Richard Sprague

Viome Recommendations

R code to compare Viome food recommendations across multiple tests and track changes over time.

Richard Sprague

I have several years worth of Viome results (located here), but how can I easily tell which recommendations have changed from test to test?

This is some R code to calculate the differences.

You have an Excel table of previous Viome food recommendations and you’d like to see which ones have changed.

The table looks like this:

Viome Recommendations
Food Oct-22 Oct-20 May-20
Abalone Enjoy Enjoy Enjoy
Anchovies Superfood Superfood Enjoy
Apple Enjoy Avoid Enjoy

I want to generate a table showing just those rows that changed. Ideally, I’ll turn this into a simple plot showing how specific food recommendations change over time.

FoodOct-22Oct-20May-20Sep-19
AbaloneEnjoyEnjoyEnjoyEnjoy
Adzuki BeansEnjoyEnjoyEnjoyEnjoy
Alfalfa SproutsEnjoySuperfoodSuperfoodSuperfood
AllspiceEnjoyEnjoyEnjoyEnjoy
Almond MilkEnjoyEnjoyEnjoyEnjoy
AlmondsEnjoyEnjoySuperfoodEnjoy

Foods with changed recommendations since the last test

Code 
# Remove non-Viome columns and any rows where results haven't changed for the last three tests.
viome_file_df %>% count()
n
245
Code 
viome_file_df %>%  filter(`Oct-22`==`Oct-20`) %>% select(1:3)
FoodOct-22Oct-20
AbaloneEnjoyEnjoy
Adzuki BeansEnjoyEnjoy
AllspiceEnjoyEnjoy
Almond MilkEnjoyEnjoy
AlmondsEnjoyEnjoy
AmaranthEnjoyEnjoy
AnchoviesSuperfoodSuperfood
Apple Cider VinegarEnjoyEnjoy
ArtichokeSuperfoodSuperfood
ArugulaEnjoyEnjoy
AvocadoEnjoyEnjoy
Avocado OilEnjoyEnjoy
Bamboo ShootsEnjoyEnjoy
BasilEnjoyEnjoy
Bay LeafEnjoyEnjoy
Beet GreensEnjoyEnjoy
Bell PepperAvoidAvoid
Black BeansEnjoyEnjoy
Black Eyed PeasEnjoyEnjoy
Black PepperEnjoyEnjoy
Black TeaEnjoyEnjoy
BlackberryEnjoyEnjoy
Bok ChoyMinimizeMinimize
Bone Broth (Poultry)EnjoyEnjoy
Brazil NutsEnjoyEnjoy
BreadfruitMinimizeMinimize
BroccoliAvoidAvoid
Brussels SproutsAvoidAvoid
BuckwheatEnjoyEnjoy
BuffaloEnjoyEnjoy
BulgurEnjoyEnjoy
Burdock RootEnjoyEnjoy
CabbageAvoidAvoid
Cane SugarMinimizeMinimize
CantaloupeEnjoyEnjoy
CapersEnjoyEnjoy
Caraway SeedEnjoyEnjoy
CardamomEnjoyEnjoy
CardoonEnjoyEnjoy
CarobEnjoyEnjoy
CarrotsEnjoyEnjoy
