RDAmaker.R

##### RDA MAKER ####
# preps dataframe for use in RShiny app #
library(tidyverse) #General everything

source("functions.R") # necessary for surface area, volume calculations

# Load finalized dataset.

human <- read_csv("Humans_Clean_Final.csv", guess_max = 10000) %>% 
  #make new variables with names to match aquatic
  mutate(particle.volume.um3 = particle.volume.um) %>%  
  mutate(size.length.um.used.for.conversions = size.length.um.used.for.conversion) %>%   
  mutate(dose.particles.mL.master = dose.particles.L.master/1000)

#### Welcome Setup ####

# All text inputs below.


#### Exploration Human Setup ####

human_v1 <- human %>% # start with original data set
  #full dataset filters.
  mutate(effect_h_f = factor(case_when(effect == "Y" ~ "Yes",
                                       effect == "N" ~ "No"),
                             levels = c("No", "Yes"))) %>% #Note: this drops effect metric data which is designated as 'NA' for effect
  
  # removing NAs to make data set nicer
  replace_na(list(size.category = 0, shape = "Not Reported", polymer = "Not Reported", exposure.route = "Not Applicable", life.stage = "Not Reported")) 

human_setup <- human_v1 %>% # start with original data set
  mutate(size_h_f = factor(case_when(
    size.category == 1 ~ "1nm < 100nm",
    size.category == 2 ~ "100nm < 1µm",
    size.category == 3 ~ "1µm < 100µm",
    size.category == 4 ~ "100µm < 1mm",
    size.category == 0 ~ "Not Reported"), 
    levels = c("1nm < 100nm", "100nm < 1µm", "1µm < 100µm", "100µm < 1mm", "Not Reported"))) %>% #Renames for widget
  mutate(shape_h_f = factor(case_when(
    shape == "fragment" ~ "Fragment",
    shape == "sphere" ~ "Sphere",
    shape == "Not Reported" ~ "Not Reported"),
    levels = c("Fragment", "Sphere", "Not Reported"))) %>% #Renames for widget
  mutate(poly_h_f = factor(case_when(
    polymer == "PA" ~ "Polyamide",
    polymer == "PE" ~ "Polyethylene",
    polymer == "PMMA" ~ "Polymethylmethacrylate",
    polymer == "PP" ~ "Polypropylene",
    polymer == "PS" ~ "Polystyrene",
    polymer == "PUR" ~ "Polyurathane",
    polymer == "PVC" ~ "Polyvinylchloride",
    polymer == "TR" ~ "Tire Rubber",
    polymer == "Not Reported" ~ "Not Reported"))) %>% #Renames for widget
  mutate(lvl1_h_f = factor(case_when(lvl1 == "alimentary.excretory" ~ "Alimentary, Excretory",
                                     lvl1 == "behavior.sense.neuro" ~ "Behavioral, Sensory, Neurological",
                                     lvl1 == "cell.growth.proliferation" ~ "Cell Growth and Proliferation",
                                     lvl1 == "cell.morphology.structure" ~ "Cell Morphology and Structure",
                                     lvl1 == "circulatory" ~ "Circulatory",
                                     lvl1 == "cytotoxicity" ~ "Cytotoxicity",
                                     lvl1 == "endocrine.signaling" ~ "Endocrine Signaling",
                                     lvl1 == "fitness" ~ "Fitness",
                                     lvl1 == "immune" ~ "Immune",
                                     lvl1 == "metabolism" ~ "Metabolism",
                                     lvl1 == "microbiome" ~ "Microbiome",
                                     lvl1 == "respiratory" ~ "Respiratory",
                                     lvl1 == "stress" ~ "Stress"))) %>% #Renames for widget
  # Level 2 Data tidying
  mutate(lvl2_h_f = factor(case_when(lvl2 == "actinobacteria" ~ "Actinobacteria",
                                     lvl2 == "amino.acid.metabolism" ~ "Amino Acid Metabolism",
                                     lvl2 == "apoptosis.cell.cycle"~"Apoptosis and Cell Cycle",
                                     lvl2 == "anxiety" ~ "Anxiety",
                                     lvl2 == "bacteroidetes"~ "Bacteriodetes",
                                     lvl2 == "bile.acid" ~ "Bile Acid",
                                     lvl2 == "blood.gen" ~ "Blood",
                                     lvl2 == "body.condition"~"Body Condition",
                                     lvl2 == "brain.histo" ~ "Brain Histological Abnormalities",
                                     lvl2 == "carb.metabolism"~"Carb Metabolism",
                                     lvl2 == "cell.aggregation"~"Cell Aggregation",
                                     lvl2 == "cell.membrane"~"Cell Membrane",
                                     lvl2 == "circulatory"~"Circulatory",
                                     lvl2 == "complement"~"Complement",
                                     lvl2 == "coordination"~"Coordination",
                                     lvl2 == "cytotoxicity"~"Cytotoxicity",
                                     lvl2 == "development" ~ "Development",
                                     lvl2 == "digestive.tract.histo"~"Digestive Tract Histological Abnormalities",
                                     lvl2 == "diversity"~ "Diversity",
                                     lvl2 == "dna.damage" ~ "DNA Damage",
                                     lvl2 == "energy.metabolism" ~ "Energy Metabolism",
                                     lvl2 == "exploration" ~ "Exploration",
                                     lvl2 == "feeding" ~ "Feeding", 
                                     lvl2 == "firmicutes"~ "Firmicutes",
                                     lvl2 == "gen.stress" ~ "General Stress",
                                     lvl2 == "heart.tissue" ~ "Heart Tissue",
                                     lvl2 == "hemolysis" ~ "Hemolysis",
                                     lvl2 == "immune.cells"~"Immune Cells",
                                     lvl2 == "immune.other"~"Immune Other ",
                                     lvl2 == "inflammation" ~ "Inflammation",
                                     lvl2 == "intestinal.inflammation" ~ "Intestinal Inflammation",
                                     lvl2 == "intestinal.ion.transport" ~ "Intestinal Ion Transport",
                                     lvl2 == "intestinal.mucus.secretion" ~ "Intestinal Mucus Secretion",
                                     lvl2 == "intestinal.permeability" ~ "Intestinal Permeability",
                                     lvl2 == "intestinal.tight.junctions" ~ "Intestinal Tight Junctions",
                                     lvl2 == "kidney.histo"~"Kidney Histological abnormalities",
                                     lvl2 == "lipid.metabolism"~"Lipid Metabolism",
                                     lvl2 == "liver.histo"~"Liver Histological Abnormalities",
                                     lvl2 == "liver.kidney.products" ~ "Liver & Kidney Products",
                                     lvl2 == "locomotion"~"Locomotion",
                                     lvl2 == "lungs.histo" ~ "Lung Histological Abnormalities",
                                     lvl2 == "lysosome" ~ "Lyosome",
                                     lvl2 == "melainabacteria" ~ "Melainabacteria",
                                     lvl2 == "morphology.gen" ~ "General Morphology",
                                     lvl2 == "mortality"~"Mortality",
                                     lvl2 == "nervous.system"~"Nervous System",
                                     lvl2 == "nucleus" ~ "Nucleus",
                                     lvl2 == "oxidative.stress"~"Oxidative Stress",
                                     lvl2 == "patescibacteria" ~ "Patescibacteria",
                                     lvl2 == "permeability" ~ "Permeability",
                                     lvl2 == "predator.avoidance" ~ "Predator Avoidance",
                                     lvl2 == "proliferation" ~ "Proliferation",
                                     lvl2 == "proteobacteria"~"Protebacteria",
                                     lvl2 == "reproduction" ~ "Reproduction",
                                     lvl2 == "reproductive.tissue" ~ "Reproductive Tissues",
                                     lvl2 == "reproductive.endocrine.signaling" ~ "Reproductive Endocrine Signaling",
                                     lvl2 == "respiration"~"Respiration",
                                     lvl2 == "spleen.histo" ~ "Spleen Histological Abnormalities",
                                     lvl2 == "tenericutes" ~ "Tenericutes",
                                     lvl2 == "thyroid" ~ "Thyroid",
                                     lvl2 == "verrucomicrobiae" ~ "Verrucomicrobiae",
                                     lvl2 == "vision" ~ "Vision"))) %>% #Renames for widget
  #Level 3 Data Tidying
  mutate(lvl3_h_f = factor(case_when(lvl3 == "3hydroxyhexadecanoylcarnitine.con" ~ "3 Hydroxyhexadecanoylcarnitine Concentration",
                                     lvl3 == "3hydroxyhexadecenoylcarnitine.con" ~ "3 Hydroxyhexadecenoylcarnitine Concentration",
                                     lvl3 == "3hydroxyoctadecenoylcarnitine.con" ~ "3 Hydroxyoctadecenoylcarnitine Concentration",
                                     lvl3 == "3hydroxytetradecanoylcarnitine.con" ~ "3 Hydroxytetradecanoylcarnitine Concentration",
                                     lvl3 == "a.proteobacteria.genomicdna" ~ "a Proteobacteria Genomic DNA",
                                     lvl3 == "aat.proteinexpression" ~ "aat protein expression",
                                     lvl3 == "abcb11.mrnaexpression" ~ "abcb11 mRNA expression",
                                     lvl3 == "abp.mrnaexpression" ~ "abp mRNA expression",
                                     lvl3 == "acc.mrnaexpression" ~ "acc mRNA expression",
                                     lvl3 == "acetylcarnitine.con" ~ "Acetylcarnitine Concentration",
                                     lvl3 == "ache.activity" ~ "AchE Activity",
                                     lvl3 == "acl.mrnaexpression" ~ "acl mRNA expression",
                                     lvl3 == "acox.mrnaexpression" ~ "acox mRNA expression",
                                     lvl3 == "actinobacteria.genomicdna" ~ "Actinobacteria Genomic DNA",
                                     lvl3 == "adipylcarnite.con" ~ "Adipylcarnite Concentration",
                                     lvl3 == "akkermansia.geonmicdna" ~ "Akkermansia Genomic DNA",
                                     lvl3 == "alanine.con" ~ "Alanine Concentration",
                                     lvl3 == "alpha.smooth.muscle.actin.protein.expression.reproduction" ~ "Alpha Smooth Muscle Actin Protein Expression (Reproductive Tissue)",
                                     lvl3 == "alpha.smooth.muscle.actin.protein.expression.cardio" ~ "Alpha Smooth Muscle Actin Protein Expression (Cardiovascular Tissue)",
                                     lvl3 == "alt.con" ~ "Alanine Aminotransferase Concentration",
                                     lvl3 == "alternation" ~ "Alternation",
                                     lvl3 == "annexinv" ~ "Annexin V",
                                     lvl3 == "annexinv.binding" ~ "Annexin V Binding",
                                     lvl3 == "ano1.mrnaexpression" ~ "ano1 mRNA expression",
                                     lvl3 == "anti.mullerian.hormone.con" ~ "Anti Mullerian Hormone Concentration",
                                     lvl3 == "ap1.proteinexpression" ~ "ap1 protein expression",
