将 RMarkdown 编织到 HTML 时出错（HTML 中没有显示图表）

Question

Question about knitting RMarkdown.

I am having issues when knitting a Rmarkdown file to HTML/pdf. When I run my chunks of code in the Rmarkdown file everything runs smoothly (and I get my graphs made with ggplot) but when knitting I get an output with no graphs and errors (error in eval, error in ggplot, error in print). Does anyone have experience with this?

The errors:

Error in eval(lhs, parent): object 'iso3166' not found

Error in ggplot(inci_100k, aes(long, lat, map.id=mapname,fill=inci)): object 'inci_100k' not found

Error in print(INCIPLOT): object 'INCIPLOT' not found

The code:

---
title: "R Markdown MAP"
author: "Alexandra V"
date: "1/4/2020"
output:
  html_document: default
  pdf_document: default
  word_document: default
---
```{r,echo = FALSE, warning = FALSE, message=FALSE, error=TRUE}
knitr::opts_chunk$set(cache=TRUE)
knitr::opts_chunk$set(echo = TRUE)
knitr::opts_chunk$set(error = TRUE)
```

Loading the packages we will need for the following analysis.
```{r echo=FALSE, warning=FALSE}
library(tidyverse)
library(lubridate)
library(ggmap)
library(countrycode)
library(grid)
library(gridExtra)
```

To only keep the data needed to make a worldmap of TB incidences, only the relevant data will be taken from the TB_burden_countries_2020-01-04.csv file. Column 1: country names, column 3: iso3 (country codes), column 6: years, column 8: e_inc_100k (estimated incidence all TB forms per 100.000). To make the file easier to work with the names of the columns will be changed to: country, code, year and inci respectively. 

```{r, message=FALSE}
TB.burden <- read.csv("TB_burden_countries_2020-01-04.csv")
TBworldINC.map <- as.data.frame(TB.burden[,c(1,3,6,8)], drop=false)
write.csv(TBworldINC.map, 'TBworldINC.map.csv', row.names = FALSE) 
tb.INC <- read_csv("TBworldINC.map.csv") %>%
  setNames(c("country", "code", "year", "inci"))
```

```{r}
world <- map_data("world")
tb_some_years <- tb.INC %>%
  filter(year %in% c(2005, 2010, 2015, 2018))
inci_100k <- tb_some_years %>%
  inner_join(iso3166 %>% select(a3, mapname), by = c(code = "a3")) %>%
  left_join(world, by = c(country = "region"))

INCIPLOT <- ggplot(inci_100k, aes(long, lat, map_id = mapname, 
                                                fill = inci)) +
  geom_map(map = world) +
  scale_fill_gradient(low = "blue", high = "yellow") +
  theme_void() +
  coord_map(xlim = c(-180, 180)) +
  labs(fill = "Incidence per year") +
  facet_wrap(~ year, ncol = 2)
print(INCIPLOT)
```

picture of the output I get in Rstudio

Answer 1

I have had similar issues when making maps in R. One work around is to create your graphs and to save it locally and including the images. The syntax for adding images in R Markdown is