Read in the data from the .txt file, Since this file was difficult
to read a clean up was conducted.
gut <- readLines("~/Desktop/BIN512L-assignments/biosample_result (1).txt")
check <- grep("^Attributes:", gut)
attributes <- gut[(check + 1):length(gut)]
attributes <- trimws(attributes)
attributes <- strsplit(attributes, "\t")
Turned the cleaned up data into a dataframe, and continued to clean
up any unwanted data.
survey <- do.call(rbind, attributes)
survey <- as.data.frame(survey, stringsAsFactors = FALSE)
colnames(survey) <- c("variable", "value")
survey$variable <- sub("/", "", survey$variable)
survey <- survey[-(1:10), ]
survey2 <- as.data.frame(t(survey$value))
colnames(survey2) <- survey$variable
survey2
## acid_reflux acne_medication acne_medication_otc
## 1 i do not have this condition no no
## add_adhd age_cat alcohol_consumption
## 1 i do not have this condition 30s yes
## alcohol_frequency alcohol_types_beercider alcohol_types_red_wine
## 1 occasionally (1-2 times/week) TRUE TRUE
## alcohol_types_sour_beers alcohol_types_spiritshard_alcohol
## 1 TRUE TRUE
## alcohol_types_unspecified alcohol_types_white_wine
## 1 FALSE FALSE
## allergic_to_i_have_no_food_allergies_that_i_know_of allergic_to_peanuts
## 1 FALSE FALSE
## allergic_to_shellfish allergic_to_tree_nuts allergic_to_unspecified
## 1 FALSE FALSE FALSE
## alzheimers anonymized_name antibiotic_history
## 1 i do not have this condition X00185902 year
## appendix_removed artificial_sweeteners asd
## 1 no rarely (a few times/month) i do not have this condition
## autoimmune beet_frequency birth_year
## 1 i do not have this condition rarely (less than once/week) 1990
## bmi_cat bowel_movement_frequency
## 1 overweight one
## bowel_movement_quality breastmilk_formula_ensure
## 1 i tend to have normal formed stool - type 3 and 4 no
## cancer cardiovascular_disease cat
## 1 i do not have this condition i do not have this condition no
## cdiff chickenpox clinical_condition
## 1 i do not have this condition yes i do not have this condition
## collection_timestamp consume_animal_products_abx contraceptive
## 1 1.60803E+12 not sure no
## cosmetics_frequency country_of_birth country_residence covid_anxious
## 1 never china united states not at all
## covid_chronic_conditions_any_autoimmune_disease
## 1 FALSE
## covid_chronic_conditions_arthritis
## 1 FALSE
## covid_chronic_conditions_asthma_or_other_lung_problems
## 1 FALSE
## covid_chronic_conditions_atrial_fibrillation_or_atrial_flutter
## 1 FALSE
## covid_chronic_conditions_cancer
## 1 FALSE
## covid_chronic_conditions_chronic_obstructive_pulmonary_disease_copd
## 1 FALSE
## covid_chronic_conditions_congestive_heart_failure
## 1 FALSE
## covid_chronic_conditions_deep_vein_thrombosis
## 1 FALSE
## covid_chronic_conditions_diabetes_or_high_blood_sugar
## 1 FALSE
## covid_chronic_conditions_epilepsy_or_seizures
## 1 FALSE
## covid_chronic_conditions_frequent_or_very_bad_headaches
## 1 FALSE
## covid_chronic_conditions_heart_disease__myocardial_infarction
## 1 FALSE
## covid_chronic_conditions_heart_problems covid_chronic_conditions_hiv
## 1 FALSE FALSE
## covid_chronic_conditions_hypertension
## 1 FALSE
## covid_chronic_conditions_immune_disorder
## 1 FALSE
## covid_chronic_conditions_kidney_problems
## 1 FALSE
## covid_chronic_conditions_pulmonary_embolism
## 1 FALSE
## covid_chronic_conditions_seasonal_allergies
## 1 FALSE
## covid_chronic_conditions_serious_acne_or_skin_problems
## 1 FALSE
## covid_chronic_conditions_serious_stomach_or_bowel_problems
## 1 FALSE