                                     lvl3 == "apoptosis" ~ "Apoptosis",
                                     lvl3 == "arginine.con" ~ "Arginine Concentration",
                                     lvl3 == "asc.proteinexpression" ~ "ASC protein expression",
                                     lvl3 == "ast.con" ~ "Aspartate Transaminase Concentration",
                                     lvl3 == "atp.con" ~ "ATP Concentration",
                                     lvl3 == "bcatenin.proteinexpression.reproduction" ~ "Beta Catenin Protein Expression (Reproductive Tissue)",
                                     lvl3 == "p-bcatenin.proteinexpression.reproduction" ~ "Phosphorylated Beta Catenin Protein Expression (Reproductive Tissue)",
                                     lvl3 == "bcatenin.proteinexpression.cardio" ~ "Beta Catenin Protein Expression (Cardiovascular Tissue)",
                                     lvl3 == "p-bcatenin.proteinexpression.cardio" ~ "Phosphorylated Beta Catenin Protein Expression (Cardiovascular Tissue)",
                                     lvl3 == "bcl2.proteinexpression" ~ "BCL2 Protein Expression",
                                     lvl3 == "blood.testis.barrier.disruption" ~ "Blood Testes Barrier Disruption",
                                     lvl3 == "b.cells" ~ "B Cells",
                                     lvl3 == "b.proteobacteria.genomicdna" ~ "B Proteobacteria Genomic DNA",
                                     lvl3 == "bacteriodetes.genomicdna" ~ "Bacteriodetes Genomic DNA",
                                     lvl3 == "ballooning.degeneration" ~ "Ballooning Degeneration",
                                     lvl3 == "basophil.count" ~ "Basophil Count",
                                     lvl3 == "bax.bcl2.proteinexpression" ~ "BAX/BCL2 protein expression",
                                     lvl3 == "bax.proteinexpression" ~ "BAX protein expression",
                                     lvl3 == "beam.crossings" ~ "Beam Crossings",
                                     lvl3 == "bgalactosidase.staining" ~ "B Galactosidase Staining",
                                     lvl3 == "bileacid.con" ~ "Bile Acid Concentration",
                                     lvl3 == "blautia.genomicdna" ~ "Blautia Genomic DNA",
                                     lvl3 == "body.weight" ~ "Body Weight",
                                     lvl3 == "brain.histo" ~ "Brain Histology",
                                     lvl3 == "butyrylcarnitine.con" ~ "Butyrylcarnitine Concentration",
                                     lvl3 == "c0.c16.c18.ratio" ~ "C0/C16/C18 Ratio",
                                     lvl3 == "callogen.proteinexpression" ~ "Callogen Protein Expression",
                                     lvl3 == "callogen3.proteinexpression" ~ "Callogen 3 Protein Expression",
                                     lvl3 == "caspase.activation" ~ "Caspase Activation",
                                     lvl3 == "casp3.con" ~ "Caspase 3 Concentration",
                                     lvl3 == "caspase3.activity" ~ "Caspase 3 Activity",
                                     lvl3 == "caspase1.mrnaexpression" ~ "Caspase 1 mRNA expression",
                                     lvl3 == "caspase1.proteinexpression" ~ "Caspase 1 protein expression",
                                     lvl3 == "caspase3.proteinexpression" ~ "Caspase 3 protein expression",
                                     lvl3 == "caspase8.proteinexpression" ~ "Caspase 8 protein expression",
                                     lvl3 == "caspase9.proteinexpression" ~ "Caspase 9 protein expression",
                                     lvl3 == "cat.activity" ~ "Catalase Activity",
                                     lvl3 == "ccl22.mrnaexpression" ~ "ccl22 mRNA expression",
                                     lvl3 == "ccnd.mrnaexpression" ~ "ccnd mRNA expression",
                                     lvl3 == "ccnd1.mrnaexpression" ~ "ccnd1 mRNA expression",
                                     lvl3 == "ccne.mrnaexpresion" ~ "ccne mRNA expression",
                                     lvl3 == "ccne1.mrnaexpression" ~ "ccne1 mRNA expression",
                                     lvl3 == "cd11b-.cd11c+.ratio" ~ "CD11b-/CD11c+ Ratio",
                                     lvl3 == "cd11b.proteinexpression" ~ "CD11b protein expression",
                                     lvl3 == "cd11b+.cd11c-.ratio" ~ "CD11b+/CD11c- Ratio",
                                     lvl3 == "cd11b+.cd11c+.ratio" ~ "CD11b+/CD11c+ Ratio",
                                     lvl3 == "cd14.proteinexpression" ~ "CD14 protein expression",
                                     lvl3 == "cd163.proteinexpression" ~ "CD163 protein expression",
                                     lvl3 == "cd200r.proteinexpression" ~ "CD200R protein expression",
                                     lvl3 == "cd206.mrnaexpression" ~ "CD 206 mRNA expression",
                                     lvl3 == "cd209.mrnaexpression" ~ "CD209 mRNA expression",
                                     lvl3 == "cd4+.cd8+.ratio" ~ "CD4+/CD8+ Ratio",
                                     lvl3 == "cd45.proteinexpression" ~ "CD45 protein expression",
                                     lvl3 == "cd61.proteinexpression" ~ "CD61 protein expression",
                                     lvl3 == "cd86.proteinexpression" ~ "CD86 protein expression",
                                     lvl3 == "cdk4.mrnaexpression" ~ "CDK4 mRNA expression",
                                     lvl3 == "cell.adhesion" ~ "Cell Adhesion",
                                     lvl3 == "cell.aggregation.size" ~ "Cell Aggregate Size",
                                     lvl3 == "cell.aggregation.small" ~ "Cell Aggregation (Small)",
                                     lvl3 == "cell.cycle" ~ "Cell Cycle",
                                     lvl3 == "cell.cycle.g0g1" ~ "Cell Cycle G0G1 Phase",
                                     lvl3 == "cell.cycle.g2m" ~ "Cell Cycle G2M Phase",
                                     lvl3 == "cell.cycle.s" ~ "Cell Cycle S Phase",
                                     lvl3 == "cell.cycle.subg0g1" ~ "Cell Cycle Sub G0G1 Phase",
                                     lvl3 == "cell.membrane.dam" ~ "Cell Membrane Damage",
                                     lvl3 == "cell.morphology" ~ "Cell Morphology",
                                     lvl3 == "cellular.hemoglobin.con" ~ "Cellular Hemoglobin Concentration",
                                     lvl3 == "cftr.mrnaexpression" ~ "cftr mRNA expression",
                                     lvl3 == "cftr.proteinexpression" ~ "cftr protein expression",
                                     lvl3 == "chao.diversity.index" ~ "Chao Diversity Index",
                                     lvl3 == "cholesterol.con" ~ "Cholesterol Concentration",
                                     lvl3 == "chrebp.mrnaexpression" ~ "chrebp mRNA expression",
                                     lvl3 == "citrulline.con" ~ "Citrulline Concentration",
                                     lvl3 == "ckmb.con" ~ "Creatine Kinase Myocardial Band",
                                     lvl3 == "claudin11.proteinexpression" ~ "claudin11 protein expression",
                                     lvl3 == "cleaved.caspase1.proteinexpression" ~ "Cleaved Caspase 1 protein expression",
                                     lvl3 == "cleaved.caspase3.proteinexpression" ~ "Cleaved Caspase 3 protein expression",
                                     lvl3 == "cleaved.gsdmd.proteinexpression" ~ "Cleaved Gasdermin D protein expression",
                                     lvl3 == "claudin1.mrnaexpression" ~ "claudin1 mRNA expression",
                                     lvl3 == "clostridiales.genomicdna" ~ "Clostridiales Genomic DNA",
                                     lvl3 == "cluster.score" ~ "Cluster Score",
                                     lvl3 == "cmyc.mrnaexpression" ~ "cmyc mRNA expression",
                                     lvl3 == "coar.mrnaexpression" ~ "coar mRNA expression",
                                     lvl3 == "coas.mrnaexpression" ~ "coas mRNA expression",
                                     lvl3 == "collagenous.fiber.staining" ~ "Collagenous Fiber Staining",
                                     lvl3 == "complement.activation.bb" ~ "Complement Activation Bb",
                                     lvl3 == "complement.activation.c3a" ~ "Complement Activation C3a",
                                     lvl3 == "complement.activation.c4d" ~ "Complement Activation C4d",
                                     lvl3 == "complement.activation.sc5b9" ~ "Complement Activation sc5b9",
                                     lvl3 == "complement.activiation.c5b9" ~ "Complement Activation c5b9",
                                     lvl3 == "complement.activiation.ic3b" ~ "Complement Activation ic3b",
                                     lvl3 == "connexin43.proteinexpression" ~ "Connexin 43 protein expression",
                                     lvl3 == "ctnl.con" ~ "Cardiac Troponin I",
                                     lvl3 == "cpt1a.mrnaexpression" ~ "cpt1a mRNA expression",
                                     lvl3 == "creatine.con" ~ "Creatine Concentration",
                                     lvl3 == "cs.mrnaexpression" ~ "cs mRNA expression",
                                     lvl3 == "cxcl10.con" ~ "cxc10 concentration",
                                     lvl3 == "cxcl2.mrnaexpression" ~ "cxcl2 mRNA expression",
                                     lvl3 == "cxcl10.mrnaexpression" ~ "cxc10 mRNA expression",
                                     lvl3 == "cyclind.proteinexpression" ~ "Cylin D protein expression",
                                     lvl3 == "cyclind1.mrnaexpression" ~ "cyclin d1 mRNA expression",
                                     lvl3 == "cyclind3.proteinexpression" ~ "cyclin d3 protein expression",
                                     lvl3 == "cycline.proteinexpression" ~ "cyclin e protein expression",
                                     lvl3 == "cyp27a1.mrnaexpression" ~ "cyp27a1 mRNA expression",
                                     lvl3 == "cyp7a1.mrnaexpression" ~ "cyp7a1 mRNA expression",
                                     lvl3 == "cyp8b1.mrnaexpression" ~ "cyp8b1 mRNA expression",
                                     lvl3 == "cytochromec.proteinexpression" ~ "Cytochrome C protein expression",
                                     lvl3 == "cytotoxicity" ~ "Cytoxicity",
                                     lvl3 == "death.after.birth" ~ "Death After Birth",
                                     lvl3 == "decadienoylcarnitine.con" ~ "Decadienoylcarnitine Concentration",
                                     lvl3 == "decanoylcarnitine.con" ~ "Decanoylcarnitine Concentration",
                                     lvl3 == "decenoylcarnitine.con" ~ "decenoylcarnitine Concentration",
                                     lvl3 == "desulfovibrio.genomicdna" ~ "Desulfovibrio Genomic DNA",
                                     lvl3 == "dgat1.mrnaexpression" ~ "dgat1 mRNA expression",
                                     lvl3 == "dgat2.mrnaexpression" ~ "dgat2 mRNA expression",
