###########################################

###########################################

############ ALIGNMENT FUNCTION ###########

###########################################

###########################################

# This script provides all necessary equations and functions to perform the food

# dilution and tissue translocation alignments ###

######## Functions ######

#function to derive correction factor (CF) from Koelmans et al (equation 2)

CFfnx = function(a, #default alpha from Koelmans et al (2020)

x2D, #set detault values to convert ranges to (1-5,000 um) #5mm is upper defuault

x1D, #1 um is lower default size

x2M, x1M){

CF = (x2D^(1-a)-x1D^(1-a))/(x2M^(1-a)-x1M^(1-a))

return(CF)

}

### Generalizable function that works on any value (alpha == 1 and == 2 are limits!)

mux_polyfnx <- function(a.x, x_UL, x_LL) {

# Validate inputs

if (length(a.x) != length(x_UL) || length(a.x) != length(x_LL)) {

stop("a.x, x_UL, and x_LL must have the same length.")

}

# Initialize result vector

mux.poly <- numeric(length(a.x))

# Loop through each element to handle row-by-row logic

for (i in seq_along(a.x)) {

if (is.na(a.x[i]) || is.na(x_UL[i]) || is.na(x_LL[i])) {

# Handle NA values

mux.poly[i] <- NA

} else if (a.x[i] == 1) {

# Special case: a.x == 1

if (x_UL[i] > 0 && x_LL[i] > 0) {

mux.poly[i] <- (x_UL[i] - x_LL[i]) / log(x_UL[i] / x_LL[i])

} else {

mux.poly[i] <- NA # Invalid input for log

}

} else if (a.x[i] == 2) {

# Special case: a.x == 2

epsilon <- 1e-10 # Small value to avoid division by zero

if (x_UL[i] > 0 && x_LL[i] > 0) {

mux.poly[i] <- log(x_UL[i] / x_LL[i]) /

((x_LL[i] + epsilon)^-1 - (x_UL[i] + epsilon)^-1)

} else {

mux.poly[i] <- NA # Invalid input for log

}

} else {

# General case: a.x != 1 and a.x != 2

if (x_UL[i] > 0 && x_LL[i] > 0) {

mux.poly[i] <- ((1 - a.x[i]) / (2 - a.x[i])) *

((x_UL[i]^(2 - a.x[i]) - x_LL[i]^(2 - a.x[i])) /

(x_UL[i]^(1 - a.x[i]) - x_LL[i]^(1 - a.x[i])))

} else {

mux.poly[i] <- NA # Invalid input for power calculations

}

}

}

# Return the result

return(mux.poly)

}

############# VOLUME ############

volumefnx <- function(R = NA, # average length-to-width ratio for environment

H_W_ratio = 0.67, # assumed 0.67 * width per Kooi et al. (2021)

length, # particle length (always known)

height = NA, # particle height (if known)

width = NA # particle width (if known)

) {

# If width unknown, use L:W ratio

width <- ifelse(is.na(width), R * length, width)

# If height unknown, use H:R ratio

height <- ifelse(is.na(height), H_W_ratio * width, height)

# Calculate volume

volume <- (4 / 3) * pi * (length / 2) * (width / 2) * (height / 2)

return(volume)

}

############### SURFACE AREA ##################

#surface area equation for elongated spheres

SAfnx = function(length,

width = NA,

height = NA,

R = NA,

H_W_ratio = 0.67# assumed 0.67 * width per Kooi et al. (2021)

) {

# If width unknown, use L:W ratio

width <- ifelse(is.na(width), R * length, width)

# If height unknown, use H:R ratio

height <- ifelse(is.na(height), H_W_ratio * width, height)

# a, b, and c are equivalent to 1/2th of the length, width, and height, respectively

a <- 0.5 * length

b <- 0.5 * width

c <- 0.5 * height

SA = (4 * pi) * ((((a*b)^1.6 + (a*c)^1.6 + (b*c)^1.6) / 3) ^ (1/1.6))

return(SA)}

################# MASS ####################

massfnx <- function(v, p) {

# If either v or p is NA, return NA for those elements

mass <- ifelse(is.na(v) | is.na(p), NA, p * v * (1 / 1e12) * 1e6) # correction factor (g to µg)

return(mass)

}

###### SSA #####

SSA.inversefnx = function(sa, # average surface area

m){ #average mass

SSA.inverse = m/sa

return(SSA.inverse)}

######################################################

############### MASTER ALIGNMENT FUNCTION ###############

########################################################

preparation_fxn <- function(df, #dataframe input

beta_log10_body_length = 0.9341, # Jâms, et al 2020 Nature paper

body_length_intercept = 1.1200, # Jâms, et al 2020 Nature paper

H_W_ratio = 0.67, # H:W ratio across all environments/particle types

R.ave.water.marine = 0.77, # average length to width ratio of microplastics in marine environment (Kooi et al. 2021)

R.ave.water.freshwater = 0.67, # average length to width ratio of microplastics in freshwater environment (Kooi et al. 2021)

R.ave.sediment.marine = 0.75, # average length to width ratio of microplastics in marine environment (Kooi et al. 2021)