## covid_chronic_conditions_stroke covid_chronic_conditions_unspecified
## 1 FALSE FALSE
## covid_depressed covid_difficulty_staying_asleep
## 1 not at all mild
## covid_family_members_fallen_ill_physically covid_family_members_hospitalized
## 1 FALSE FALSE
## covid_family_members_lost_job covid_family_members_none_of_the_above
## 1 FALSE FALSE
## covid_family_members_passed_away
## 1 FALSE
## covid_family_members_put_into_self_quarantine_with_symptoms
## 1 FALSE
## covid_family_members_put_into_self_quarantine_without_symptoms_eg_due_to_possible_exposure
## 1 FALSE
## covid_family_members_reduced_ability_to_earn_money
## 1 FALSE
## covid_family_members_unspecified covid_happened_to_you_fallen_ill_physically
## 1 FALSE FALSE
## covid_happened_to_you_hospitalized covid_happened_to_you_lost_job
## 1 FALSE FALSE
## covid_happened_to_you_none_of_the_above
## 1 FALSE
## covid_happened_to_you_put_into_self_quarantine_with_symptoms
## 1 FALSE
## covid_happened_to_you_put_into_self_quarantine_without_symptoms_eg_due_to_possible_exposure
## 1 FALSE
## covid_happened_to_you_reduced_ability_to_earn_money
## 1 FALSE
## covid_happened_to_you_unspecified covid_interest_pleasure
## 1 FALSE not at all
## covid_left_home covid_level_of_wellbeing covid_likely_exposure_no
## 1 several days per week very good TRUE
## covid_likely_exposure_unspecified
## 1 FALSE
## covid_likely_exposure_yes_someone_with_medical_diagnosis_but_no_test
## 1 FALSE
## covid_likely_exposure_yes_someone_with_positive_test
## 1 FALSE
## covid_likely_exposure_yes_someone_with_possible_symptoms_but_no_diagnosis_by_doctor
## 1 FALSE
## covid_patient_care covid_quality_of_life covid_rideshare
## 1 no barely noticeable yes
## covid_sleep_interference covid_sleep_pattern covid_suspected_positive
## 1 interfering satisfied no symptoms or signs
## covid_symptoms_chest_pain_or_tightness_in_chest covid_symptoms_cough
## 1 FALSE FALSE
## covid_symptoms_diarrhea covid_symptoms_fatigue covid_symptoms_fever
## 1 FALSE FALSE FALSE
## covid_symptoms_lack_of_appetitie covid_symptoms_loss_of_taste_or_smell
## 1 FALSE FALSE
## covid_symptoms_nausea covid_symptoms_shortness_of_breath
## 1 FALSE FALSE
## covid_symptoms_sore_throat covid_symptoms_unspecified covid_waking_up_early
## 1 FALSE FALSE mild
## covid_worried_sleep covid_worrying csection deodorant_use
## 1 a little worried not at all no i use deodorant
## diabetes diet_type dna_extracted dog dominant hand
## 1 i do not have this condition omnivore TRUE no i am right handed
## drinking_water_source drinks_per_session empo_1 empo_2
## 1 filtered 4-Mar host-associated animal
## empo_3 broad-scale environmental context
## 1 animal distal gut dense settlement biome
## local-scale environmental context environmental medium environmental package
## 1 human-associated habitat feces human-gut
## epilepsy_or_seizure_disorder exercise_frequency exercise_location
## 1 i do not have this condition regularly (3-5 times/week) both
## fed_as_infant fermented_consumed_beer
## 1 a mixture of breast milk and formula FALSE
## fermented_consumed_chicha fermented_consumed_cider
## 1 FALSE FALSE
## fermented_consumed_cottage_cheese fermented_consumed_fermented_beansmisonatto
## 1 FALSE FALSE
## fermented_consumed_fermented_breadsourdoughinjera
## 1 FALSE
## fermented_consumed_fermented_fish fermented_consumed_fermented_tofu
## 1 FALSE FALSE
## fermented_consumed_fish_sauce fermented_consumed_kefir_milk
## 1 FALSE FALSE
## fermented_consumed_kefir_water fermented_consumed_kimchi
## 1 FALSE FALSE
## fermented_consumed_kombucha