                                     lvl3 == "d.lactate.con" ~ "D Lactate Concentration",
                                     lvl3 == "dao.activity" ~ "DAO Activity",
                                     lvl3 == "dazl.mrnaexpression" ~ "dazl mRNA expression",
                                     lvl3 == "dna.damage" ~ "DNA Damage",
                                     lvl3 == "dodecanoylcarnitine.con" ~ "Dodecanoylcarnitine Concentration",
                                     lvl3 == "dodecenoylcarnitine.con" ~ "Dodecenoylcarnitine Concentration",
                                     lvl3 == "dr5.proteinexpression" ~ "dr5 protein expression",
                                     lvl3 == "dubosiella.genomicdna" ~ "dubosiella Genomic DNA",
                                     lvl3 == "duodenum.histo" ~ "Duodenum Histology",
                                     lvl3 == "edema" ~ "Edema",
                                     lvl3 == "eosinophil.count" ~ "Eosinophil Count",
                                     lvl3 == "epididymis.histo" ~ "Epididymis Histology",
                                     lvl3 == "epididymis.somatic.index" ~ "Epididymis Somatic Index",
                                     lvl3 == "epithelial.cell.count" ~ "Epithelial Cell Count",
                                     lvl3 == "erk.mrnaexpression" ~ "erk mRNA expression",
                                     lvl3 == "erk1.mrnaexpression" ~ "erk1 mRNA expression",
                                     lvl3 == "erythema" ~ "Erythema",
                                     lvl3 == "fabp1.mrnaexpression" ~ "fabp1 mRNA expression",
                                     lvl3 == "fas.mrnaexpression" ~ "fas mRNA expression",
                                     lvl3 == "fat.index" ~ "Fat Index",
                                     lvl3 == "fat.mrnaexpression" ~ "fat mRNA expression",
                                     lvl3 == "fat.vacuoles" ~ "Fat Vacuoles",
                                     lvl3 == "fibronectin.proteinexpression.reproduction" ~ "Fibronectin protein expression (Reproductive Tissue)",
                                     lvl3 == "fibronectin.proteinexpression.cardio" ~ "Fibronectin protein expression (Cardiovascular Tissue)",
                                     lvl3 == "focaladhesionkinase.proteinexpression" ~ "Focal Adhesion Kinase protein expression",
                                     lvl3 == "folliclestimulatinghormone.con" ~ "Follicle Stimulating Hormone Concentration",
                                     lvl3 == "fsh.mrnaexpression" ~ "Follicle Stimulating Hormone mRNA expression",
                                     lvl3 == "food.intake" ~ "Food Intake",
                                     lvl3 == "fatp2.mrnaexpression" ~ "fatp2 mRNA expression",
                                     lvl3 == "firmicutes.genomicdna" ~ "Firmicutes Genomic DNA",
                                     lvl3 == "freecarnitine.con" ~ "Free Carnitine Concentration",
                                     lvl3 == "ft3.con" ~ "Free T3 Concentration",
                                     lvl3 == "ft3.ft4.ratio" ~ "Free T3/Free T4 Ratio",
                                     lvl3 == "ft4.con" ~ "Free T4 Concentration",
                                     lvl3 == "fumarylacetoacetatehydrolase.con" ~ "Fumarylacetoacetatehydrolase Concentration",
                                     lvl3 == "fxr.mrnaexpression" ~ "fxr mRNA expression",
                                     lvl3 == "gcsf.release" ~ "gcsf mRNA expression",
                                     lvl3 == "gestation.period" ~ "Gestation Period",
                                     lvl3 == "germinal.epithelium.height" ~ "Germinal Epithelium Cell Height",
                                     lvl3 == "gk.mrnaexpression" ~ "gk mRNA expression",
                                     lvl3 == "glucose.con" ~ "Glucose Concentration",
                                     lvl3 == "glut2.mrnaexpression" ~ "glut2 mRNA expression",
                                     lvl3 == "glutamicoxaloacetictransminase.con" ~ "Glutamicoxaloacetictransminase Concentration",
                                     lvl3 == "glutamicpyruvictransaminase.con" ~ "Glutamicpyruvictransaminase Concentration",
                                     lvl3 == "glutarylcarnitine.con" ~ "Glutarylcarnitine Concentration",
                                     lvl3 == "glycine.con" ~ "Glycine Concentration",
                                     lvl3 == "gpat.mrnaexpression" ~ "gpat mRNA expression",
                                     lvl3 == "gpx.activity" ~ "Glutathione Peroxidase Activity",
                                     lvl3 == "gsh.con" ~ "Glutathione Concentration",
                                     lvl3 == "gsdmd.proteinexpression" ~ "Gasdermin D protein expression",
                                     lvl3 == "gstp1.mrnaexpression" ~ "gstp1 mRNA expression",
                                     lvl3 == "gut.mucus.secretion" ~ "Gut Muscus Secretion",
                                     lvl3 == "heart.histo" ~ "Heart Histology",
                                     lvl3 == "heart.rate" ~ "Heart Rate",
                                     lvl3 == "hematocrit" ~ "Hematocrit",
                                     lvl3 == "hemoglobin.con" ~ "Hemoglobulin Concentration",
                                     lvl3 == "hemoglobin.distribution.width" ~ "Hemoglobulin Distribution Width",
                                     lvl3 == "hemolysis" ~ "Hemolysis",
                                     lvl3 == "hexadecenoylcarnitine.con" ~ "Hexadecenoylcarnitine Concentration",
                                     lvl3 == "hexanoylcarnitine.con" ~ "Hexanoylcarnitine Concentration",
                                     lvl3 == "hexaoylcarnitine.con" ~ "Hexaoylcarnitine Concentration",
                                     lvl3 == "highdensitylipoprotein.con" ~ "HDL Concentration",
                                     lvl3 == "histamine.release" ~ "Histamine Release",
                                     lvl3 == "histone.acetylation" ~ "Histone Acetylation",
                                     lvl3 == "ho1.mrnaexpression" ~ "ho1 mRNA expression",
                                     lvl3 == "ho1.proteinexpression" ~ "ho1 protein expression",
                                     lvl3 == "hsp70.mrnaexpression" ~ "hsp70 mRNA expression",
                                     lvl3 == "ic3b.con" ~ "iC3b Concentration",
                                     lvl3 == "ifny.con" ~ "Interferon y Concentration",
                                     lvl3 == "IgA.con" ~ "IgA Concentration",
                                     lvl3 == "IgE.con" ~ "IgE Concentration",
                                     lvl3 == "IgG.con" ~ "IgG Concentration",
                                     lvl3 == "IgM.con" ~ "IgM Concentration",
                                     lvl3 == "ikba.proteinexpression" ~ "ikba protein expression",
                                     lvl3 == "il1.mrnaexpression" ~ "il1 mRNA expression",
                                     lvl3 == "il1.release" ~ "IL1 Release",
                                     lvl3 == "il10.release" ~ "IL10 Release",
                                     lvl3 == "il1a.release" ~ "IL1a Release",
                                     lvl3 == "il1b.mrnaexpression" ~ "IL1b mRNA expression",
                                     lvl3 == "il1b.proteinexpression" ~ "IL1b protein expression",
                                     lvl3 == "il1b.release" ~ "IL1b Release",
                                     lvl3 == "il1b.con" ~ "IL1b Concentration",
                                     lvl3 == "il2.release" ~ "IL2 Release",
                                     lvl3 == "il5.release" ~ "IL5 Release",
                                     lvl3 == "il6.proteinexpression" ~ "IL6 protein expression",
                                     lvl3 == "il6.mrnaexpression" ~ "IL6 mRNA expression",
                                     lvl3 == "il6.release" ~ "IL6 Release",
                                     lvl3 == "il6.con" ~ "Interleukin 6 Concentration",
                                     lvl3 == "il8.mrnaexpression" ~ "IL8 mRNA expression",
                                     lvl3 == "il8.proteinexpression" ~ "IL8 protein expression",
                                     lvl3 == "il18.proteinexpression" ~ "IL18 protein expression",
                                     lvl3 == "il8.release" ~ "IL8 Release",
                                     lvl3 == "il8.con" ~ "IL8 Concentration",
                                     lvl3 == "il18.con" ~ "IL18 Concentration",
                                     lvl3 == "il9.release" ~ "IL9 Release",
                                     lvl3 == "immune.cell.proliferation" ~ "Immune Cell Proliferation",
                                     lvl3 == "immune.cell.protein.con" ~ "Immune Cell Protein Concentration",
                                     lvl3 == "inflammatory.cell.infiltration" ~ "Inflammatory Cell Infiltration",
                                     lvl3 == "intestinal.permeability" ~ "Intestinal Permeability",
                                     lvl3 == "intestinal.tissue.inflammation" ~ "Intestinal Tissue Inflammation",
                                     lvl3 == "inos.mrnaexpression" ~ "iNOS mRNA expression",
                                     lvl3 == "intracellular.ca.level" ~ "Intracellular Calcium Levels",
                                     lvl3 == "invariant.natural.killer.cells" ~ "Invariant Natural Killer Cells",
                                     lvl3 == "irf5.proteinexpression" ~ "irf5 protein expression",
                                     lvl3 == "isovalerylcarnitine.con" ~ "Isovalerylcarnitine Concentration",
                                     lvl3 == "keap1.proteinexpression" ~ "keap1 protein expression",
                                     lvl3 == "kidney.tissue.inflammation" ~ "Kidney Tissue Inflammation",
                                     lvl3 == "ki67.mrnaexpression" ~ "ki67 mRNA expression",
                                     lvl3 == "kidney.histo" ~ "Kidney Histology",
                                     lvl3 == "klf4.mrnaexpression" ~ "klf4 mRNA expression",
                                     lvl3 == "lactobacillus.genomicdna" ~ "Lactobacillus Genomic DNA",
                                     lvl3 == "large.intestine.histo" ~ "Large Intestine Histology",
                                     lvl3 == "ldh.activity" ~ "Lactate Dehydrogenase Activity",
                                     lvl3 == "ldh.con" ~ "Lactate Dehydrogenase Concentration",
                                     lvl3 == "ldh.release" ~ "Lactate Dehydrogenase Release",
                                     lvl3 == "leucine.con" ~ "Leucine Concentration",
                                     lvl3 == "leukocyte.adhesion" ~ "Leukocyte Adhesion",
                                     lvl3 == "lh.mrnaexpression"~ "lh mRNA expression",
                                     lvl3 == "linoleylcarnitine.con" ~ "Linoleylcarnitine Concentration",
                                     lvl3 == "lipid.droplets" ~ "Lipid Droplets",
                                     lvl3 == "liver.histo" ~ "Liver Histology",
