我如何使用模型和运行 F-test ggplot

Question

我有一个小问题，我已经为不同的数据子集拟合了一个模型。我现在想在进行 F 检验之前将每个模型绘制在包含所有点的数据上，以查看包含“Site_class”变量是否对模型有任何好处。

数据：

sitedata <- structure(list(Site_class = c("1", "1", "1", "1", "1", "1", "1", 
"1", "1", "1", "1", "1", "4", "4", "4", "4", "4", "4", "4", "4", 
"4", "4", "4", "4", "All", "All", "All", "All", "All", "All", 
"All", "All", "All", "All", "All", "All", "All", "All", "All", 
"All", "All", "All", "All", "All", "All", "All", "All", "All", 
"All", "All", "All", "All", "All", "All", "All", "All", "All", 
"All", "All", "All", "All", "All", "All", "All", "All", "All", 
"All", "All", "All", "All", "All", "All", "All", "All", "All", 
"All", "All", "All", "All", "All", "All", "All", "All"), VarA = c(2.4, 
6.5, 11.3, 16.1, 20.5, 24.3, 27.4, 30, 32, 33.6, 34.9, 36, 0.75, 
2.45, 4.75, 7.45, 10.3, 13.05, 15.55, 17.7, 19.4, 20.75, 21.9, 
22.8, 2.4, 6.5, 11.3, 16.1, 20.5, 24.3, 27.4, 30, 32, 33.6, 34.9, 
36, 1.85, 5.15, 9.1, 13.2, 17.1, 20.55, 23.45, 25.9, 27.8, 29.3, 
30.55, 31.6, 1.3, 3.8, 6.95, 10.35, 13.7, 16.8, 19.5, 21.8, 23.6, 
25.05, 26.25, 27.2, 0.75, 2.45, 4.75, 7.45, 10.3, 13.05, 15.55, 
17.7, 19.4, 20.75, 21.9, 22.8, 1.1, 2.6, 4.6, 6.9, 9.3, 11.6, 
13.6, 15.2, 16.5, 17.55, 18.4), VarB = c(12, 81, 220, 403, 605, 
806, 991, 1153, 1288, 1399, 1495, 1578, 1, 11, 45, 106, 189, 
283, 381, 473, 552, 619, 675, 723, 12, 81, 220, 403, 605, 806, 
991, 1153, 1288, 1399, 1495, 1578, 4, 51, 148, 286, 446, 609, 
760, 893, 1008, 1105, 1186, 1255, 2, 27, 93, 190, 307, 433, 557, 
670, 766, 848, 917, 975, 1, 11, 45, 106, 189, 283, 381, 473, 
552, 619, 675, 723, 2, 11, 42, 94, 161, 234, 304, 368, 423, 469, 
508)), row.names = c(NA, -83L), class = c("grouped_df", "tbl_df", 
"tbl", "data.frame"), groups = structure(list(Site_class = c("1", 
"4", "All"), .rows = list(1:12, 13:24, 25:83)), row.names = c(NA, 
-3L), class = c("tbl_df", "tbl", "data.frame"), .drop = FALSE))

这就是我到目前为止的工作方式。

library(dplyr)
library(tidyr)
library(purrr)
library(ggplot2)

#Create model
modfit <- function(df){
  nls(VarB ~ a * (VarA^b), data=df, start=c(a=1,b=1))
}

#Nest the original data.frame
sitedata <- sitedata %>% group_by(Site_class) %>% nest()

#Fit the models
sitedata_model <- sitedata %>% mutate(
  Model= map(.x=data, .f= modfit)
)

#Attempt to plot the models:
ggplot(sitedata_model[[2]][[3]], aes(x=VarA,y=VarB)) + #All the data
  geom_point()+
  geom_function(fun=~sitedata_model[[3]][[1]]) + # I assume I will have to plot them separately?
  geom_function(fun=~sitedata_model[[3]][[2]]) +
  geom_function(fun=~sitedata_model[[3]][[3]])

看来我已经成功创建了模型，但是它不理解我对它们进行绘图的调用。我也尝试过使用 predict，但没有成功。

我怎样才能：

将它们绘制在我的图表上 &
运行对所有 3 个模型进行 F 检验，看看是否存在差异？

Answer 1

geom_function 需要一个函数。不是公式，不是模型，而是函数.

我对这个 geom 没有太多经验，而且我不确定以下是否有效，但它似乎确实适用于您的用例：

sitedata_model <- sitedata %>% 
  #Fit the models
  mutate(Model = purrr::map(.x=data, .f= modfit)) %>%
  
  # extract formula from each model, convert to one-sided form, &
  # replace coefficients with fitted values, & store in dataframe
  # as character string 
  rowwise() %>%
  mutate(func = formula(Model) %>% 
           as.character() %>% 
           magrittr::extract(3) %>%
           gsub("VarA", ".x", ., fixed = T) %>%
           gsub("a", Model$m$getPars()[1], .) %>%
           gsub("b", Model$m$getPars()[2], .) %>%
           paste("~", ., collapse = "")) %>%
  ungroup()

# plot
ggplot(data = sitedata_model$data[[3]]) +
  geom_point(aes(x = VarA, y = VarB)) + 
  
  # add formula in each row as a separate geom_function layer
  lapply(seq(1, nrow(sitedata_model)),
         function(i) geom_function(fun = rlang::as_function(formula(sitedata_model$func[i])),
                                   aes(colour = sitedata_model$Site_class[i]))) +
  
  # change legend name (can also change palette / labels / etc.)
  scale_colour_discrete(name = "Site class")

至于运行 F-test，你指的是ANOVA吗？

> anova(sitedata_model$Model[[1]], sitedata_model$Model[[2]], sitedata_model$Model[[3]])
Analysis of Variance Table

Model 1: VarB ~ a * (VarA^b)
Model 2: VarB ~ a * (VarA^b)
Model 3: VarB ~ a * (VarA^b)
  Res.Df Res.Sum Sq  Df  Sum Sq F value Pr(>F)
1     10      60.14                           
2     10      90.36   0    0.00               
3     57     741.38 -47 -651.02  1.5328 0.2386

有关如何解释 ANOVA 输出的说明，请参阅 here。

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我如何使用模型和运行 F-test ggplot