fermented_consumed_mead
## 1 FALSE FALSE
## fermented_consumed_pickled_vegetables fermented_consumed_sauerkraut
## 1 FALSE FALSE
## fermented_consumed_sour_creamcreme_fraiche fermented_consumed_tempeh
## 1 FALSE FALSE
## fermented_consumed_unspecified fermented_consumed_wine
## 1 FALSE FALSE
## fermented_consumed_yogurtlassi fermented_plant_frequency
## 1 FALSE occasionally (1-2 times/week)
## fermented_produce_commercial_beer fermented_produce_commercial_chicha
## 1 FALSE FALSE
## fermented_produce_commercial_cider
## 1 FALSE
## fermented_produce_commercial_cottage_cheese
## 1 FALSE
## fermented_produce_commercial_fermented_beansmisonatto
## 1 FALSE
## fermented_produce_commercial_fermented_breadsourdoughinjera
## 1 FALSE
## fermented_produce_commercial_fermented_fish
## 1 FALSE
## fermented_produce_commercial_fermented_tofu
## 1 FALSE
## fermented_produce_commercial_fish_sauce
## 1 FALSE
## fermented_produce_commercial_kefir_milk
## 1 FALSE
## fermented_produce_commercial_kefir_water fermented_produce_commercial_kimchi
## 1 FALSE FALSE
## fermented_produce_commercial_kombucha fermented_produce_commercial_mead
## 1 FALSE FALSE
## fermented_produce_commercial_pickled_vegetables
## 1 FALSE
## fermented_produce_commercial_sauerkraut
## 1 FALSE
## fermented_produce_commercial_sour_creamcreme_fraiche
## 1 FALSE
## fermented_produce_commercial_tempeh fermented_produce_commercial_unspecified
## 1 FALSE FALSE
## fermented_produce_commercial_wine fermented_produce_commercial_yogurtlassi
## 1 FALSE FALSE
## fermented_produce_personal_beer fermented_produce_personal_chicha
## 1 FALSE FALSE
## fermented_produce_personal_cider fermented_produce_personal_cottage_cheese
## 1 FALSE FALSE
## fermented_produce_personal_fermented_beansmisonatto
## 1 FALSE
## fermented_produce_personal_fermented_breadsourdoughinjera
## 1 FALSE
## fermented_produce_personal_fermented_fish
## 1 FALSE
## fermented_produce_personal_fermented_tofu
## 1 FALSE
## fermented_produce_personal_fish_sauce fermented_produce_personal_kefir_milk
## 1 FALSE FALSE
## fermented_produce_personal_kefir_water fermented_produce_personal_kimchi
## 1 FALSE FALSE
## fermented_produce_personal_kombucha fermented_produce_personal_mead
## 1 FALSE FALSE
## fermented_produce_personal_pickled_vegetables
## 1 FALSE
## fermented_produce_personal_sauerkraut
## 1 FALSE
## fermented_produce_personal_sour_creamcreme_fraiche
## 1 FALSE
## fermented_produce_personal_tempeh fermented_produce_personal_unspecified
## 1 FALSE FALSE
## fermented_produce_personal_wine fermented_produce_personal_yogurtlassi
## 1 FALSE FALSE
## flossing_frequency flu_vaccine_date food_source_human_food
## 1 daily month FALSE
## food_source_pet_store_food food_source_unspecified food_source_wild_food
## 1 FALSE FALSE FALSE
## food_special_grain_free food_special_organic food_special_unspecified
## 1 FALSE FALSE FALSE
## frozen_dessert_frequency fruit_frequency
## 1 occasionally (1-2 times/week) occasionally (1-2 times/week)
## fungal_overgrowth gluten high_fat_red_meat_frequency
## 1 i do not have this condition no rarely (less than once/week)
## homecooked_meals_frequency host age host_age_normalized_years
## 1 daily 30.3 30.3
## host body habitat host body mass index host body product host tissue sampled
## 1 uberon:feces 29.2 uberon:feces uberon:feces
## host common name host height host_height_units
## 1 human 175 cm
## host subject id
## 1 ['82ac58c085b81ce5bdacb775910b2a31e40ed1fc8b00558b6f55f50d4f768f74af3333a8accd9fa196d2ba8a9ca63874a2493047029ce7b5b44816e03e1f052c']