                                     lvl3 == "liver.index" ~ "Liver Index",
                                     lvl3 == "liver.tissue.inflammation" ~ "Liver Tissue Inflammation",
                                     lvl3 == "lowdensitylipoprotein.con" ~ "Low Density Lipoprotein Concentration",
                                     lvl3 == "lung.histo" ~ "Lung Histology",
                                     lvl3 == "lung.tissue.inflammation" ~ "Lung Tissue Inflammation",
                                     lvl3 == "luteinizinghormone.con" ~ "Luteinizinghormone Concentration",
                                     lvl3 == "lymphocyte.count" ~ "Lymphocyte Count",
                                     lvl3 == "lysosomal.integrity" ~ "Lysosomal Integrity",
                                     lvl3 == "lysosomal.protonation" ~ "Lyosomal Protonation",
                                     lvl3 == "macrophage.cell.count" ~ "Macrophage Count",
                                     lvl3 == "macrophage.polarization" ~ "Macrophage Polarization",
                                     lvl3 == "malonylcarnitine.con" ~ "Malonylcarnitine Concentration",
                                     lvl3 == "mcad.mrnaexpression" ~ "mcad mRNA expression",
                                     lvl3 == "mcp1.con" ~ "mcp1 Concentration",
                                     lvl3 == "mcp1.mrnaexpression" ~ "mcp1 mRNA expression",
                                     lvl3 == "mda.activity" ~ "Malondialdehyde Activity",
                                     lvl3 == "mda.con" ~ "Malondialdehyde Concentration",
                                     lvl3 == "mean.corpuscular.hemoglobin" ~ "Mean Corpuscular Hemoglobin",
                                     lvl3 == "mean.corpuscular.hemoglobin.con" ~ "Mean Corpuscular Hemoglobin Concentration",
                                     lvl3 == "mean.corpuscular.volume" ~ "Mean Corpuscular Volume",
                                     lvl3 == "mean.platelet.volume" ~ "Mean Platelet Volume",
                                     lvl3 == "mek.mrnaexpression" ~ "mek mRNA expression",
                                     lvl3 == "melainabacteria.genomicdna" ~ "Melainabacteria Genomic DNA",
                                     lvl3 == "mem.il12.release" ~ "Membrane IL12 Release",
                                     lvl3 == "mem.il1b.release" ~ "Membrane IL1B Release",
                                     lvl3 == "mem.il2.release" ~ "Membrane IL2 Release",
                                     lvl3 == "mem.tnfa.release" ~ "Membrane TNFa Release",
                                     lvl3 == "meprinb.mrnaexpression" ~ "meprinb mRNA expression",
                                     lvl3 == "methionine.con" ~ "Methionine Concentration",
                                     lvl3 == "methylmalonic.con" ~ "Methylmalonic Concentration",
                                     lvl3 == "mice.in.predator.field.of.view" ~ "Within Predator Field of View",
                                     lvl3 == "micronuclei.freq" ~ "Micronuclei Frequency",
                                     lvl3 == "mitochondria.membrane.potential" ~ "Mitochondrial Membrane Potential",
                                     lvl3 == "mitochondria.num" ~ "Number of Mitochondria",
                                     lvl3 == "mitochondrial.ros.prod" ~ "Mitochondria ROS Production",
                                     lvl3 == "monocyte.adhesion" ~ "Monocyte Adhesion",
                                     lvl3 == "monocyte.count" ~ "Monocyte Count",
                                     lvl3 == "mortality" ~ "Mortality",
                                     lvl3 == "mrp2.mrnaexpression" ~ "mrp2 mRNA expression",
                                     lvl3 == "mrp3.mrnaexpression" ~ "mrp3 mRNA expression",
                                     lvl3 == "mtp.mrnaexpression" ~ "mtp mRNA expression",
                                     lvl3 == "muc1.mrnaexpression" ~ "muc1 mRNA expression",
                                     lvl3 == "muc2.mrnaexpression" ~ "muc2 mRNA expression",
                                     lvl3 == "muc3.mrnaexpression" ~ "muc mRNA expression",
                                     lvl3 == "muribaculum.genomicdna" ~ "Muribaculum Genomic DNA",
                                     lvl3 == "nadh.levels" ~ "NADH Levels",
                                     lvl3 == "natural.killer.cells" ~ "Natural Killer Cell Count",
                                     lvl3 == "ncadherin.proteinexpression" ~ "N-cadherin protein expression",
                                     lvl3 == "neutrophil.count" ~ "Neutrophil Count",
                                     lvl3 == "nfkb.mrnaexpression" ~ "nfkB mRNA expression",
                                     lvl3 == "nfkb.proteinexpression" ~ "nfkB protein expression",
                                     lvl3 == "nfkb1.mrnaexpression" ~ "nfkb1 mRNA expression",
                                     lvl3 == "nfkbp75.proteinexpression" ~ "nfkbp75 protein expression",
                                     lvl3 == "nhe3.mrnaexpression" ~ "nhe3 mRNA expression",
                                     lvl3 == "nkcc1.mrnaexpression" ~ "nkcc1 mRNA expression",
                                     lvl3 == "nkcc1.proteinexpression" ~ "nkcc1 protein expression",
                                     lvl3 == "nlrp3.proteinexpression" ~ "nlrp3 protein expression",
                                     lvl3 == "nonestrifiedfattyacid.con" ~ "Nonestrified Fatty Acid Concentration",
                                     lvl3 == "nos2.proteinexpression" ~ "nos2 protein expression",
                                     lvl3 == "nqo1.proteinexpression" ~ "nqo1 protein expression",
                                     lvl3 == "nrf2.mrnaexpression" ~ "nrf2 mRNA expression",
                                     lvl3 == "nrf2.proteinexpression" ~ "nrf2 protein expression",
                                     lvl3 == "ntcp.mrnaexpression" ~ "ntcp mRNA expression",
                                     lvl3 == "nuclear.intensity" ~ "Nuclear Intensity",
                                     lvl3 == "nuclear.size" ~ "Nuclear Size",
                                     lvl3 == "nucleaus.cytoplasm.ratio" ~ "Nucleaus Cytoplasm Ratio",
                                     lvl3 == "number.of.growing.follicles" ~ "Number of Growing Follicles",
                                     lvl3 == "number.of.live.births" ~ "Number of Live Births",
                                     lvl3 == "occludin.proteinexpression" ~ "Occludin protein expression",
                                     lvl3 == "octanoylcarnitine.con" ~ "Octanoylcarnitine Concentration",
                                     lvl3 == "octenoylcarnitine.con" ~ "Octenoylcarnitine Concentration",
                                     lvl3 == "odoribacter.genomicdna" ~ "Odoribacter Genomic DNA",
                                     lvl3 == "oleylcarnitine.con" ~ "Oleylcarnitine Concentration",
                                     lvl3 == "open.arm.entries" ~ "Open Arm Entries",
                                     lvl3 == "open.arm.time" ~ "Open Arm Time",
                                     lvl3 == "open.field.test.anxiety.index" ~ "Anxiety Index (Open Field Test)",
                                     lvl3 == "open.field.test.distance.traveled" ~ "Distance Traveled (Open Field Test)",
                                     lvl3 == "open.field.test.locomotion.speed" ~ "Locomotion Speed (Open Field Test)",
                                     lvl3 == "opsonization" ~ "Opsonization",
                                     lvl3 == "ornithine.con" ~ "Ornithine Concentration",
                                     lvl3 == "ovary.histo" ~ "Ovary Histology",
                                     lvl3 == "p-ikba.proteinexpression" ~ "p-ikba protein expression",
                                     lvl3 == "p-nfkbp75.proteinexpression" ~ "p-nfkbp75 protein expression",
                                     lvl3 == "p38.mrnaexpression" ~ "p38 mRNA expression",
                                     lvl3 == "p38.phosphorylation" ~ "p38 Phosphorylation",
                                     lvl3 == "p38.proteinexpression" ~ "p38 protein expression",
                                     lvl3 == "p53.mrnaexpression" ~ "p53 mRNA expression",
                                     lvl3 == "p53.proteinexpression" ~ "p53 protein expression",
                                     lvl3 == "p70s6k.proteinexpression" ~ "p70s6k protein expression",
                                     lvl3 == "palmitoylcarnitine.con" ~ "Palmitoylcarnitine Concentration",
                                     lvl3 == "parabacteroides.genomicdna" ~ "Parabacteroides Genomic DNA",
                                     lvl3 == "patescibacteria.genomicdna" ~ "Patescibacteria Genomic DNA",
                                     lvl3 == "p-bcatenin.proteinexpression" ~ "p-Bcatenin protein expression",
                                     lvl3 == "pge2.release" ~ "pge2 Release",
                                     lvl3 == "phagocytosis" ~ "Phagocytosis",
                                     lvl3 == "phenylalanine.con" ~ "Phenylalanine Concentration",
                                     lvl3 == "p-ikba.proteinexpression" ~ "p-ikba protein expression",
                                     lvl3 == "pk.mrnaexpression" ~ "pk mRNA expression",
                                     lvl3 == "platelet.count" ~ "Platelet Count",
                                     lvl3 == "plzf.mrnaexpression" ~ "plzf mRNA expression",
                                     lvl3 == "pnfkb.nfkb.ratio.proteinexpression" ~ "p-nfkB/nfkB Ratio protein expression",
                                     lvl3 == "p-nfkb.proteinexpression" ~ "p-nfkB protein expression",
                                     lvl3 == "p-p38.proteinexpression" ~ "p-p38 protein expression",
                                     lvl3 == "ppara.mrnaexpression" ~ "ppar a mRNA expression",
                                     lvl3 == "pparr.mrnaexpression" ~ "ppar r mRNA expression",
                                     lvl3 == "ppary.mrnaexpression" ~ "ppar y mRNA expression",
                                     lvl3 == "ppary.con" ~ "ppar y Concentration",
                                     lvl3 == "proliferation" ~ "Proliferation",
                                     lvl3 == "immune.cell.proliferation" ~ "Immune Cell Proliferation",
                                     lvl3 == "proline.con" ~ "Proline Concentration",
                                     lvl3 == "propionylcarnitine.con" ~ "Propionylcarnitine Concentration",
                                     lvl3 == "protein.con" ~ "Protein Concentration",
                                     lvl3 == "immune.cell.protein.con" ~ "Immune Cell Protein Concentration",
                                     lvl3 == "proteobactria.genomicdna" ~ "Proteobactria Genomic DNA",
                                     lvl3 == "pulmonary.arterial.pressure" ~ "Pulmonary Arterial Pressure",
                                     lvl3 == "pyruvate.con" ~ "Pyruvate Concentration",
                                     lvl3 == "rantes.release" ~ "RANTES Release",
