I am currently working on a whale catalogue which we use to identify certain individuals to conduct research on these animals. The reports include tables, ggplots and photographs.
I wrote a markdown script to create these reports as .pdfs. I spend quite some time to finalize the layout, positions etc. as this is the first time I am using markdown.
However, I was happy with the single reports. But as there are hundreds of those report-pdfs which need to be created, I want to run an R script with a for loop to create all those reports automatically.
When I use
for (whale in all_data$ID){
rmarkdown::render(input = "C:/Users/NK/Desktop/research_elding/minke_whale_catalogue/minke_whale_catalogue_final_test1/file_2.Rmd",
output_format = "pdf_document",
output_file = paste("test_report_", whale, ".pdf", sep=''),
output_dir = "C:/Users/NK/Desktop/research_elding/minke_whale_catalogue/minke_whale_catalogue_final_test1/reports",
clean=TRUE)
}
in my R script, I get different kinds of errors and the script stopps. I guess I am somehow missing an option to tell the r script that the styling of the .Rmd file needs to be used.
I use MikTex with the LaTex engine pdflatex.
I tracked the problems down to the alignment settings fig.align, fig.height, fig.width and kable and kable_styling.
an example:
When I change
kable(ins,format="latex",booktabs=TRUE,align="c") %>%
kable_styling(full_width = T,font_size = 20)
to
kable(ins)
in the Rmd-file the r-script works fine but off course my format, alignment etc. is gone.
Same is true for my ggplots:
an example:
When I change
h_map <- ggplot(date_f, aes(year,month)) +
geom_tile(aes(fill=Sightings), colour="white") + scale_fill_gradient(low="white",high="black") +
labs(x="Year", y="Month") + #change axis labels
theme(axis.ticks=element_blank()) + #remove ticks
theme(axis.text=element_text(size=13)) #change axis title size
h_map
to
h_map <- ggplot(date_f, aes(year,month)) +
geom_tile(aes(fill=Sightings), colour="white") + scale_fill_gradient(low="white",high="black") +
labs(x="Year", y="Month") + #change axis labels
theme(axis.ticks=element_blank()) + #remove ticks
theme(axis.text=element_text(size=13)) #change axis title size
h_map
in the Rmd-file the r-script works but the formats of the plot are gone and it looks really ■■■■.
I appreciate any help!