## host taxonomy ID host_weight host_weight_units ibd
## 1 9606 89.35780316 kg i do not have this condition
## ibs kidney_disease lactose
## 1 i do not have this condition i do not have this condition no
## last_move
## 1 i have lived in my current state of residence for more than a year.
## last_travel level_of_education life stage liver_disease
## 1 1 year bachelor's degree adult i do not have this condition
## livingwith lung_disease meat_eggs_frequency mental_illness
## 1 yes i do not have this condition daily no
## mental_illness_type_anorexia_nervosa mental_illness_type_bipolar_disorder
## 1 FALSE FALSE
## mental_illness_type_bulimia_nervosa mental_illness_type_depression
## 1 FALSE FALSE
## mental_illness_type_ptsd_post_traumatic_stress_disorder
## 1 FALSE
## mental_illness_type_schizophrenia mental_illness_type_substance_abuse
## 1 FALSE FALSE
## mental_illness_type_unspecified migraine
## 1 FALSE i do not have this condition
## milk_cheese_frequency milk_substitute_frequency multivitamin
## 1 occasionally (1-2 times/week) rarely (less than once/week) no
## nail_biter non_food_allergies_beestings non_food_allergies_drug_eg_penicillin
## 1 no FALSE FALSE
## non_food_allergies_pet_dander non_food_allergies_poison_ivyoak
## 1 FALSE FALSE
## non_food_allergies_sun non_food_allergies_unspecified
## 1 FALSE FALSE
## olive_oil one_liter_of_water_a_day_frequency
## 1 rarely (less than once/week) daily
## other_supplement_frequency pets_other physical_specimen_location
## 1 no no ucsdmi
## physical_specimen_remaining pku
## 1 yes i do not have this condition
## plant_protein_frequency pool_frequency
## 1 occasionally (1-2 times/week) rarely (a few times/month)
## poultry_frequency pregnant prepared_meals_frequency
## 1 regularly (3-5 times/week) no regularly (3-5 times/week)
## probiotic_frequency public race
## 1 rarely (a few times/month) TRUE asian or pacific islander
## ready_to_eat_meals_frequency red_meat_frequency roommates_in_study
## 1 regularly (3-5 times/week) regularly (3-5 times/week) no
## salted_snacks_frequency sample name sample type
## 1 occasionally (1-2 times/week) qiita_sid_10317:10317.X00185902 stool
## scientific_name seafood_frequency seasonal_allergies sex
## 1 human gut metagenome regularly (3-5 times/week) no male
## sibo skin_condition sleep_duration
## 1 i do not have this condition i do not have this condition 7-8 hours
## smoking_frequency softener specialized_diet_exclude_dairy
## 1 rarely (a few times/month) yes FALSE
## specialized_diet_exclude_nightshades specialized_diet_exclude_refined_sugars
## 1 FALSE FALSE
## specialized_diet_fodmap specialized_diet_halaal
## 1 FALSE FALSE
## specialized_diet_i_do_not_eat_a_specialized_diet specialized_diet_kosher
## 1 TRUE FALSE
## specialized_diet_modified_paleo_diet
## 1 FALSE
## specialized_diet_other_restrictions_not_described_here
## 1 FALSE
## specialized_diet_paleo_diet_or_primal_diet specialized_diet_raw_food_diet
## 1 FALSE FALSE
## specialized_diet_unspecified
## 1 FALSE
## specialized_diet_weston_price_or_other_low_grain_low_processed_food_diet
## 1 FALSE
## sugar_sweetened_drink_frequency sugary_sweets_frequency
## 1 rarely (less than once/week) occasionally (1-2 times/week)
## teethbrushing_frequency thyroid tonsils_removed
## 1 daily i do not have this condition no
## types_of_plants vegetable_frequency vitamin_b_supplement_frequency
## 1 6 to 10 regularly (3-5 times/week) never
## vitamin_d_supplement_frequency vivid_dreams
## 1 never rarely (a few times/month)
## weight_change whole_eggs
## 1 increased more than 10 pounds rarely (less than once/week)
## whole_grain_frequency Description: american gut project stool sample
## 1 occasionally (1-2 times/week) Description: american gut project stool sample
## Accession: SAMEA112990854
## 1 ID: 34470136
colnames(survey2)