R.ave.sediment.freshwater = 0.70, # average length to width ratio of microplastics in freshwater environment (Kooi et al. 2021)

p.ave.marine = 1.10, #average density in marine surface water

alpha.marine = 2.07, #table s4 for marine surface water. length

a.sa.marine = 1.50, #marine surface area power law

a.v.marine = 1.48, #a_V for marine surface water volume

a.m.marine = 1.32, # upper limit fora_m for mass for marine surface water in table S4

a.ssa.marine = 1.98, # A_SSA for marine surface water

p.ave.freshwater = 1.04, #average density in freshwater surface water

alpha.freshwater = 2.64, #table s4 for freshwater surface water. length

a.sa.freshwater = 2.00, #freshwater surface area power law

a.v.freshwater = 1.68, #a_V for freshwater surface water volume

a.m.freshwater = 1.65, # upper limit fora_m for mass for freshwater surface water in table S4

a.ssa.freshwater = 2.71 # A_SSA for freshwater surface water

){

# Check if columns exist and conditionally create them

if (!"dose.mg.kg.sed.measured" %in% names(df)) {

df <- df %>%

mutate(dose.mg.kg.sed.measured = measured.dose.mg.kg.sediment)

}

if (!"dose.mg.kg.sed.nominal" %in% names(df)) {

df <- df %>%

mutate(dose.mg.kg.sed.nominal = nominal.dose.mg.kg.sediment)

}

if (!"dose.particles.kg.sed.nominal" %in% names(df)) {

df <- df %>%

mutate(dose.particles.kg.sed.nominal = nominal.dose.particles.kg.sediment)

}

if (!"environment" %in% names(df)){

df <- df %>%

mutate(environment = env_f)

}

df_prepared <- df %>%

mutate(beta_log10_body_length = !!beta_log10_body_length,

body_length_intercept = !!body_length_intercept,

H_W_ratio = !!H_W_ratio,

R.ave.water.marine = !!R.ave.water.marine,

R.ave.water.freshwater = !!R.ave.water.freshwater,

R.ave.sediment.marine = !!R.ave.sediment.marine,

R.ave.sediment.freshwater = !!R.ave.sediment.freshwater,

p.ave.marine = !!p.ave.marine,

alpha.marine = !!alpha.marine,

a.sa.marine = !!a.sa.marine,

a.v.marine = !!a.v.marine,

a.m.marine = !!a.m.marine,

a.ssa.marine = !!a.ssa.marine,

p.ave.freshwater = !!p.ave.freshwater,

alpha.freshwater = !!alpha.freshwater,

a.sa.freshwater = !!a.sa.freshwater,

a.v.freshwater = !!a.v.freshwater,

a.m.freshwater = !!a.m.freshwater,

a.ssa.freshwater = !!a.ssa.freshwater) %>%

##### define environment-specific alpha parameters ###############

mutate(alpha = case_when(environment == "Marine" & exposure.route == "water" ~ alpha.marine,

environment == "Freshwater" & exposure.route == "water" ~ alpha.freshwater),

a.sa = case_when(environment == "Marine" & exposure.route == "water" ~ a.sa.marine,

environment == "Freshwater" & exposure.route == "water" ~ a.sa.freshwater),

a.v = case_when(environment == "Marine" & exposure.route == "water" ~ a.v.marine,

environment == "Freshwater" & exposure.route == "water" ~ a.v.freshwater),

a.m = case_when(environment == "Marine" & exposure.route == "water" ~ a.m.marine,

environment == "Freshwater" & exposure.route == "water" ~ a.m.freshwater),

a.ssa = case_when(environment == "Marine" & exposure.route == "water" ~ a.ssa.marine,

environment == "Freshwater" & exposure.route == "water" ~ a.ssa.freshwater),

R.ave = case_when(environment == "Marine" & exposure.route == "water" ~ R.ave.water.marine,

environment == "Freshwater" & exposure.route == "water" ~ R.ave.water.freshwater,

environment == "Marine" & exposure.route == "sediment" ~ R.ave.sediment.marine,

environment == "Freshwater" & exposure.route == "sediment" ~ R.ave.sediment.freshwater),

p.ave = case_when(environment == "Marine" & exposure.route == "water" ~ p.ave.marine,

environment == "Freshwater" & exposure.route == "water" ~ p.ave.freshwater,

environment == "Marine" & exposure.route == "sediment" ~ p.ave.marine,

environment == "Freshwater" & exposure.route == "sediment" ~ p.ave.freshwater),

H_W_ratio = H_W_ratio # currently just using one value for all environments

) %>%

mutate(shape = shape_f) %>%

## calculate size parameters using compartment characteristics

mutate(size.width.min.um.used.for.conversions = case_when(

shape == "sphere" ~ size.length.min.um.used.for.conversions, #all dims same

shape == "fiber" ~ R.ave * size.length.min.um.used.for.conversions, #median holds for all particles (Kooi et al 2021)

shape == "Not Reported" ~ R.ave * size.length.min.um.used.for.conversions, # average width to length ratio in the marine environment (kooi et al 2021)

shape == "fragment" ~ R.ave * 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" ~ R.ave * H_W_ratio * size.length.min.um.used.for.conversions, # average width to length ratio in the marine environment (kooi et al 2021)

shape == "fiber" ~ R.ave * size.length.min.um.used.for.conversions, #height same as width for fibers

shape == "fragment" ~ R.ave * H_W_ratio * 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" ~ R.ave * size.length.max.um.used.for.conversions, #median holds for all particles (Kooi et al 2021) #there are no fibers

shape == "Not Reported" ~ R.ave * size.length.max.um.used.for.conversions, # average width to length ratio in the marine environment (kooi et al 2021)

shape == "fragment" ~ R.ave * 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" ~ R.ave * H_W_ratio * size.length.max.um.used.for.conversions, # average width to length ratio in the marine environment (kooi et al 2021)

shape == "fiber" ~ R.ave * size.length.max.um.used.for.conversions, #hieght same as width

shape == "fragment" ~ R.ave * H_W_ratio * 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)