                                     lvl3 == "ras.mrnaexpression" ~ "ras mRNA expression",
                                     lvl3 == "red.blood.cell.count" ~ "Red Blood Cell Count",
                                     lvl3 == "red.blood.cell.distribution.width" ~ "Red Blood Cell Distribution Width",
                                     lvl3 == "renlb.mrnaexpression" ~ "renlb mRNA expression",
                                     lvl3 == "respiration.rate" ~ "Respiration Rate",
                                     lvl3 == "reticulocyte" ~ "Reticulocyte",
                                     lvl3 == "retnlb.mrnaexpression" ~ "retnlb mRNA expression",
                                     lvl3 == "ros.prod" ~ "ROS Production",
                                     lvl3 == "sc5b9.con" ~ "sc5b9 Concentration",
                                     lvl3 == "scd1.mrnaexpression" ~ "scd1 mRNA expression",
                                     lvl3 == "sdh.activity" ~ "Succinate dehydrogenase Activity",
                                     lvl3 == "seminal.vesicle.histo" ~ "Seminal Vesicle Histology",
                                     lvl3 == "seminiferous.tubules.diameter" ~ "Seminiferous Tubules Diameter",
                                     lvl3 == "sex.ratio" ~ "Sex Ratio",
                                     lvl3 == "shaking.frequency" ~ "Shaking Frequency",
                                     lvl3 == "shannon.index" ~ "Shannon Index",
                                     lvl3 == "slc26a3.mrnaexpression" ~ "slc26a3 mRNA expression",
                                     lvl3 == "slc26a6.mrnaexpression" ~ "slc26a6 mRNA expression",
                                     lvl3 == "slc26a6.proteinexpression" ~ "slc26a6 protein expression",
                                     lvl3 == "small.intestine.histo" ~ "Small Intestine Histology",
                                     lvl3 == "sod.activity" ~ "SOD Activity",
                                     lvl3 == "sod2.mrnaexpression" ~ "sod2 mRNA expression",
                                     lvl3 == "sperm.count" ~ "Sperm Count",
                                     lvl3 == "sperm.deformity" ~ "Sperm Deformity",
                                     lvl3 == "sperm.dna.damage" ~ "Sperm DNA damage",
                                     lvl3 == "sperm.maturity" ~ "Sperm Maturity",
                                     lvl3 == "sperm.motility" ~ "Sperm Motility",
                                     lvl3 == "sperm.viability" ~ "Sperm Viability",
                                     lvl3 == "spermatogenic.cell.con" ~ "Spermatogenic Cell Concentration",
                                     lvl3 == "spleen.histo" ~ "Spleen Histology",
                                     lvl3 == "spleen.tissue.inflammation" ~ "Spleen Tissue Inflammation",
                                     lvl3 == "srebp1c.mrnaexpression" ~ "srebp1c mRNA expression",
                                     lvl3 == "staphylococcus.genomicdna" ~ "Staphylococcus Genomic DNA",
                                     lvl3 == "stat1.phosphorylation" ~ "stat1 Phosphorylation",
                                     lvl3 == "stat6.phosphorylation" ~ "stat6 Phosphorylation",
                                     lvl3 == "stearoylcarnitine.con" ~ "Stearoylcarnitine Concentration",
                                     lvl3 == "stomach.histo" ~ "Stomach Histology",
                                     lvl3 == "succinylacetone.con" ~ "Succinylacetone Concentration",
                                     lvl3 == "suzuki.score" ~ "Suzuki Score",
                                     lvl3 == "t.cells" ~ "T Cell Count",
                                     lvl3 == "t3.con" ~ "T3 Concentration",
                                     lvl3 == "t3.t4.ratio" ~ "T3/T4 Ratio",
                                     lvl3 == "t4.con" ~ "T4 Concentration",
                                     lvl3 == "tenericutes.genomicdna" ~ "Tenericutes Genomic DNA",
                                     lvl3 == "testis.histo" ~ "Testis Histology",
                                     lvl3 == "testis.somatic.index" ~ "Testis Somatic Index",
                                     lvl3 == "testicular.capsule.diameter" ~ "Testicular Capsule Diameter",
                                     lvl3 == "testosterone.con" ~ "Testosterone Concentration",
                                     lvl3 == "tetradecadienoylcarnitine.con" ~ "Tetradecadienoylcarnitine Concentration",
                                     lvl3 == "tetradecanocarnitine.con" ~ "Tetradecanocarnitine Concentration",
                                     lvl3 == "tetradecenoylcarnitine.con" ~ "Tetradecenoylcarnitine Concentration",
                                     lvl3 == "tf.proteinexpression" ~ "tf protein expression",
                                     lvl3 == "tgfb.proteinexpression" ~ "tbfb protein expression",
                                     lvl3 == "tgfb1.mrnaexpression" ~ "tgfb1 mRNA expression",
                                     lvl3 == "tgfb1.release" ~ "tgfb1 Release",
                                     lvl3 == "th17.cell.count" ~ "TH17 Cell Count",
                                     lvl3 == "th17.treg.ratio" ~ "TH17/Treg Ratio",
                                     lvl3 == "thymus.histo" ~ "Thymus Histology",
                                     lvl3 == "tiglylcarnitine.con" ~ "Tiglycarnitine Concentration",
                                     lvl3 == "time.in.dark" ~ "Time in Dark",
                                     lvl3 == "time.rotarod" ~ "Time Rotarod",
                                     lvl3 == "intestinal.tissue.inflammation" ~ "Intestinal Tissue Inflammation",
                                     lvl3 == "kidney.tissue.inflammation" ~ "Kidney Tissue Inflammation",
                                     lvl3 == "liver.tissue.inflammation" ~ "Liver Tissue Inflammation",
                                     lvl3 == "vision.tissue.inflammation" ~ "Vision Tissue Inflammation",
                                     lvl3 == "lung.tissue.inflammation" ~ "Lung Tissue Inflammation",
                                     lvl3 == "spleen.tissue.inflammation" ~ "Spleen Tissue Inflammation",
                                     lvl3 == "tlr4.proteinexpression" ~ "tlr4 protein expression",
                                     lvl3 == "tnfa.mrnaexpression" ~ "tnfa mRNA expression",
                                     lvl3 == "tnfa.proteinexpression" ~ "tnfa protein expression",
                                     lvl3 == "tnfa.release" ~ "TNFa Release",
                                     lvl3 == "tnfa.con" ~ "TNFa Concentration",
                                     lvl3 == "total.arm.entries" ~ "Total Arm Entries",
                                     lvl3 == "total.arm.entries.5min" ~ "TOtal Arm Entries (5 min)",
                                     lvl3 == "transepithelial.elec.res.respiratory" ~ "Transepithelial Electric Resistance (Respiratory)",
                                     lvl3 == "transepithelial.elec.res.intestinal" ~ "Transepithelial Electric Resistance (Intestinal)",
                                     lvl3 == "transepithelial.elec.res" ~ "Transepithelial Electric Resistance",
                                     lvl3 == "treg.cell.count" ~ "Treg Count",
                                     lvl3 == "triglyceride.con" ~ "Triglyceride Concentration",
                                     lvl3 == "trpv1.mrnaexpression" ~ "trpv1 mRNA expression",
                                     lvl3 == "troponin1.con" ~ "Troponin 1 Concentration",
                                     lvl3 == "tsh.con" ~ "TSH Concentration",
                                     lvl3 == "tunel.staining" ~ "TUNEL staining",
                                     lvl3 == "tyrosine.con" ~ "Tyrosine Concentration",
                                     lvl3 == "unifrac.diversity" ~ "Unifrac Diversity",
                                     lvl3 == "uterus.histo" ~ "Uterus Histology",
                                     lvl3 == "valine.con" ~ "Valine Concentration",
                                     lvl3 == "verrucomicrobia.genomicdna" ~ "Verrucomicrobia Genomic DNA",
                                     lvl3 == "vision.tissue.inflammation" ~ "",
                                     lvl3 == "water.intake" ~ "Water Intake",
                                     lvl3 == "weight.gain" ~ "Weight Gain",
                                     lvl3 == "white.blood.cell.count" ~ "White Blood Cell Count",
                                     lvl3 == "wnt.proteinexpression" ~ "wnt protein expression",
                                     lvl3 == "y.proteobacteria.genomicdna" ~ "y Proteobacteria Genomic DNA",
                                     lvl3 == "zo1.mrnaexpression" ~ "zo1 mRNA expression",
                                     lvl3 == "zo1.proteinexpression" ~ "zo1 protein expression"))) %>% 
  mutate(bio_h_f = factor(case_when(bio.org == "cell"~"Cell", #Renames for widget
                                    bio.org == "organism"~"Organism",
                                    bio.org == "subcell"~"Subcell",
                                    bio.org == "tissue" ~ "Tissue")))%>%
  mutate(vivo_h_f = factor(case_when(invitro.invivo == "invivo"~"In Vivo",
                                     invitro.invivo == "invitro"~"In Vitro")))%>% ##Renames for widget 
  mutate(life_h_f = factor(case_when(life.stage == "early,f1"~"Early, F1 Generation",
                                     life.stage == "early,f2"~"Early, F2 Generation",
                                     life.stage == "adult"~"Adult",
                                     life.stage == "Not Reported"~"Not Reported")))%>% #Renames for widget
  mutate(exposure_route_h_f = factor(case_when(exposure.route == "drinking.water" ~ "Drinking Water",
                                               exposure.route == "food" ~ "Food",
                                               exposure.route == "gavage" ~ "Gavage",
                                               exposure.route == "gestation" ~ "Gestation",
                                               exposure.route == "gestation,lactation" ~ "Gestation & Lactation",
                                               exposure.route == "Not Applicable"~"In Vitro",
                                               exposure.route == "iv.injection" ~ "IV Injection",
                                               exposure.route == "inhalation" ~ "Inhalation",
                                               exposure.route == "intratracheal.instillation" ~ "Intratracheal Instillation")))%>%
  mutate(species_h_f = factor(case_when(species == "aries"~"(Sheep) Ovis aries",
                                        species == "sapiens"~"(Human) Homo sapiens",
                                        species == "musculus"~"(Mouse) Mus musculus",
                                        species == "cuniculus"~"(Rabbit) Oryctolagus cuniculus",
                                        species == "domesticus" ~ "(Pig) Sus domesticus",
                                        species == "norvegicus"~"(Rat) Rattus norvegicus"))) %>% 
  #Make factor for experiment type
  mutate(exp_type_f = factor(if_else(is.na(chem), "Particle Only", "Chemical Co-Exposure"))) %>% 
  