## [1] "acid_reflux"
## [2] "acne_medication"
## [3] "acne_medication_otc"
## [4] "add_adhd"
## [5] "age_cat"
## [6] "alcohol_consumption"
## [7] "alcohol_frequency"
## [8] "alcohol_types_beercider"
## [9] "alcohol_types_red_wine"
## [10] "alcohol_types_sour_beers"
## [11] "alcohol_types_spiritshard_alcohol"
## [12] "alcohol_types_unspecified"
## [13] "alcohol_types_white_wine"
## [14] "allergic_to_i_have_no_food_allergies_that_i_know_of"
## [15] "allergic_to_peanuts"
## [16] "allergic_to_shellfish"
## [17] "allergic_to_tree_nuts"
## [18] "allergic_to_unspecified"
## [19] "alzheimers"
## [20] "anonymized_name"
## [21] "antibiotic_history"
## [22] "appendix_removed"
## [23] "artificial_sweeteners"
## [24] "asd"
## [25] "autoimmune"
## [26] "beet_frequency"
## [27] "birth_year"
## [28] "bmi_cat"
## [29] "bowel_movement_frequency"
## [30] "bowel_movement_quality"
## [31] "breastmilk_formula_ensure"
## [32] "cancer"
## [33] "cardiovascular_disease"
## [34] "cat"
## [35] "cdiff"
## [36] "chickenpox"
## [37] "clinical_condition"
## [38] "collection_timestamp"
## [39] "consume_animal_products_abx"
## [40] "contraceptive"
## [41] "cosmetics_frequency"
## [42] "country_of_birth"
## [43] "country_residence"
## [44] "covid_anxious"
## [45] "covid_chronic_conditions_any_autoimmune_disease"
## [46] "covid_chronic_conditions_arthritis"
## [47] "covid_chronic_conditions_asthma_or_other_lung_problems"
## [48] "covid_chronic_conditions_atrial_fibrillation_or_atrial_flutter"
## [49] "covid_chronic_conditions_cancer"
## [50] "covid_chronic_conditions_chronic_obstructive_pulmonary_disease_copd"
## [51] "covid_chronic_conditions_congestive_heart_failure"
## [52] "covid_chronic_conditions_deep_vein_thrombosis"
## [53] "covid_chronic_conditions_diabetes_or_high_blood_sugar"
## [54] "covid_chronic_conditions_epilepsy_or_seizures"
## [55] "covid_chronic_conditions_frequent_or_very_bad_headaches"
## [56] "covid_chronic_conditions_heart_disease__myocardial_infarction"
## [57] "covid_chronic_conditions_heart_problems"
## [58] "covid_chronic_conditions_hiv"
## [59] "covid_chronic_conditions_hypertension"
## [60] "covid_chronic_conditions_immune_disorder"
## [61] "covid_chronic_conditions_kidney_problems"
## [62] "covid_chronic_conditions_pulmonary_embolism"
## [63] "covid_chronic_conditions_seasonal_allergies"
## [64] "covid_chronic_conditions_serious_acne_or_skin_problems"
## [65] "covid_chronic_conditions_serious_stomach_or_bowel_problems"
## [66] "covid_chronic_conditions_stroke"
## [67] "covid_chronic_conditions_unspecified"
## [68] "covid_depressed"
## [69] "covid_difficulty_staying_asleep"
## [70] "covid_family_members_fallen_ill_physically"
## [71] "covid_family_members_hospitalized"
## [72] "covid_family_members_lost_job"
## [73] "covid_family_members_none_of_the_above"
## [74] "covid_family_members_passed_away"
## [75] "covid_family_members_put_into_self_quarantine_with_symptoms"
## [76] "covid_family_members_put_into_self_quarantine_without_symptoms_eg_due_to_possible_exposure"