# first ensure that width and height are filled out (sometimes there are reported, but if not, some default assumptions are made to estimate them)

mutate(size.width.um.used.for.conversions = case_when(

is.na(size.width.um.used.for.conversions) & shape_f == "Fiber" ~ 15, # assume 15 um width for fibers unless already known (kooi et al. 2021)

is.na(size.width.um.used.for.conversions) & shape_f == "Sphere" ~ size.length.um.used.for.conversions, # W = L for spheres

is.na(size.width.um.used.for.conversions) & shape_f == "Fragment" ~ size.length.um.used.for.conversions * R.ave, #use average width:length ratio for fragments

T ~ size.width.um.used.for.conversions # if available, use as-is

)) %>%

#estimate height based on shape (data doesn't exist in ToMEx for monodisperse, because never reported)

mutate(size.height.um.used.for.conversions = case_when(

shape_f == "Sphere" ~ size.length.um.used.for.conversions, # if spherical, height = length

shape_f != "Sphere" ~ size.width.um.used.for.conversions * H_W_ratio # if not spherical, height = width * H:W ratio

)) %>%

#### use assessment factors to get chronic NOECs ##

# mutate(dose.particles.mL.AF.corrected = dose.particles.mL.master / (af.time * af.noec)) %>%

# if NA, then there's missing AFs - data are considered invalid #

# drop_na(dose.particles.mL.AF.corrected) %>%

# rename

# mutate(dose.particles.mL.master = dose.particles.mL.AF.corrected) %>%

# calculate volume for monodisperse particles #

mutate(particle.volume.um3 = volumefnx(R = R.ave,

length = size.length.um.used.for.conversions,

width = size.width.um.used.for.conversions,

height = size.height.um.used.for.conversions

)) %>%

# calculate min and max volume when polydisperse particles are used (being sure to use ingestion-restricted sizes)

mutate(particle.volume.um3.min = volumefnx(R = R.ave,

length = size.length.min.um.used.for.conversions,

width = size.width.min.um.used.for.conversions,

height = size.height.min.um.used.for.conversions),

particle.volume.um3.max = volumefnx(R = R.ave,

length = size.length.max.um.used.for.conversions,

width = size.width.max.um.used.for.conversions,

height = size.height.max.um.used.for.conversions)) %>%

# calculate surface are for monodisperse particles

mutate(particle.surface.area.um2 = SAfnx(length = size.length.um.used.for.conversions,

width = size.width.um.used.for.conversions,

height = size.height.um.used.for.conversions,

R = R.ave,

H_W_ratio = H_W_ratio)) %>%

# calculate min/max SA for polydisperse mixtures (being sure to use translocation-restricted polydisperse upper sizes)

mutate(particle.surface.area.um2.min = SAfnx(length = size.length.min.um.used.for.conversions,

width = size.width.min.um.used.for.conversions,

height = size.height.min.um.used.for.conversions,

R = R.ave,

H_W_ratio = H_W_ratio),

particle.surface.area.um2.max = SAfnx(length = size.length.max.um.used.for.conversions,

width = size.width.max.um.used.for.conversions,

height = size.height.max.um.used.for.conversions,

R = R.ave,

H_W_ratio = H_W_ratio)) %>%

#calculate minimum and maximum mass for polydisperse particles

mutate(mass.per.particle.mg.min = massfnx(v = particle.volume.um3.min, p = density.g.cm3) * 1e-3) %>% #equation uses g/cm3

mutate(mass.per.particle.mg.max = massfnx(v = particle.volume.um3.max, p = density.g.cm3) * 1e-3) %>% #equation uses g/cm3

mutate(mass.per.particle.mg = massfnx(v = particle.volume.um3, p = density.g.cm3) * 1e-3) %>% #equation uses g/cm3

########## DOSE METRICS ################

#calcualte 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) %>%

#Sediment-based concentration metrics

mutate(dose.mg.kg.sediment.master = if_else(!is.na(dose.mg.kg.sed.measured), dose.mg.kg.sed.measured, dose.mg.kg.sed.nominal)) %>% #Create master column with measured concentrations preferred

mutate(dose.particles.kg.sediment.master = dose.particles.kg.sed.nominal) %>% #Create master column with measured concentrations preferred (only nominal concentrations available)

#Create reported vs. converted columns for sediment-based metrics

mutate(dose.mg.kg.sediment.master.converted.reported = if_else(!is.na(dose.mg.kg.sediment.master), "reported", NA_character_)) %>%

mutate(dose.particles.kg.sediment.master.converted.reported = if_else(!is.na(dose.particles.kg.sediment.master), "reported", NA_character_)) %>%