CashewsEnjoyEnjoy
CassavaMinimizeMinimize
CatfishEnjoyEnjoy
CauliflowerMinimizeMinimize
Cayenne PepperEnjoyEnjoy
CeleriacEnjoyEnjoy
CeleryEnjoyEnjoy
Celery SeedEnjoyEnjoy
ChardEnjoyEnjoy
Chayote SquashEnjoyEnjoy
CherryEnjoyEnjoy
ChervilEnjoyEnjoy
Chia SeedsEnjoyEnjoy
Chicken (White Meat)EnjoyEnjoy
ChickpeasEnjoyEnjoy
Chili PowderEnjoyEnjoy
ClamsEnjoyEnjoy
CoffeeEnjoyEnjoy
Collard GreensEnjoyEnjoy
Crab (Pacific)EnjoyEnjoy
CranberryEnjoyEnjoy
CucumberEnjoyEnjoy
CuminEnjoyEnjoy
DatesMinimizeMinimize
DillEnjoyEnjoy
EelEnjoyEnjoy
Egg Whites (Chicken)MinimizeMinimize
ElderberryEnjoyEnjoy
EndiveEnjoyEnjoy
EscaroleEnjoyEnjoy
Flax SeedsEnjoyEnjoy
GarlicMinimizeMinimize
Goat MilkEnjoyEnjoy
Green TeaSuperfoodSuperfood
Halibut (Pacific)EnjoyEnjoy
HazelnutsEnjoyEnjoy
HerringEnjoyEnjoy
HoneyEnjoyEnjoy
Honeydew MelonEnjoyEnjoy
HorseradishMinimizeMinimize
JackfruitMinimizeMinimize
Jerusalem ArtichokeSuperfoodSuperfood
JicamaEnjoyEnjoy
KaleMinimizeMinimize
KefirEnjoyEnjoy
Kidney BeansEnjoyEnjoy
KimchiEnjoyEnjoy
KiwiSuperfoodSuperfood
KohlrabiMinimizeMinimize
LemonEnjoyEnjoy
LentilsEnjoyEnjoy
LettuceEnjoyEnjoy
LycheeMinimizeMinimize
Macademia NutsEnjoyEnjoy
MackerelEnjoyEnjoy
Maple SyrupMinimizeMinimize
MCT OilEnjoyEnjoy
MisoEnjoyEnjoy
MolassesMinimizeMinimize
MusselsEnjoyEnjoy
Mustard GreensAvoidAvoid
NattoEnjoyEnjoy
Navy BeansEnjoyEnjoy
OlivesEnjoyEnjoy
OnionMinimizeMinimize
OystersEnjoyEnjoy
ParsleyEnjoyEnjoy
PeachEnjoyEnjoy
PeanutsEnjoyEnjoy
PearEnjoyEnjoy
PeasEnjoyEnjoy
PersimmonEnjoyEnjoy
PickleEnjoyEnjoy
PineappleEnjoyEnjoy
PistachiosSuperfoodSuperfood
PlumEnjoyEnjoy
PumpkinEnjoyEnjoy
QuinoaEnjoyEnjoy
RadicchioEnjoyEnjoy
RadishEnjoyEnjoy
Ricotta Cottage CheeseEnjoyEnjoy
SalmonSuperfoodSuperfood
SaltMinimizeMinimize
Sheep MilkEnjoyEnjoy
Snap PeasEnjoyEnjoy
Soy MilkEnjoyEnjoy
SpinachSuperfoodSuperfood
Sprouted RyeEnjoyEnjoy
Sprouted WheatEnjoyEnjoy
StrawberryEnjoyEnjoy
Sunflower SeedsSuperfoodSuperfood
Sweet Potato or YamEnjoyEnjoy
TaroEnjoyEnjoy
TempehEnjoyEnjoy
TofuEnjoyEnjoy
TunaEnjoyEnjoy
Turkey (White Meat)EnjoyEnjoy
VealEnjoyEnjoy
WalnutsEnjoyEnjoy
White MushroomSuperfoodSuperfood
White RiceMinimizeMinimize
Winter SquashEnjoyEnjoy
YogurtEnjoyEnjoy