## [77] "covid_family_members_reduced_ability_to_earn_money"
## [78] "covid_family_members_unspecified"
## [79] "covid_happened_to_you_fallen_ill_physically"
## [80] "covid_happened_to_you_hospitalized"
## [81] "covid_happened_to_you_lost_job"
## [82] "covid_happened_to_you_none_of_the_above"
## [83] "covid_happened_to_you_put_into_self_quarantine_with_symptoms"
## [84] "covid_happened_to_you_put_into_self_quarantine_without_symptoms_eg_due_to_possible_exposure"
## [85] "covid_happened_to_you_reduced_ability_to_earn_money"
## [86] "covid_happened_to_you_unspecified"
## [87] "covid_interest_pleasure"
## [88] "covid_left_home"
## [89] "covid_level_of_wellbeing"
## [90] "covid_likely_exposure_no"
## [91] "covid_likely_exposure_unspecified"
## [92] "covid_likely_exposure_yes_someone_with_medical_diagnosis_but_no_test"
## [93] "covid_likely_exposure_yes_someone_with_positive_test"
## [94] "covid_likely_exposure_yes_someone_with_possible_symptoms_but_no_diagnosis_by_doctor"
## [95] "covid_patient_care"
## [96] "covid_quality_of_life"
## [97] "covid_rideshare"
## [98] "covid_sleep_interference"
## [99] "covid_sleep_pattern"
## [100] "covid_suspected_positive"
## [101] "covid_symptoms_chest_pain_or_tightness_in_chest"
## [102] "covid_symptoms_cough"
## [103] "covid_symptoms_diarrhea"
## [104] "covid_symptoms_fatigue"
## [105] "covid_symptoms_fever"
## [106] "covid_symptoms_lack_of_appetitie"
## [107] "covid_symptoms_loss_of_taste_or_smell"
## [108] "covid_symptoms_nausea"
## [109] "covid_symptoms_shortness_of_breath"
## [110] "covid_symptoms_sore_throat"
## [111] "covid_symptoms_unspecified"
## [112] "covid_waking_up_early"
## [113] "covid_worried_sleep"
## [114] "covid_worrying"
## [115] "csection"
## [116] "deodorant_use"
## [117] "diabetes"
## [118] "diet_type"
## [119] "dna_extracted"
## [120] "dog"
## [121] "dominant hand"
## [122] "drinking_water_source"
## [123] "drinks_per_session"
## [124] "empo_1"
## [125] "empo_2"
## [126] "empo_3"
## [127] "broad-scale environmental context"
## [128] "local-scale environmental context"
## [129] "environmental medium"
## [130] "environmental package"
## [131] "epilepsy_or_seizure_disorder"
## [132] "exercise_frequency"
## [133] "exercise_location"
## [134] "fed_as_infant"
## [135] "fermented_consumed_beer"
## [136] "fermented_consumed_chicha"
## [137] "fermented_consumed_cider"
## [138] "fermented_consumed_cottage_cheese"
## [139] "fermented_consumed_fermented_beansmisonatto"
## [140] "fermented_consumed_fermented_breadsourdoughinjera"
## [141] "fermented_consumed_fermented_fish"
## [142] "fermented_consumed_fermented_tofu"
## [143] "fermented_consumed_fish_sauce"
## [144] "fermented_consumed_kefir_milk"
## [145] "fermented_consumed_kefir_water"
## [146] "fermented_consumed_kimchi"
## [147] "fermented_consumed_kombucha"
## [148] "fermented_consumed_mead"
## [149] "fermented_consumed_pickled_vegetables"
## [150] "fermented_consumed_sauerkraut"
## [151] "fermented_consumed_sour_creamcreme_fraiche"
## [152] "fermented_consumed_tempeh"
## [153] "fermented_consumed_unspecified"
## [154] "fermented_consumed_wine"
## [155] "fermented_consumed_yogurtlassi"
## [156] "fermented_plant_frequency"
## [157] "fermented_produce_commercial_beer"
## [158] "fermented_produce_commercial_chicha"
## [159] "fermented_produce_commercial_cider"
## [160] "fermented_produce_commercial_cottage_cheese"
## [161] "fermented_produce_commercial_fermented_beansmisonatto"