#Sediment Mass (converted)

mutate(dose.mg.kg.sediment.master = ifelse(is.na(dose.mg.kg.sediment.master), (dose.particles.kg.sediment.master)*mass.per.particle.mg, dose.mg.kg.sediment.master)) %>%

mutate(dose.mg.kg.sediment.master.converted.reported = factor(ifelse((!is.na(dose.mg.kg.sediment.master)&is.na(dose.mg.kg.sediment.master.converted.reported)), "converted", dose.mg.kg.sediment.master.converted.reported))) %>%

#Sediment Count (converted)

mutate(dose.particles.kg.sediment.master = ifelse(is.na(dose.particles.kg.sediment.master), (dose.mg.kg.sediment.master)/mass.per.particle.mg, dose.particles.kg.sediment.master)) %>%

mutate(dose.particles.kg.sediment.master.converted.reported = factor(ifelse((!is.na(dose.particles.kg.sediment.master)&is.na(dose.particles.kg.sediment.master.converted.reported)), "converted", dose.particles.kg.sediment.master.converted.reported))) %>%

#Volume

mutate(dose.um3.mL.master = particle.volume.um3 * dose.particles.mL.master) %>% #calculate volume/mL

mutate(dose.um3.kg.sediment.master = particle.volume.um3 * dose.particles.kg.sediment.master) %>% #calculate volume/kg sediment

#Surface Area

mutate(dose.um2.mL.master = as.numeric(particle.surface.area.um2) * dose.particles.mL.master) %>%

mutate(dose.um2.kg.sediment.master = as.numeric(particle.surface.area.um2) * dose.particles.kg.sediment.master) %>%

#Specific Surface Area

mutate(dose.um2.ug.mL.master = dose.um2.mL.master / (mass.per.particle.mg / 1000)) %>% #correct mg to ug

mutate(dose.um2.ug.kg.sediment.master = dose.um2.kg.sediment.master/(mass.per.particle.mg / 1000)) %>%

################## BIOAVAILABILITY ##############

#### Estimate ingestible plastic size

mutate(max.size.ingest.um = 1000 * (10^(beta_log10_body_length * log10(body.length.cm * 10) - body_length_intercept)))#(Jâms, et al 2020 Nature paper)correction for cm to mm

return(df_prepared)

}

######################### ALIGNMENT FUNCTION #############

alignment_fxn <- function(df_prepared, #dataframe input

x1D_set = 1, # lower default distribution (typically 1 um)

x2D_set = 5000, # upper default distribution (typically 5000 um)

x1M_set = 1, # lower bioavailable size limit (typically 1 um)

upper.tissue.trans.size.um = 88, # Coffin et al. (2025)

beta_log10_body_length = 0.9341, # Jâms, et al 2020 Nature paper

body_length_intercept = 1.1200, # Jâms, et al 2020 Nature paper

H_W_ratio = 0.67, # H:W ratio across all environments/particle types

R.ave.water.marine = 0.77, # average length to width ratio of microplastics in marine environment (Kooi et al. 2021)

R.ave.water.freshwater = 0.67, # average length to width ratio of microplastics in freshwater environment (Kooi et al. 2021)

R.ave.sediment.marine = 0.75, # average length to width ratio of microplastics in marine environment (Kooi et al. 2021)

R.ave.sediment.freshwater = 0.70, # average length to width ratio of microplastics in freshwater environment (Kooi et al. 2021)

p.ave.marine = 1.10, #average density in marine surface water

alpha.marine = 2.07, #table s4 for marine surface water. length

a.sa.marine = 1.50, #marine surface area power law

a.v.marine = 1.48, #a_V for marine surface water volume

a.m.marine = 1.32, # upper limit fora_m for mass for marine surface water in table S4

a.ssa.marine = 1.98, # A_SSA for marine surface water

p.ave.freshwater = 1.04, #average density in freshwater surface water

alpha.freshwater = 2.64, #table s4 for freshwater surface water. length

a.sa.freshwater = 2.00, #freshwater surface area power law

a.v.freshwater = 1.68, #a_V for freshwater surface water volume

a.m.freshwater = 1.65, # upper limit fora_m for mass for freshwater surface water in table S4

a.ssa.freshwater = 2.71 # A_SSA for freshwater surface water

){

### Create EC_mono_p.particles.mL only if it doesn't already exist (ensures compatibility with Shiny app) ##

if (!"EC_mono_p.particles.mL" %in% names(df_prepared)) {

df_prepared <- df_prepared %>%

mutate(EC_mono_p.particles.mL = dose.particles.mL.master)

}

# Check if columns exist and conditionally create them

if (!"dose.mg.kg.sed.measured" %in% names(df_prepared)) {

df_prepared <- df_prepared %>%

mutate(dose.mg.kg.sed.measured = measured.dose.mg.kg.sediment)

}

if (!"dose.mg.kg.sed.nominal" %in% names(df_prepared)) {

df_prepared <- df_prepared %>%

mutate(dose.mg.kg.sed.nominal = nominal.dose.mg.kg.sediment)

}

if (!"dose.particles.kg.sed.nominal" %in% names(df_prepared)) {

df_prepared <- df_prepared %>%

mutate(dose.particles.kg.sed.nominal = nominal.dose.particles.kg.sediment)