  
  #### Recalculation of surface area and volume based on shape ####

#calculate particle surface area based on shape
mutate(particle.surface.area.um2 = case_when(shape == "sphere" ~ SAfnx(a = size.length.um.used.for.conversions,
                                                                       b = size.length.um.used.for.conversions,
                                                                       c = size.length.um.used.for.conversions),
                                             shape == "fiber" ~ SAfnx_fiber(width = 15, length = size.length.um.used.for.conversions), #assum 15 um width (kooi et al 2021)
                                             #shape == "fiber" & !is.na(size.width.um.used.for.conversions) ~ SAfnx_fiber(width = size.width.um.used.for.conversions, length = size.length.um.used.for.conversions), #if width is known
                                             shape == "fragment" ~ SAfnx(a = size.length.um.used.for.conversions,
                                                                         b = 0.77 * size.length.um.used.for.conversions,
                                                                         c = 0.77 * 0.67 * size.length.um.used.for.conversions))) %>% 
  #calculate particle volume
  mutate(particle.volume.um3 = case_when(shape == "sphere" ~ particle.volume.um3, #sphere volume is correct in excel
                                         shape == "fiber"  ~ volumefnx_fiber(width = 15, length = size.length.um.used.for.conversions), #assume 15 um as width (kooi et al 2021)
                                        # shape == "fiber" & !is.na(size.width.um.used.for.conversions) ~ volumefnx_fiber(width = size.width.um.used.for.conversions, length = size.length.um.used.for.conversions), #if width reported
                                         shape == "fragment" ~ volumefnx(R = 0.77, L = size.length.um.used.for.conversions))) %>% 
  
  #calculate particle mass
  mutate(particle.mass.mg = particle.volume.um3*density.mg.um3) %>%
  
  #Count
  mutate(dose.particles.mL.master = if_else(dose.particles.L.master.reported.converted == "converted",
                                            (dose.mg.mL.master/particle.mass.mg),
                                            dose.particles.L.master/1000)) %>%
  
  #calculate dose metrics accordingly
  mutate(dose.surface.area.um2.mL.master = particle.surface.area.um2 * dose.particles.mL.master) %>% 
  mutate(particle.surface.area.um2.mg = particle.surface.area.um2 / mass.per.particle.mg) %>% 
  
  # create label for polydispersity
  mutate(polydispersity = case_when(
    is.na(size.length.min.mm.nominal) ~ "monodisperse",
    !is.na(size.length.min.mm.nominal) ~ "polydisperse")) %>% 
  
