R中的错误：找不到对象，代码不工作R Markdown

Question

我有一个奇怪的情况，当我在控制台中运行它时，一大块代码正在为我工​​作，但是当我试图编织它时R Markdown文件，我收到错误。下面是代码：

{r,echo=FALSE, message=FALSE, fig.width=3, fig.height=3} 
    library(cdcfluview) 
    library(mosaic) 
    library(ggplot2) 
    library(dplyr) 

    neflu <- get_flu_data("census", "1", "ilinet", years=1997:2016) 
    neflu[neflu=="X"]<-NA 

    wk_new <- rep(NA, nrow(neflu)) 
    season_new <- rep('0', nrow(neflu)) 

    for(i in 1:nrow(neflu)){ 
    if(neflu$WEEK[i] == 40){ 
     wk_num <- 1 
    } 
    wk_new[i] <- wk_num 
    wk_num <- wk_num+1 

    if(neflu$WEEK[i] < 40) { 
     season_new[i] <- paste(neflu$YEAR[i]-1, '-', neflu$YEAR[i]) 
    } else { 
     season_new[i] <- paste(neflu$YEAR[i], '-', neflu$YEAR[i]+1) 
    } 
    } 

    neflu_new <- cbind(neflu, wk_new, season_new) 


    neflu_agg <- neflu_new %>% 
    mutate(weighted_ili = as.numeric(X..WEIGHTED.ILI))%>% 
    group_by(REGION.TYPE, season_new) %>% 
    summarize(peak_ili = max(weighted_ili, na.rm=TRUE), 
     cum_ili = sum(weighted_ili,na.rm=TRUE), 
     peak_wk = wk_new[which.max(weighted_ili)]) 

    neflu_agg2 <- subset(neflu_agg, peak_wk != 5, select=c(REGION.TYPE,season_new,peak_ili,cum_ili, peak_wk)) 

    plot(peak_wk, peak_ili, main= "Peak ILI vs Peak Week", xlab= "Peak Week", ylab= "Peak ILI") 
    nelm1 <- lm(peak_ili~1+peak_wk) 
    abline(nelm1, col='red') 
    plot(peak_ili, cum_ili, main= "Cumulative ILI vs Peak ILI", xlab= "Peak ILI", ylab= "Cumulative ILI") 
    nelm2 <- lm(cum_ili~1+peak_ili) 
    abline(nelm2, col='blue') 

，这里是错误消息我得到：

The object peak_wk not found Calls:<Anonymous> . . . 
    WithCallingHandlers -> withVisible -> eval -> eval -> plot execution halted". 

我曾试图改变这个代码这一点，但我仍然得到错误：

{r,echo=FALSE, message=FALSE, fig.width=3, fig.height=3} 
    library(cdcfluview) 
    library(mosaic) 
    library(ggplot2) 
    library(dplyr) 

    neflu <- get_flu_data("census", "1", "ilinet", years=1997:2016) 
    neflu[neflu=="X"]<-NA 

    wk_new <- rep(NA, nrow(neflu)) 
    season_new <- rep('0', nrow(neflu)) 

    for(i in 1:nrow(neflu)){ 
    if(neflu$WEEK[i] == 40){ 
     wk_num <- 1 
    } 
    wk_new[i] <- wk_num 
    wk_num <- wk_num+1 

    if(neflu$WEEK[i] < 40) { 
     season_new[i] <- paste(neflu$YEAR[i]-1, '-', neflu$YEAR[i]) 
    } else { 
     season_new[i] <- paste(neflu$YEAR[i], '-', neflu$YEAR[i]+1) 
    } 
    } 

    neflu_new <- cbind(neflu, wk_new, season_new) 

    weighted_ili <- mutate(neflu_new, weighted_ili = as.numeric(X..WEIGHTED.ILI)) 
    peak_ili <- max(weighted_ili, na.rm=TRUE) 
    cum_ili <- sum(weighted_ili,na.rm=TRUE) 
    peak_wk <- wk_new[which.max(weighted_ili)] 

    neflu_agg <- neflu_new %>% 
    mutate(weighted_ili = as.numeric(X..WEIGHTED.ILI))%>% 
    group_by(REGION.TYPE, season_new) %>% 
    summarize(peak_ili = max(weighted_ili, na.rm=TRUE), 
     cum_ili = sum(weighted_ili,na.rm=TRUE), 
     peak_wk = wk_new[which.max(weighted_ili)]) 

    neflu_agg2 <- subset(neflu_agg, peak_wk != 5, select=c(REGION.TYPE,season_new,peak_ili,cum_ili, peak_wk)) 

    plot(peak_wk, peak_ili, main= "Peak ILI vs Peak Week", xlab= "Peak Week", ylab= "Peak ILI") 
    nelm1 <- lm(peak_ili~1+peak_wk) 
    abline(nelm1, col='red') 
    plot(peak_ili, cum_ili, main= "Cumulative ILI vs Peak ILI", xlab= "Peak ILI", ylab= "Cumulative ILI") 
    nelm2 <- lm(cum_ili~1+peak_ili) 
    abline(nelm2, col='blue') 

这里是我现在得到的错误：

Error in FUN(X[[i]],...): only defined on data frame with all 
    numeric variables Calls: 

任何帮助只是让这个代码编织将不胜感激。我相信我只是错过了一些非常明显的东西，但我无法弄清楚。

Answer 1

我现在明白为什么我从LMO收到错误，有帮助：

peak_wk，peak_ili和cum_ili没有在全球环境中定义。我不得不指定plot（）函数从哪里提取数据：

attach(neflu_agg2) 

这工作得很好。