}

if (!"environment" %in% names(df)){

df_prepared <- df_prepared %>%

mutate(environment = env_f)

}

df_aligned <- df_prepared %>%

mutate(x1D_set = !!x1D_set,

x2D_set = !!x2D_set,

x1M_set = !!x1M_set,

upper.tissue.trans.size.um = !!upper.tissue.trans.size.um,

beta_log10_body_length = !!beta_log10_body_length,

body_length_intercept = !!body_length_intercept,

H_W_ratio = !!H_W_ratio,

R.ave.water.marine = !!R.ave.water.marine,

R.ave.water.freshwater = !!R.ave.water.freshwater,

R.ave.sediment.marine = !!R.ave.sediment.marine,

R.ave.sediment.freshwater = !!R.ave.sediment.freshwater,

p.ave.marine = !!p.ave.marine,

alpha.marine = !!alpha.marine,

a.sa.marine = !!a.sa.marine,

a.v.marine = !!a.v.marine,

a.m.marine = !!a.m.marine,

a.ssa.marine = !!a.ssa.marine,

p.ave.freshwater = !!p.ave.freshwater,

alpha.freshwater = !!alpha.freshwater,

a.sa.freshwater = !!a.sa.freshwater,

a.v.freshwater = !!a.v.freshwater,

a.m.freshwater = !!a.m.freshwater,

a.ssa.freshwater = !!a.ssa.freshwater) %>%

## assign alpha values

mutate(environment = env_f) %>%

mutate(alpha = case_when(environment == "Marine" & exposure.route == "water" ~ alpha.marine,

environment == "Freshwater" & exposure.route == "water" ~ alpha.freshwater),

a.sa = case_when(environment == "Marine" & exposure.route == "water" ~ a.sa.marine,

environment == "Freshwater" & exposure.route == "water" ~ a.sa.freshwater),

a.v = case_when(environment == "Marine" & exposure.route == "water" ~ a.v.marine,

environment == "Freshwater" & exposure.route == "water" ~ a.v.freshwater),

a.m = case_when(environment == "Marine" & exposure.route == "water" ~ a.m.marine,

environment == "Freshwater" & exposure.route == "water" ~ a.m.freshwater),

a.ssa = case_when(environment == "Marine" & exposure.route == "water" ~ a.ssa.marine,

environment == "Freshwater" & exposure.route == "water" ~ a.ssa.freshwater),

R.ave = case_when(environment == "Marine" & exposure.route == "water" ~ R.ave.water.marine,

environment == "Freshwater" & exposure.route == "water" ~ R.ave.water.freshwater,

environment == "Marine" & exposure.route == "sediment" ~ R.ave.sediment.marine,

environment == "Freshwater" & exposure.route == "sediment" ~ R.ave.sediment.freshwater),

p.ave = case_when(environment == "Marine" & exposure.route == "water" ~ p.ave.marine,

environment == "Freshwater" & exposure.route == "water" ~ p.ave.freshwater,

environment == "Marine" & exposure.route == "sediment" ~ p.ave.marine,

environment == "Freshwater" & exposure.route == "sediment" ~ p.ave.freshwater),

H_W_ratio = H_W_ratio # currently just using one value for all environments

) %>%

##### filter out undesired data ####

# ensure no nanoparticle (or simply particles outside desired range) studies are used

filter(size.length.um.used.for.conversions >= x1D_set,

size.length.um.used.for.conversions <= x2D_set) %>%

mutate(nanoparticle_polydisperse = case_when(

polydispersity == "polydisperse" & size.length.min.um.used.for.conversions < x1D_set ~ "nanoparticle_filter out",

T ~ "don't filter out")) %>%

filter(nanoparticle_polydisperse == "don't filter out") %>%

############################

######### BIOAVAILABILITY##########

#################################

mutate(max.size.ingest.um = 1000 * (10^(beta_log10_body_length * log10(body.length.cm * 10) - body_length_intercept))) %>% #(Jâms, et al 2020 Nature paper)correction for cm to mm

# max ingestible particle size for bioavailability restriction

mutate(x2M_ingest = case_when(max.size.ingest.um < x2D_set ~ max.size.ingest.um,

max.size.ingest.um >= x2D_set ~ x2D_set), #if max ingestible size is bigger than default distribution size, then just use that

# max translocatable particle size for bioavailability restriction

x2M_trans = case_when(max.size.ingest.um < upper.tissue.trans.size.um ~ max.size.ingest.um,

max.size.ingest.um >= upper.tissue.trans.size.um ~ upper.tissue.trans.size.um)) %>%

# tag whether monodisperse particles are ingestible/translocatable for each species #

mutate(ingestible = case_when(

polydispersity == "monodisperse" & size.length.um.used.for.conversions <= x2M_ingest ~ "ingestible",

polydispersity == "monodisperse" & size.length.um.used.for.conversions > x2M_ingest ~ "not ingestible"),

translocatable = case_when(

polydispersity == "monodisperse" & size.length.um.used.for.conversions <= x2M_trans ~ "translocatable",

polydispersity == "monodisperse" & size.length.um.used.for.conversions > x2M_trans ~ "not translocatable"),

