # Replace with your desired point codes (e.g., 1=circle, 17=triangle)

This bypasses the internal pch assignment in accumcomp and lets you specify exactly what shapes you want.

Solution 2: Modify the accumcomp Function Source (For Repeated Use) #

If you need to use this custom styling regularly, you can tweak the accumcomp function to respect your pch input:

1. First, view the function's source code to find where pch is hardcoded:

print(accumcomp)

2.Look for the line where accumplot is called inside accumcomp—it will likely have something like:

accumplot(result1, addit = addit, xlab = xlab, ylab = ylab, xlim = xlim, 
          ylim = ylim, type = type, pch = 1:length(levels(factor)), ...)

3. Replace that section with code that checks for your custom pch first, falling back to the default if none is provided:

# Check if user provided pch; use default if not
custom_pch <- list(...)$pch
if (is.null(custom_pch)) {
  custom_pch <- 1:length(levels(factor))
}

# Call accumplot with the resolved pch value
accumplot(result1, addit = addit, xlab = xlab, ylab = ylab, xlim = xlim, 
          ylim = ylim, type = type, pch = custom_pch, ...)

4. Re-define the modified accumcomp function in your R environment. Now you can call it directly with pch=c() like you originally tried:

accumcomp(fungi, y=fungi.env, factor='Stand.Composition', method='exact', 
          legend=TRUE, conditioned=TRUE, ylim=c(0,50),xlim=c(0,110),
          xlab="Seedlings",ylab="Species richness",rainbow=FALSE,labelit=FALSE,
          pch=c(16,17))

内容的提问来源于stack exchange，提问作者Natalie Scott