Introduction

In this script, we will build a foodtree with the NHANES 2-day average totals, subsetted for males, 60-79 years old.

First, we will load the QC-ed averaged totals of males 60-79 years old (n=236) and all food records (n=4,164). Then, we will keep the food records of only the individuals in males 60-79 years old and generate a foodtree with the filtered food data.


Load functions and packages

Name the path to DietR directory where input files are pulled.

main_wd <- "~/GitHub/DietR"

Load the reshape2 package necessary for tree building, and if it is not installed, install it.

if (!require("reshape2", quietly = TRUE))install.packages("reshape2")

Load the data.tree package necessary for newick.tree.r, and if it is not installed, install it.

if (!require("data.tree", quietly = TRUE))install.packages("data.tree")

Load the necessary functions.

source("lib/specify_data_dir.R")

source("lib/Food_tree_scripts/newick.tree.r")
source("lib/Food_tree_scripts/make.food.tree.r") # This needs 'newick.tree.r' already loaded.
source("lib/Food_tree_scripts/make.food.ifc.r")
source("lib/Food_tree_scripts/make.fiber.ifc.r")
source("lib/Food_tree_scripts/make.dhydrt.ifc.r")

You can come back to the main directory by:

setwd(main_wd)


Load and prep data for generating foodtrees

Specify the directory where the data is.

SpecifyDataDirectory(directory.name = "eg_data/NHANES/Laboratory_data")


Load the males60to79 people. Note this is a total data (1 row/person).

totals_males60to79 <- read.table("QCtotal_d_ga_body_meta_glu_comp_2_males60to79.txt", 
                                 sep="\t", header=T)

Make the individuals as a vector.

selectedind <- totals_males60to79$SEQN

Load the input file (all food record data) to be filtered.

all.food.record <- read.table("../Food_D12_FC_QC_demo_QCed.txt", sep="\t", header=T)

Select only the individuals listed in selectedind.

sel.food.record <- all.food.record[all.food.record$SEQN %in% selectedind, ]

Confirm the two contains the same set of individuals.

identical(unique(sel.food.record$SEQN), selectedind)
## [1] TRUE

Save. This will be the input for the following procedures.

write.table(sel.food.record, "Food_D12_FC_QC_demo_QCed_males60to79.txt", 
            sep="\t", row.names=F, quote=F)


Create foodtrees

Create a foodtree with the foods classified at a desired level of classification (Lv. 1-6).

“NodeLabelsMCT.txt” has a list of food levels and names, which comes with the DietR package.

MakeFoodTree(nodes_fn= "../../Food_tree_eg/NodeLabelsMCT.txt", 
             addl_foods_fn = NULL,
             num_levels = 3,
             food_database_fn =            "Food_D12_FC_QC_demo_QCed_males60to79.txt",  
             output_tree_fn =     "Foodtree/Food_D12_FC_QC_demo_QCed_males60to79_3Lv.nwk", 
             output_taxonomy_fn = "Foodtree/Food_D12_FC_QC_demo_QCed_males60to79_3Lv.tax.txt")
Arguments Description
nodes_fn he food level (node) information for each food item
addl_foods_fn List of foods not present in the list can be added. NULL by default
num_levels Number of food levels (1 - 5) to save
food_database_fn Your food item data
output_tree_fn Output tree file name. Should end with “.nwk”
output_taxonomy_fn Output taxonomy file (to be used later) name

The xxx.nwk is the foodtree, and xxx.tax.txt is the taxonomy file that is to be used to IFC tables next.


Generate IFC tables for downstream analyses.

Note that this may take some time.

Make the standard food ifc table with data in gram weights of food. For the food_records_fn argument, you need to supply sel.food.records file that have FoodAmt column.

It is OK to see see a warning message: “In write.table(dhydrt.ifc, output_fn, sep =”, quote = F, append = TRUE) :
appending column names to file”

MakeFoodIfc(food_records_fn=  "Food_D12_FC_QC_demo_QCed_males60to79.txt",   
            food_record_id =  "SEQN",                              
            food_taxonomy_fn= "Foodtree/Food_D12_FC_QC_demo_QCed_males60to79_3Lv.tax.txt",       
            output_fn =       "Foodtree/Food_D12_FC_QC_demo_QCed_males60to79_3Lv.food.ifc.txt")  
## Warning in write.table(food.ifc, output_fn, sep = "\t", quote = F, append =
## TRUE): appending column names to file
Arguments Description
food_records_fn Same as food_records_fn in MakeFoodTree
food_record_id The colunmname of your participants’ ID
food_taxonomy_fn Taxonomy file produced by MakeFoodTree
output_fn Name output ifc file to be saved


Make a food ifc table with data in grams of fiber per food.

MakeFiberIfc(food_records_fn=  "Food_D12_FC_QC_demo_QCed_males60to79.txt", 
             food_record_id=   "SEQN", 
             food_taxonomy_fn= "Foodtree/Food_D12_FC_QC_demo_QCed_males60to79_3Lv.tax.txt", 
             output_fn=        "Foodtree/Food_D12_FC_QC_demo_QCed_males60to79_3Lv.fiber.ifc.txt")
## Warning in write.table(fiber.ifc, output_fn, sep = "\t", quote = F, append =
## TRUE): appending column names to file


Make a food ifc table as dehydrated grams per kcal.

MakeDhydrtIfc(food_records_fn=  "Food_D12_FC_QC_demo_QCed_males60to79.txt", 
              food_record_id =  "SEQN", 
              food_taxonomy_fn= "Foodtree/Food_D12_FC_QC_demo_QCed_males60to79_3Lv.tax.txt", 
              output_fn =       "Foodtree/Food_D12_FC_QC_demo_QCed_males60to79_3Lv.dhydrt.ifc.txt")  
## Warning in write.table(dhydrt.ifc, output_fn, sep = "\t", quote = F, append =
## TRUE): appending column names to file


Come back to the main directory.

setwd(main_wd)