#### tag whether polydipserse particles are ingestible/translocatable

ingestible_poly = case_when(

polydispersity == "polydisperse" & size.length.max.um.used.for.conversions <= x2M_ingest & size.length.min.um.used.for.conversions <= x2M_ingest ~ "ingestible (all)",

polydispersity == "polydisperse" & size.length.max.um.used.for.conversions > x2M_ingest & size.length.min.um.used.for.conversions <= x2M_ingest ~ "ingestible (some)",

polydispersity == "polydisperse" & size.length.max.um.used.for.conversions > x2M_ingest & size.length.min.um.used.for.conversions > x2M_ingest ~ "not ingestible"),

translocatable_poly = case_when(

polydispersity == "polydisperse" & size.length.max.um.used.for.conversions <= x2M_trans & size.length.min.um.used.for.conversions <= x2M_trans ~ "translocatable (all)",

polydispersity == "polydisperse" & size.length.max.um.used.for.conversions > x2M_trans & size.length.min.um.used.for.conversions <= x2M_trans ~ "translocatable (some)",

polydispersity == "polydisperse" & size.length.max.um.used.for.conversions > x2M_trans & size.length.min.um.used.for.conversions > x2M_trans ~ "not translocatable")

) %>%

# filter out studies that are not translocatable (as they will not be used in any alignments)

filter(!grepl("not", translocatable_poly)) %>%

filter(!grepl("not", translocatable)) %>%

# correct for partially translocatable particles by calculating translocatable fraction

mutate(CF_bioavailable_trans = case_when(

translocatable_poly == "translocatable (some)" ~ CFfnx(a = alpha,

x1D = size.length.min.um.used.for.conversions,

x2D = x2M_trans,

x1M = size.length.min.um.used.for.conversions,

x2M = size.length.max.um.used.for.conversions),

T ~ 1)) %>%

# calculate translocatable dose using correction factor (fraction)

mutate(EC_mono_p.particles.mL_trans = case_when(

translocatable_poly == "translocatable (some)" ~ CF_bioavailable_trans * EC_mono_p.particles.mL,

T ~ EC_mono_p.particles.mL)

) %>%

# determine fraction of partially ingestible particles using correction factor

mutate(CF_bioavailable_ingest = case_when(

ingestible_poly == "ingestible (some)" ~ CFfnx(a = alpha,

x1D = size.length.min.um.used.for.conversions,

x2D = x2M_ingest,

x1M = size.length.min.um.used.for.conversions,

x2M = size.length.max.um.used.for.conversions),

T ~ 1 )) %>%

# calculate ingestible particle effect concentration using correction factoor (fraction)

mutate(EC_mono_p.particles.mL_ingest = case_when(

ingestible_poly == "ingestible (some)" ~ CF_bioavailable_ingest * EC_mono_p.particles.mL,

T ~ dose.particles.mL.master)) %>%

## restrict size range of partially bioavailable polydisperse mixtures to bioavailable fractions (just the max sizes in each dimension)

mutate(size.length.max.um.trans = case_when(

translocatable_poly == "translocatable (some)" ~ x2M_trans,

T ~ size.length.max.um.used.for.conversions),

# adjust width based on existing L:W ratio, and fraction of length that's used

size.width.max.um.trans = case_when(

translocatable_poly == "translocatable (some)" ~ size.width.max.um.used.for.conversions * (x2M_trans / size.length.max.um.trans),

T ~ size.width.max.um.used.for.conversions),

# adjust height based on existing H:L ratio, and fraction of length that's used

size.height.max.um.trans = case_when(

translocatable_poly == "translocatable (some)" ~ size.height.max.um.used.for.conversions * (x2M_trans / size.length.max.um.trans),

T ~ size.height.max.um.used.for.conversions),

#### perform same operations for partially ingestible particles

size.length.max.um.ingest = case_when(

ingestible_poly == "ingestible (some)" ~ x2M_ingest,

T ~ size.length.max.um.used.for.conversions),

# adjust width based on existing L:W ratio, and fraction of length that's used

size.width.max.um.ingest = case_when(

ingestible_poly == "ingestible (some)" ~ size.width.max.um.used.for.conversions * (x2M_ingest / size.length.max.um.ingest),

T ~ size.width.max.um.used.for.conversions),

# adjust height based on existing H:L ratio, and fraction of length that's used

size.height.max.um.ingest = case_when(

ingestible_poly == "ingestible (some)" ~ size.height.max.um.used.for.conversions * (x2M_ingest / size.length.max.um.ingest),

T ~ size.height.max.um.used.for.conversions),

) %>%

###################################################

###################### Re-calculate surface area/volume with bioavailable polydisperse fractions