Foods whose recommendation has changed since the last test

Code 
viome_file_df %>%  filter(`Oct-22`!=`Oct-20`) %>% select(1:3)
FoodOct-22Oct-20
Alfalfa SproutsEnjoySuperfood
AppleEnjoyAvoid
ApricotEnjoySuperfood
AsparagusAvoidEnjoy
BananaEnjoyMinimize
BarleySuperfoodEnjoy
BeefAvoidEnjoy
Beef (Fatty)AvoidEnjoy
BeetsEnjoySuperfood
BlueberryAvoidEnjoy
Bone Broth (Fish)SuperfoodEnjoy
Bone Broth (Mammal)EnjoySuperfood
BoysenberryEnjoySuperfood
Brown RiceEnjoySuperfood
ButterMinimizeEnjoy
Caviar or RoeAvoidEnjoy
CheeseAvoidEnjoy
ChestnutsEnjoyMinimize
Chicken (Dark Meat)MinimizeEnjoy
Chicory RootEnjoySuperfood
CinnamonSuperfoodEnjoy
Coconut MeatAvoidEnjoy
Coconut MilkAvoidEnjoy
Coconut OilAvoidEnjoy
Coconut WaterEnjoyMinimize
CodAvoidEnjoy
CornEnjoyMinimize
CouscousEnjoyMinimize
Dandelion GreensEnjoySuperfood
Dragon FruitEnjoyMinimize
DuckAvoidEnjoy
Egg Yolk (Chicken)AvoidMinimize
EggplantEnjoyAvoid
Fennel BulbEnjoySuperfood
FigSuperfoodMinimize
GheeMinimizeEnjoy
GingerEnjoySuperfood
GoatAvoidEnjoy
Goji BerryEnjoyMinimize
GrapefruitAvoidSuperfood
GrapesSuperfoodMinimize
GuavaEnjoySuperfood
HaddockAvoidEnjoy
Heavy Cream (Cow Milk)AvoidEnjoy
Hemp HeartsEnjoyAvoid
HuckleberryEnjoySuperfood
LambAvoidSuperfood
LeekSuperfoodEnjoy
LobsterAvoidEnjoy
MangoEnjoyMinimize
MangosteenEnjoyMinimize
Mung Bean SproutsEnjoySuperfood
NectarineSuperfoodEnjoy
OatsMinimizeEnjoy
OkraEnjoyAvoid
OreganoEnjoySuperfood
PapayaEnjoySuperfood
PaprikaEnjoyAvoid
ParsnipEnjoyMinimize
PecansSuperfoodEnjoy
Pepino MelonEnjoyAvoid
Pinto BeansEnjoySuperfood
PlantainEnjoyMinimize
PorkAvoidMinimize
PotatoEnjoyAvoid
PrunesEnjoyMinimize
PummeloEnjoyMinimize
RaspberrySuperfoodEnjoy
RhubarbEnjoyAvoid
Rice MilkEnjoyMinimize
Rice NoodlesEnjoyMinimize
SardinesEnjoySuperfood
SauerkrautSuperfoodEnjoy
ScallopsAvoidEnjoy
Seaweed (Fresh)MinimizeEnjoy
Sheep CheeseAvoidEnjoy
ShrimpAvoidMinimize
SoybeanSuperfoodEnjoy
SprilinaMinimizeEnjoy
SteviaEnjoyMinimize
TomatoSuperfoodAvoid
Trout (Cold Water)SuperfoodEnjoy
Turkey (Dark Meat)MinimizeSuperfood
TurmericAvoidSuperfood
TurnipAvoidEnjoy
Water ChestnutsEnjoyMinimize
WatermelonAvoidEnjoy
Whole MilkAvoidEnjoy

Food recommendation counts per test

Code 
x <- rbind(viome_file_df %>% count(`Oct-22`)  %>% t()  %>% as_tibble() %>% slice(2),
      viome_file_df %>% count(`Oct-20`) %>% (t) %>% as_tibble() %>% slice(2))
Warning: The `x` argument of `as_tibble.matrix()` must have unique column names if
`.name_repair` is omitted as of tibble 2.0.0.
ℹ Using compatibility `.name_repair`.
Code 
names(x) <- c(c("Avoid","Minimize","Enjoy","Superfood"),"NA")
x$date <- c("Oct-22","Oct-20")
x <- x %>% relocate(1:5,.after = last_col())
x %>% knitr::kable()
date Avoid Minimize Enjoy Superfood NA
Oct-22 31 160 25 27 2
Oct-20 14 149 40 31 11

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