make_multi_pheno_trend_plot: Combine multiple phenology contour plots in one figure

In chillR: Statistical Methods for Phenology Analysis in Temperate Fruit Trees

Combine multiple phenology contour plots in one figure

Description

For multiple datasets, this function plots surface plots relating mean temperatures during specified periods to annually recurring variables (e.g. flowering). It produces one panel per dataset and plots them all in one figure. Plots can be produced in R or directly exported as .png files.

Usage

make_multi_pheno_trend_plot(
  pheno_list,
  fixed_weather,
  split_month = 6,
  outpath = NA,
  file_name = NA,
  image_type = "png",
  fonttype = "serif",
  percol = 5,
  xlabel = NA,
  ylabel = NA,
  height_factor = 0.8
)

Arguments

pheno_list	a data.frame with the following columns: varieties (contains a character string), Start_chill (the start of the chill period, in Julian days), End_chill (the end of the chill period, in Julian days), Start_heat (the start of the forcing period, in Julian days), End_heat (the end of the forcing period, in Julian days), Link (the complete path to a csv file that contains all the annual observations for the dataset, with columns Year and pheno)
fixed_weather	daily weather, as produced with the fix_weather function
split_month	the month after which to start a new season. Defaults to 6, meaning the new season will start in July.
outpath	Path to the folder where the images should be saved. Should include a trailing "/". The folder must already exists.
file_name	name of the image file to be produced, if image_type='png'.
image_type	Character string indicating the file format that should be output. Image files are only produced for the moment, if this is "png". All other values, as well as the default NA lead to output as an R plot only.
fonttype	The type of font to be used for the figures. Can be 'serif' (default) for a Times New Roman like font, 'sans' for an Arial type font or 'mono' for a typewriter type font.
percol	number of plots to be placed in a column.
xlabel	label for the x-axis (if unhappy with the default).
ylabel	label for the y-axis (if unhappy with the default).
height_factor	height of the resulting png figure (if this is a png) relative to the width of the plot (e.g. 1 or 0.7, defaults to 0.8).

Details

This function is only useful, if you want to plot several surface plots in the same figure. These must relate to the same weather dataset. Arguably, this function isn't quite ready to be released, but it performs some useful functions that you may be interested in...

Value

Only a side effect is produced: either a .png file or an R graphic showing the multi-panel contour figure.

Author(s)

Eike Luedeling

Examples

#this example uses arbitrarily modified versions of the KA_bloom dataset, and the starts
#end ends of the periods are also arbitraty. So the outputs may not make a lot of sense...

weather<-fix_weather(KA_weather[which(KA_weather$Year>2000),])
pheno_list<-data.frame(varieties=c("KA1","KA2","KA3","KA4"), Start_chill=c(270,305,315,320),
  End_chill=c(15,20,35,40), Start_heat=c(17,25,40,45),End_heat=c(90,100,110,115),
  Link=c("KA1.csv","KA2.csv","KA3.csv","KA4.csv"))
  
 # write.csv(KA_bloom,"KA1.csv",row.names=FALSE)
 KA_bloom$pheno<-as.numeric(as.character(KA_bloom$pheno))+10
 # write.csv(KA_bloom,"KA2.csv",row.names=FALSE)
 KA_bloom$pheno<-KA_bloom$pheno+10
 # write.csv(KA_bloom,"KA3.csv",row.names=FALSE)
 KA_bloom$pheno<-KA_bloom$pheno+10
 # write.csv(KA_bloom,"KA4.csv",row.names=FALSE)

# make_multi_pheno_trend_plot(pheno_list,weather, split_month=6,
#            outpath=NA,file_name=NA,image_type="",fonttype="serif",percol=2)

 

chillR documentation built on Nov. 28, 2023, 1:09 a.m.