############################################################

# calculate min and max volume when polydisperse particles are used (being sure to use ingestion-restricted sizes)

mutate(particle.volume.um3.min = volumefnx(R = R.ave,

length = size.length.min.um.used.for.conversions,

width = size.width.min.um.used.for.conversions,

height = size.height.min.um.used.for.conversions),

particle.volume.um3.max = volumefnx(R = R.ave,

length = size.length.max.um.ingest,

width = size.width.max.um.ingest,

height = size.height.max.um.ingest)) %>%

# calculate surface are for monodisperse particles

mutate(particle.surface.area.um2 = SAfnx(length = size.length.um.used.for.conversions,

width = size.width.um.used.for.conversions,

height = size.height.um.used.for.conversions,

R = R.ave,

H_W_ratio = H_W_ratio)) %>%

# calculate min/max SA for polydisperse mixtures (being sure to use translocation-restricted polydisperse upper sizes)

mutate(particle.surface.area.um2.min = SAfnx(length = size.length.min.um.used.for.conversions,

width = size.width.min.um.used.for.conversions,

height = size.height.min.um.used.for.conversions,

R = R.ave,

H_W_ratio = H_W_ratio),

particle.surface.area.um2.max = SAfnx(length = size.length.max.um.trans,

width = size.width.max.um.trans,

height = size.height.max.um.trans,

R = R.ave,

H_W_ratio = H_W_ratio)) %>%

#####################################################

##################### ALIGNMENTS ####################

#########################################################

##### Determine CF_bio for ERM of interest ###

# calculate CF_bio for translocation

mutate(CF_bio_trans = CFfnx(x1M = x1M_set,#lower size bin

x2M = x2M_trans, #upper translocatable

x1D = x1D_set, #default

x2D = x2D_set, #default

a = alpha),

CF_bio_ingest = CFfnx(x1M = x1M_set,#lower size bin

x2M = x2M_ingest, #upper ingestible length

x1D = x1D_set, #default

x2D = x2D_set, #default upper size range

a = alpha)) %>%

################################################

############## Particle ERM #####################

################################################

### Particle ERM ###

# calculate effect threshold for particles

mutate(mu.p.mono = 1) %>% #mu_x_mono is always 1 for particles to particles

#### translocation-limited ####

mutate(mu.p.poly_trans = mux_polyfnx(a.x = alpha, x_UL = x2M_trans, x_LL = x1M_set)) %>%

# polydisperse effect threshold for particles

mutate(EC_poly_p.particles.mL_trans = (EC_mono_p.particles.mL_trans * mu.p.mono)/mu.p.poly_trans) %>%

## Calculate environmentally relevant effect threshold for particles

mutate(EC_env_p.particles.mL_trans = EC_poly_p.particles.mL_trans * CF_bio_trans) %>% #aligned particle effect concentration (1-5000 um)

##### Ingestion-limited ###

mutate(mu.p.poly_ingest = mux_polyfnx(a.x = alpha, x_UL = x2M_ingest, x_LL = x1M_set)) %>%

# polydisperse effect threshold for particles

mutate(EC_poly_p.particles.mL_ingest = (EC_mono_p.particles.mL_ingest * mu.p.mono)/mu.p.poly_ingest) %>%

## Calculate environmentally relevant effect threshold for particles

mutate(EC_env_p.particles.mL_ingest = EC_poly_p.particles.mL_ingest * CF_bio_ingest) %>% #aligned particle effect concentration (1-5000 um)

################################################

################### FOOD DILUTION ERM ##########

###############################################

# calculate volume for monodisperse particles #

mutate(particle.volume.um3 = volumefnx(R = R.ave,

length = size.length.um.used.for.conversions,

width = size.width.um.used.for.conversions,

height = size.height.um.used.for.conversions

)) %>%

# calculate min and max volume when polydisperse particles are used (being sure to use ingestion-restricted sizes)

mutate(particle.volume.um3.min = volumefnx(R = R.ave,

length = size.length.min.um.used.for.conversions,

width = size.width.min.um.used.for.conversions,

height = size.height.min.um.used.for.conversions),

particle.volume.um3.max = volumefnx(R = R.ave,

length = size.length.max.um.ingest,

width = size.width.max.um.ingest,

height = size.height.max.um.ingest)) %>%

# now determine mu.v.mono for monodisperse and polydisperse lab exposure particles

mutate(mu.v.mono = case_when(

polydispersity == "monodisperse" ~ particle.volume.um3, # use reported volume in monodisperse

polydispersity == "polydisperse" ~ mux_polyfnx(a.x = a.v,

x_LL = particle.volume.um3.min,

x_UL = particle.volume.um3.max))) %>%

#### INGESTION-LIMITED ####

#ingestion-limited lower/upper bioavailability limits

mutate(x_LL_v_ingest = volumefnx(length = x1D_set,

width = x1D_set,

height = x1D_set),

x_UL_v_ingest = volumefnx(length = x2M_ingest,

width = x2M_ingest,

height = x2M_ingest)) %>%

# translate to environmental

mutate(mu.v.poly_ingest = mux_polyfnx(a.v, x_UL_v_ingest, x_LL_v_ingest),

EC_poly_v.particles.mL_ingest = (EC_mono_p.particles.mL_ingest * mu.v.mono)/mu.v.poly_ingest,

EC_env_v.particles.mL_ingest = EC_poly_v.particles.mL_ingest * CF_bio_ingest#,

# final ingestion-based ERM excludes algae

# EC_env_v.particles.mL_ingest = case_when(

# Group == "Algae" ~ NA,

# T ~ EC_env_v.particles.mL_ingest)

) %>%

mutate(particles.mL.food.dilution = EC_env_v.particles.mL_ingest) %>%

#### TRANSLOCATION_LIMITED###

mutate(x_LL_v_trans = volumefnx(length = x1D_set,

width = x1D_set,

height = x1D_set),

x_UL_v_trans = volumefnx(length = x2M_trans,

width = x2M_trans,

height = x2M_trans)) %>%

# translate to environmental

mutate(mu.v.poly_trans = mux_polyfnx(a.v, x_UL_v_trans, x_LL_v_trans),

EC_poly_v.particles.mL_trans = (EC_mono_p.particles.mL_trans * mu.v.mono)/mu.v.poly_trans,