  ####prioritize measured parameters for conversions ###
  # minima
  mutate(size.length.min.um.used.for.conversions = case_when(
    is.na(size.length.min.mm.measured) ~ size.length.min.mm.nominal * 1000,
    !is.na(size.length.min.mm.measured) ~ size.length.min.mm.measured * 1000)) %>% 
  mutate(size.width.min.um.used.for.conversions = case_when(
    shape == "sphere" ~ size.length.min.um.used.for.conversions, #all dims same
    shape == "fiber" ~ 0.77 * size.length.min.um.used.for.conversions, #median holds for all particles (Kooi et al 2021)
    shape == "Not Reported" ~ 0.77 * size.length.min.um.used.for.conversions, # average width to length ratio in the marine environment (kooi et al 2021)
    shape == "fragment" ~ 0.77 * size.length.min.um.used.for.conversions)) %>% # average width to length ratio in the marine environment (kooi et al 2021)
  mutate(size.height.min.um.used.for.conversions = case_when(
    shape == "sphere" ~ size.length.min.um.used.for.conversions, #all dims same
    shape == "Not Reported" ~ 0.77 * 0.67 * size.length.min.um.used.for.conversions, # average width to length ratio in the marine environment (kooi et al 2021)
    shape == "fiber" ~  0.77 * size.length.min.um.used.for.conversions, #height same as width for fibers
    shape == "fragment" ~ 0.77 * 0.67 * size.length.min.um.used.for.conversions)) %>% # average width to length ratio in the marine environment AND average height to width ratio (kooi et al 2021)
  # maxima
  mutate(size.length.max.um.used.for.conversions = case_when(
    is.na(size.length.max.mm.measured) ~ size.length.max.mm.nominal * 1000,
    !is.na(size.length.max.mm.measured) ~ size.length.max.mm.measured * 1000)) %>% 
  mutate(size.width.max.um.used.for.conversions = case_when(
    shape == "sphere" ~ size.length.max.um.used.for.conversions, #all dims same
    shape == "fiber" ~ 0.77 * size.length.max.um.used.for.conversions, #median holds for all particles (Kooi et al 2021) #there are no fibers
    shape == "Not Reported" ~ 0.77 * size.length.max.um.used.for.conversions, # average width to length ratio in the marine environment (kooi et al 2021)
    shape == "fragment" ~ 0.77 * size.length.max.um.used.for.conversions)) %>% # average width to length ratio in the marine environment (kooi et al 2021)
  mutate(size.height.max.um.used.for.conversions = case_when(
    shape == "sphere" ~ size.length.max.um.used.for.conversions, #all dims same
    shape == "Not Reported" ~ 0.77 * 0.67 * size.length.max.um.used.for.conversions, # average width to length ratio in the marine environment (kooi et al 2021)
    shape == "fiber" ~ 0.77 * size.length.max.um.used.for.conversions, #hieght same as width
    shape == "fragment" ~ 0.77 * 0.67 * size.length.max.um.used.for.conversions)) %>%  # average width to length ratio in the marine environment AND average height to width ratio (kooi et al 2021)
  
  #calculate minimum and maximum surface area for polydisperse particles
  mutate(particle.surface.area.um2.min = SAfnx(a = size.length.min.um.used.for.conversions,
                                               b = size.width.min.um.used.for.conversions,
                                               c = size.height.min.um.used.for.conversions)) %>%
  mutate(particle.surface.area.um2.max = SAfnx(a = size.length.max.um.used.for.conversions,
                                               b = size.width.max.um.used.for.conversions,
                                               c = size.height.max.um.used.for.conversions)) %>% 
  #calculate minimum and maximum volume for polydisperse particles
  mutate(particle.volume.um3.min = volumefnx_poly(length = size.length.min.um.used.for.conversions,
                                                  width =  size.width.min.um.used.for.conversions)) %>% 
  mutate(particle.volume.um3.max = volumefnx_poly(length = size.length.max.um.used.for.conversions,
                                                  width = size.width.max.um.used.for.conversions)) %>% 
  #calculate minimum and maximum volume for polydisperse particles
  mutate(mass.per.particle.mg.min = massfnx_poly(length = size.length.min.um.used.for.conversions,
                                                 width = size.width.min.um.used.for.conversions,
                                                 p = density.g.cm3)) %>% #equation uses g/cm3
  mutate(mass.per.particle.mg.max = massfnx_poly(length = size.length.max.um.used.for.conversions,
                                                 width = size.width.max.um.used.for.conversions,
                                                 p = density.g.cm3)) %>%   #equation uses g/cm3
  
  #Mass
  mutate(dose.ug.mL.master = if_else(dose.mg.mL.master.reported.converted == "converted",
                                    (dose.particles.mL.master*particle.mass.mg)/1000,
                                     dose.particles.mL.master)/1000) %>%
  
  #Volume
  mutate(dose.um3.mL.master = particle.volume.um3 * dose.particles.mL.master) %>%  #calculate volume/mL
  
  #Surface Area
  mutate(dose.um2.mL.master = as.numeric(particle.surface.area.um2) * dose.particles.mL.master) %>% 
  
  #Specific Surface Area
  mutate(dose.um2.ug.mL.master = dose.um2.mL.master / (mass.per.particle.mg / 1000)) %>% #correct mg to ug
  
  #Additional tidying for nicer values
  mutate(authors = gsub(".", " & ", as.character(authors), fixed = TRUE)) %>% 
  mutate(exposure.media = gsub(".", " ", as.character(exposure.media), fixed = TRUE)) %>%
  mutate(detergent = gsub(".", " ", as.character(detergent), fixed = TRUE)) %>%
  mutate(chem = gsub(".", " ", as.character(chem), fixed = TRUE)) %>%
  mutate(exposure.route = gsub(".", " ", as.character(exposure.route), fixed = TRUE)) %>% 
  mutate(sol.rinse = gsub(".", " ", as.character(sol.rinse), fixed = TRUE)) %>%
  mutate(sol.rinse = if_else(sol.rinse == "N", "No", sol.rinse)) %>% 
  mutate(clean.method = gsub(".", " ", as.character(clean.method), fixed = TRUE)) %>% 
  mutate(clean.method = if_else(clean.method == "N", "Not Cleaned", clean.method)) %>% 
  mutate(particle.behavior = gsub(".", " ", as.character(particle.behavior), fixed = TRUE)) %>% 
  mutate(particle.behavior = if_else(particle.behavior == "N", "Not Evaluated", particle.behavior)) %>%
  mutate(tissue.distribution = gsub(".", " ", as.character(tissue.distribution), fixed = TRUE)) %>%   
  
  #Create factors for red criteria screening
  mutate(particle_red_criteria = factor(case_when(
    is.na(particle.1) ~ "Scoring Not Available",
    particle.1 == 0|particle.2 == 0|particle.3 == 0|particle.4 == 0 ~ "Fail",
    particle.1 != 0 & particle.2 != 0 & particle.3 != 0 & particle.4 != 0 ~ "Pass"))) %>%
  mutate(design_red_criteria = factor(case_when(
    is.na(design.1) ~ "Scoring Not Available",
    design.3 == 0|design.4 == 0|design.6 == 0|design.7 == 0|design.9 == 0|design.10 == 0|design.11 == 0 ~ "Fail",
    design.3 != 0 & design.4 != 0 & design.6 != 0 & design.7 != 0 & design.9 != 0 & design.10 != 0 & design.11 != 0 ~ "Pass"))) %>% 
  mutate(risk_red_criteria = factor(case_when(
    is.na(risk.1) ~ "Scoring Not Available",
    risk.2 == 0|risk.3 == 0|risk.5 == 0 ~ "Fail",
    risk.2 != 0 & risk.3 != 0 & risk.5 != 0 ~ "Pass")))  

#### Endpoint Category Setup ####

human_endpoint <- human_setup %>% 
  group_by(vivo_h_f, lvl1_h_f,lvl2_h_f,lvl3_h_f,bio_h_f) %>% 
  summarise()

#### Search Setup ####

human_search <- human_setup %>%
  #general
  dplyr::select(doi, authors, year, particle_red_criteria, design_red_criteria, risk_red_criteria, species_h_f, life_h_f, vivo_h_f, sex,
                #experimental parameters
                exp_type_f, exposure_route_h_f, mix, negative.control, reference.material, exposure.media, solvent, detergent,
                media.ph, media.sal, media.temp, media.temp.min, media.temp.max, exposure.duration.d, 
                treatment, replicates, sample.size, dosing.frequency, chem, chem.dose.ug.L.nominal, chem.dose.ug.L.measured, 
                chem.dose.umol.kg.bw.day, chem.dose.uM, 
                #master doses
                dose.particles.mL.master, dose.particles.L.master.reported.converted, dose.ug.mL.master, dose.mg.mL.master.reported.converted,
                dose.um3.mL.master, 
                #biological effects
                effect_h_f, direction, lvl1_h_f, lvl2_h_f, lvl3_h_f, bio_h_f, target.organelle.cell.tissue, 
                #particle characteristics
                poly_h_f, shape_h_f, density.g.cm3, density.reported.estimated, charge, zetapotential, zeta.potential.media, functional.group,
                size.length.um.used.for.conversion, size_h_f, particle.volume.um,
                mass.per.particle.mg, weathered.biofouled,
                #quality
                size.valid, polymer.valid, shape.valid, particle.source, sodium.azide, contaminant.screen, clean.method, sol.rinse, background.plastics,
                con.valid, particle.behavior, uptake.valid, tissue.distribution, fed,
                #reported doses
                dose.ug.g.food.nominal, dose.uM.nominal, dose.ug.cm2.nominal, dose.particles.day.nominal, dose.particles.kg.bw.nominal,
                dose.mg.day.nominal, dose.particles.L.nominal, dose.mg.L.air.nominal, dose.mg.kg.day.bw.nominal, 
                dose.cm2.mL.nominal, 
                dose.ug.g.food.measured, dose.uM.measured, dose.ug.cm2.measured, dose.particles.day.measured, 
                dose.mg.day.measured, dose.particles.L.measured, dose.mg.L.air.measured, dose.mg.kg.day.bw.measured, 
                dose.cm2.mL.measured) %>%      
  #rename 'master' dose columns 
  rename("particles/mL (master)" = dose.particles.mL.master, "particles/mL (master), reported or converted" = dose.particles.L.master.reported.converted,
         "μg/mL (master)" = dose.ug.mL.master, "μg/mL (master), reported or converted" = dose.mg.mL.master.reported.converted,
         "μm^3/mL (master)" = dose.um3.mL.master) %>% 
  #rename 'other' dose columns
  rename("μg/g (food) - nominal" = dose.ug.g.food.nominal, "uM - nominal" = dose.uM.nominal, "μg/cm^2 - nominal" = dose.ug.cm2.nominal,
         "particles/day - nominal" = dose.particles.day.nominal, "particles/kg (body weight) - nominal" = dose.particles.kg.bw.nominal,
         "mg/day - nominal" = dose.mg.day.nominal, "particles/L - nominal" = dose.particles.L.nominal, "mg/L (air) - nominal" = dose.mg.L.air.nominal, 
         "mg/kg (body weight)/da - nominal" = dose.mg.kg.day.bw.nominal, "cm^2/mL - nominal" = dose.cm2.mL.nominal,
         