## [162] "fermented_produce_commercial_fermented_breadsourdoughinjera"
## [163] "fermented_produce_commercial_fermented_fish"
## [164] "fermented_produce_commercial_fermented_tofu"
## [165] "fermented_produce_commercial_fish_sauce"
## [166] "fermented_produce_commercial_kefir_milk"
## [167] "fermented_produce_commercial_kefir_water"
## [168] "fermented_produce_commercial_kimchi"
## [169] "fermented_produce_commercial_kombucha"
## [170] "fermented_produce_commercial_mead"
## [171] "fermented_produce_commercial_pickled_vegetables"
## [172] "fermented_produce_commercial_sauerkraut"
## [173] "fermented_produce_commercial_sour_creamcreme_fraiche"
## [174] "fermented_produce_commercial_tempeh"
## [175] "fermented_produce_commercial_unspecified"
## [176] "fermented_produce_commercial_wine"
## [177] "fermented_produce_commercial_yogurtlassi"
## [178] "fermented_produce_personal_beer"
## [179] "fermented_produce_personal_chicha"
## [180] "fermented_produce_personal_cider"
## [181] "fermented_produce_personal_cottage_cheese"
## [182] "fermented_produce_personal_fermented_beansmisonatto"
## [183] "fermented_produce_personal_fermented_breadsourdoughinjera"
## [184] "fermented_produce_personal_fermented_fish"
## [185] "fermented_produce_personal_fermented_tofu"
## [186] "fermented_produce_personal_fish_sauce"
## [187] "fermented_produce_personal_kefir_milk"
## [188] "fermented_produce_personal_kefir_water"
## [189] "fermented_produce_personal_kimchi"
## [190] "fermented_produce_personal_kombucha"
## [191] "fermented_produce_personal_mead"
## [192] "fermented_produce_personal_pickled_vegetables"
## [193] "fermented_produce_personal_sauerkraut"
## [194] "fermented_produce_personal_sour_creamcreme_fraiche"
## [195] "fermented_produce_personal_tempeh"
## [196] "fermented_produce_personal_unspecified"
## [197] "fermented_produce_personal_wine"
## [198] "fermented_produce_personal_yogurtlassi"
## [199] "flossing_frequency"
## [200] "flu_vaccine_date"
## [201] "food_source_human_food"
## [202] "food_source_pet_store_food"
## [203] "food_source_unspecified"
## [204] "food_source_wild_food"
## [205] "food_special_grain_free"
## [206] "food_special_organic"
## [207] "food_special_unspecified"
## [208] "frozen_dessert_frequency"
## [209] "fruit_frequency"
## [210] "fungal_overgrowth"
## [211] "gluten"
## [212] "high_fat_red_meat_frequency"
## [213] "homecooked_meals_frequency"
## [214] "host age"
## [215] "host_age_normalized_years"
## [216] "host body habitat"
## [217] "host body mass index"
## [218] "host body product"
## [219] "host tissue sampled"
## [220] "host common name"
## [221] "host height"
## [222] "host_height_units"
## [223] "host subject id"
## [224] "host taxonomy ID"
## [225] "host_weight"
## [226] "host_weight_units"
## [227] "ibd"
## [228] "ibs"
## [229] "kidney_disease"
## [230] "lactose"
## [231] "last_move"
## [232] "last_travel"
## [233] "level_of_education"
## [234] "life stage"
## [235] "liver_disease"
## [236] "livingwith"
## [237] "lung_disease"
## [238] "meat_eggs_frequency"
## [239] "mental_illness"
## [240] "mental_illness_type_anorexia_nervosa"
## [241] "mental_illness_type_bipolar_disorder"
## [242] "mental_illness_type_bulimia_nervosa"
## [243] "mental_illness_type_depression"
## [244] "mental_illness_type_ptsd_post_traumatic_stress_disorder"
## [245] "mental_illness_type_schizophrenia"
## [246] "mental_illness_type_substance_abuse"
## [247] "mental_illness_type_unspecified"