         "μg/g (food) - measured" = dose.ug.g.food.measured, "uM - measured" = dose.uM.measured, "μg/cm^2 - measured" = dose.ug.cm2.measured,
         "particles/day - measured" = dose.particles.day.measured, "mg/kg (body weight)/da - measured" = dose.mg.kg.day.bw.measured,
         "mg/day - measured" = dose.mg.day.measured, "particles/L - measured" = dose.particles.L.measured, "mg/L (air) - measured" = dose.mg.L.air.measured, 
         "cm^2/mL - measured" = dose.cm2.mL.measured)

#Turn all character strings into factors if they aren't already so they are searchable via dropdown
human_search[sapply(human_search, is.character)] <- lapply(human_search[sapply(human_search, is.character)], as.factor)

#Rename table columns
human_search <- human_search %>% 
  dplyr::rename('DOI' = doi,'Authors' = authors, 'Year' = year, 'Particle "Red Criteria"' = particle_red_criteria, 
                'Design "Red Criteria"' = design_red_criteria, 'Risk "Red Criteria"' = risk_red_criteria, 'Species' = species_h_f, 
                'Life Stage' = life_h_f, 'In vitro/in vivo' = vivo_h_f,
                'Sex' = sex, 'Experiment Type' = exp_type_f,
                'Exposure Route' = exposure_route_h_f, 'Particle Mix?' = mix, 'Negative Control' = negative.control, 
                'Reference Particle' = reference.material, 'Exposure Media' = exposure.media,
                'Solvent' = solvent, 'Detergent' = detergent, 'pH' = media.ph, 'Salinity (ppt)' = media.sal, 
                'Temperature (Avg)' = media.temp, 'Temperature (Min)' = media.temp.min,
                'Temperature (Max)' = media.temp.max, 'Exposure Duration (days)' = exposure.duration.d, 
                'Number of Doses' = treatment, 'Replicates' = replicates,
                'Sample Size' = sample.size, 'Dosing Frequency' = dosing.frequency, 'Chemicals Added' = chem, 
                'Added Chemical Dose μg/L (nominal)' = chem.dose.ug.L.nominal,
                'Added Chemical Dose μg/L (measured)' = chem.dose.ug.L.measured,
                'Added Chemical Dose μmol/kg/body weight/day' = chem.dose.umol.kg.bw.day,
                'Added Chemical Dose μM' = chem.dose.uM,
                'Effect' = effect_h_f, 'Direction' = direction, 'Broad Endpoint Category' = lvl1_h_f, 
                'Specific Endpoint Category' = lvl2_h_f,'Endpoint' = lvl3_h_f, 
                'Level of Biological Organization' = bio_h_f, 'Target Cell or Tissue' = target.organelle.cell.tissue, 
                'Polymer' = poly_h_f, 'Shape' = shape_h_f, 'Density (g/cm^3)' = density.g.cm3, 
                'Density, reported or estimated' = density.reported.estimated, 'Charge' = charge,
                'Zeta Potential (mV)' = zetapotential, 'Functional Group' = functional.group,
                'Particle Length (μm)' = size.length.um.used.for.conversion,
                'Size Category' = size_h_f,'Zeta Potential Media' = zeta.potential.media, 
                'Particle Volume (μm^3)' = particle.volume.um, 'Particle Mass (mg)'= mass.per.particle.mg,
                'Weathered or Biofouled?' = weathered.biofouled, 'Size Validated?' = size.valid, 
                'Polymer Validated?' = polymer.valid, 'Shape Validated' = shape.valid, 'Particle Source' = particle.source,
                'Sodium Azide Present?' = sodium.azide,
                'Screened for Chemical Contamination?' = contaminant.screen, 'Particle Cleaning?' = clean.method, 
                'Solvent Rinse'= sol.rinse, 'Background Contamination Monitored?' = background.plastics,
                'Concentration Validated?' = con.valid, 
                'Particle Behavior' = particle.behavior, 'Uptake Validated?' = uptake.valid,
                'Tissue Distribution' = tissue.distribution, 'Organisms Fed?' = fed)

#### Study Screening Setup ####

human_quality <- human_setup %>%
  filter(particle_red_criteria != "Scoring Not Available") %>% 
  filter(design_red_criteria != "Scoring Not Available") %>% 
  filter(risk_red_criteria != "Scoring Not Available") %>% 
  mutate(Study = paste0(authors, " (", year,")")) %>%
  mutate(Study_plus = as.factor(paste0(authors, " (", year,")", " (",doi,")"))) %>%  
  distinct(Study, Study_plus, doi, particle.1, particle.2, particle.3, particle.4, particle.5, particle.6, particle.7,
           design.1, design.2, design.3, design.4, design.5, design.6, design.7, design.8, design.9, design.10, design.11, design.12, 
           design.12, design.13, risk.1, risk.2, risk.3, risk.4, risk.5, risk.6,
           lvl1_h_f, lvl2_h_f, bio_h_f, effect_h_f, life_h_f, poly_h_f, shape_h_f, size_h_f, species_h_f, exposure_route_h_f, 
           particle_red_criteria, design_red_criteria, risk_red_criteria) %>%     
  
  pivot_longer(!c(Study, Study_plus, doi, lvl1_h_f, lvl2_h_f, bio_h_f, effect_h_f, life_h_f, poly_h_f, shape_h_f, size_h_f, species_h_f, exposure_route_h_f,
                  particle_red_criteria, design_red_criteria, risk_red_criteria),
               names_to ="Criteria", 
               values_to ="Score") %>% 
  #Assign descriptions to numerical scores
  mutate(Score_f = factor(case_when(Score == 0 ~ "Inadequate",
                                    Score == 1 ~ "Adequate with Restrictions",
                                    Score == 2 ~ "Adequate"))) %>%
  #Assign each criteria to appropriate category
  mutate(Category = case_when(grepl("particle", Criteria) ~ "Particle Characterization",
                              grepl("design", Criteria) ~ "Experimental Design",
                              grepl("risk", Criteria) ~ "Risk Assessment")) %>%  
  #Set order of categories so they plot in correct order
  mutate(Category_f = factor(Category, levels = c("Particle Characterization", "Experimental Design", "Risk Assessment"))) %>%   
  #Assign descriptions to each criteria
  mutate(Criteria = case_when(Criteria == "particle.1" ~ "Particle Size*",
                              Criteria == "particle.2" ~ "Particle Shape*",
                              Criteria == "particle.3" ~ "Polymer Type*",
                              Criteria == "particle.4" ~ "Particle Source*",
                              Criteria == "particle.5" ~ "Surface Chemistry",
                              Criteria == "particle.6" ~ "Chemical Purity",
                              Criteria == "particle.7" ~ "Microbial Contamination",
                              Criteria == "design.1" ~ "Concentration Units",
                              Criteria == "design.2" ~ "Particle Stability",
                              Criteria == "design.3" ~ "Test Vehicle*",
                              Criteria == "design.4" ~ "Administered Dose*",
                              Criteria == "design.5" ~ "Homogeneity of Exposure",
                              Criteria == "design.6" ~ "Administration Route*",
                              Criteria == "design.7" ~ "Test Species*",
                              Criteria == "design.8" ~ "Feeding/Housing Conditions",
                              Criteria == "design.9" ~ "Sample Size*",
                              Criteria == "design.10" ~ "Frequency/Duration of Exposure*",
                              Criteria == "design.11" ~ "Controls*",
                              Criteria == "design.12" ~ "Replicates",
                              Criteria == "design.13" ~ "Internal Dose Confirmation",
                              Criteria == "risk.1" ~ "Statistical Analysis",
                              Criteria == "risk.2" ~ "Endpoints*",
                              Criteria == "risk.3" ~ "Dose-Response*",
                              Criteria == "risk.4" ~ "Concentration Range",
                              Criteria == "risk.5" ~ "Effect Thresholds*",
                              Criteria == "risk.6" ~ "Test Particle Relevance")) %>%
  mutate(Criteria_f = factor(Criteria, levels = c("Test Particle Relevance","Effect Thresholds*","Concentration Range","Dose-Response*","Endpoints*","Statistical Analysis",
                                                  "Internal Dose Confirmation","Replicates","Controls*","Frequency/Duration of Exposure*","Sample Size*","Feeding/Housing Conditions",
                                                  "Test Species*","Administration Route*","Homogeneity of Exposure","Administered Dose*","Test Vehicle*","Particle Stability",
                                                  "Concentration Units","Microbial Contamination","Chemical Purity","Surface Chemistry","Particle Source*","Polymer Type*","Particle Shape*","Particle Size*")))

##### SAVE DATA #####
saveRDS(human, file = "human.RDS")
saveRDS(human_endpoint, file = "human_endpoint.RDS")
saveRDS(human_quality, file = "human_quality.RDS")
saveRDS(human_search, file = "human_search.RDS")
saveRDS(human_setup, file = "human_setup.RDS")
saveRDS(human_v1, file = "human_v1.RDS")