## [248] "migraine"
## [249] "milk_cheese_frequency"
## [250] "milk_substitute_frequency"
## [251] "multivitamin"
## [252] "nail_biter"
## [253] "non_food_allergies_beestings"
## [254] "non_food_allergies_drug_eg_penicillin"
## [255] "non_food_allergies_pet_dander"
## [256] "non_food_allergies_poison_ivyoak"
## [257] "non_food_allergies_sun"
## [258] "non_food_allergies_unspecified"
## [259] "olive_oil"
## [260] "one_liter_of_water_a_day_frequency"
## [261] "other_supplement_frequency"
## [262] "pets_other"
## [263] "physical_specimen_location"
## [264] "physical_specimen_remaining"
## [265] "pku"
## [266] "plant_protein_frequency"
## [267] "pool_frequency"
## [268] "poultry_frequency"
## [269] "pregnant"
## [270] "prepared_meals_frequency"
## [271] "probiotic_frequency"
## [272] "public"
## [273] "race"
## [274] "ready_to_eat_meals_frequency"
## [275] "red_meat_frequency"
## [276] "roommates_in_study"
## [277] "salted_snacks_frequency"
## [278] "sample name"
## [279] "sample type"
## [280] "scientific_name"
## [281] "seafood_frequency"
## [282] "seasonal_allergies"
## [283] "sex"
## [284] "sibo"
## [285] "skin_condition"
## [286] "sleep_duration"
## [287] "smoking_frequency"
## [288] "softener"
## [289] "specialized_diet_exclude_dairy"
## [290] "specialized_diet_exclude_nightshades"
## [291] "specialized_diet_exclude_refined_sugars"
## [292] "specialized_diet_fodmap"
## [293] "specialized_diet_halaal"
## [294] "specialized_diet_i_do_not_eat_a_specialized_diet"
## [295] "specialized_diet_kosher"
## [296] "specialized_diet_modified_paleo_diet"
## [297] "specialized_diet_other_restrictions_not_described_here"
## [298] "specialized_diet_paleo_diet_or_primal_diet"
## [299] "specialized_diet_raw_food_diet"
## [300] "specialized_diet_unspecified"
## [301] "specialized_diet_weston_price_or_other_low_grain_low_processed_food_diet"
## [302] "sugar_sweetened_drink_frequency"
## [303] "sugary_sweets_frequency"
## [304] "teethbrushing_frequency"
## [305] "thyroid"
## [306] "tonsils_removed"
## [307] "types_of_plants"
## [308] "vegetable_frequency"
## [309] "vitamin_b_supplement_frequency"
## [310] "vitamin_d_supplement_frequency"
## [311] "vivid_dreams"
## [312] "weight_change"
## [313] "whole_eggs"
## [314] "whole_grain_frequency"
## [315] "Description:"
## [316] "american gut project stool sample"
## [317] "Accession: SAMEA112990854"
Choose which data to keep and which data to omit.
keep <- c("age_cat", "bmi_cat", "bowel_movement_frequency",
"bowel_movement_quality", "antibiotic_history",
"diet_type", "exercise_frequency", "probiotic_frequency",
"fruit_frequency", "vegetable_frequency", "meat_eggs_frequency",
"milk_cheese_frequency", "smoking_frequency", "sex",
"sample type")
survey_final <- survey2[, keep]
Created a final csv file of the cleaned/titled data.
write.csv(survey_final, "American_Gut_cleaned.csv", row.names = FALSE)
head(survey_final)
## age_cat bmi_cat bowel_movement_frequency
## 1 30s overweight one
## bowel_movement_quality antibiotic_history
## 1 i tend to have normal formed stool - type 3 and 4 year
## diet_type exercise_frequency probiotic_frequency
## 1 omnivore regularly (3-5 times/week) rarely (a few times/month)
## fruit_frequency vegetable_frequency meat_eggs_frequency
## 1 occasionally (1-2 times/week) regularly (3-5 times/week) daily
## milk_cheese_frequency smoking_frequency sex sample type
## 1 occasionally (1-2 times/week) rarely (a few times/month) male stool