EC_env_v.particles.mL_trans = EC_poly_v.particles.mL_trans * CF_bio_trans) %>%

###############################################

################ TISSUE TRANSLOCATION ERM #######

##################################################

# step 1: ensure particle surface area is estimated for exposure particles

mutate(particle.surface.area.um2 = SAfnx(length = size.length.um.used.for.conversions,

width = size.width.um.used.for.conversions,

height = size.height.um.used.for.conversions,

R = R.ave,

H_W_ratio = H_W_ratio)) %>%

# calculate min/max SA for polydisperse mixtures (being sure to use translocation-restricted polydisperse upper sizes)

mutate(particle.surface.area.um2.min = SAfnx(length = size.length.min.um.used.for.conversions,

width = size.width.min.um.used.for.conversions,

height = size.height.min.um.used.for.conversions,

R = R.ave,

H_W_ratio = H_W_ratio),

particle.surface.area.um2.max = SAfnx(length = size.length.max.um.trans,

width = size.width.max.um.trans,

height = size.height.max.um.trans,

R = R.ave,

H_W_ratio = H_W_ratio)) %>%

# calculate mu.sa.mono for mono and polydisperse particles

# mu.x_poly equation must be used in case of polydisperse exposure concentrations

mutate(mu.sa.mono = case_when(

polydispersity == "monodisperse" ~ particle.surface.area.um2, # use reported surface area in monodisperse

polydispersity == "polydisperse" ~ mux_polyfnx(a.x = a.sa,

x_LL = particle.surface.area.um2.min,

x_UL = particle.surface.area.um2.max))) %>%

#TRANSLOCATION-LIMTED #

#calculate lower translocatable surface area using spherical assumption

mutate(x_LL_sa_trans = SAfnx(length = x1D_set,

width = x1D_set,

height = x1D_set),

#calculate upper translocatable surface area using spherical assumption

x_UL_sa_trans = SAfnx(length = x2M_trans,

width = x2M_trans,

height = x2M_trans)) %>%

#calculate SA mu_poly and EC_poly_SA (translocatation-limited)

mutate(mu.sa.poly_trans = mux_polyfnx(a.sa, x_UL_sa_trans, x_LL_sa_trans),

EC_poly_sa.particles.mL_trans = (EC_mono_p.particles.mL_trans * mu.sa.mono)/mu.sa.poly_trans,

# calculate EC_env_sa (translocation limited). This is the Tissue Translocation ERM Value!

EC_env_sa.particles.mL_trans = EC_poly_sa.particles.mL_trans * CF_bio_trans,

particles.mL.tissue.translocation = EC_env_sa.particles.mL_trans) %>%

#INGESTION-LIMITED

#calculate lower ingestible surface area using spherical assumption

mutate(x_LL_sa_ingest = SAfnx(length = x1D_set,

width = x1D_set,

height = x1D_set),

#calculate upper ingestible surface area using spherical assumption

x_UL_sa_ingest = SAfnx(length = x2M_ingest,

width = x2M_ingest,

height = x2M_ingest)) %>%

#calculate SA mu_poly and EC_poly_SA (ingestion-limited)

mutate(mu.sa.poly_ingest = mux_polyfnx(a.sa, x_UL_sa_ingest, x_LL_sa_ingest),

EC_poly_sa.particles.mL_ingest = (EC_mono_p.particles.mL_ingest * mu.sa.mono)/mu.sa.poly_ingest,

# calculate EC_env_sa (ingestion limited). This is the Tissue ingestlocation ERM Value!

EC_env_sa.particles.mL_ingest = EC_poly_sa.particles.mL_ingest * CF_bio_ingest) %>%

#################################################

################ MASS ERM ######################

####################################################

#calculate lower ingestible mass (translocation-limited)

mutate(x_LL_m_trans = massfnx(v = x_LL_v_trans, p = p.ave),

x_UL_m_trans = massfnx(v = x_UL_v_trans, p = p.ave)) %>% #average density

#calculate lower ingestible mass (ingestion-limited)

mutate(x_LL_m_ingest = massfnx(v = x_LL_v_ingest, p = p.ave),

x_UL_m_ingest = massfnx(v = x_UL_v_ingest, p = p.ave)) %>% #average density

# calculate mu.m.poly (trans / ingest)

mutate(mu.m.poly_trans = mux_polyfnx(a.m, x_UL_m_trans, x_LL_m_trans),

mu.m.poly_ingest = mux_polyfnx(a.m, x_UL_m_ingest, x_LL_m_ingest)

) %>%

##--- laboratory calculations ---###

## define mu_x_mono OR mu_x_poly (lab) for alignment to ERM #

#(note that if mixed particles were used, a different equation must be used)

mutate(mu.m.mono = case_when(

polydispersity == "monodisperse" ~ mass.per.particle.mg * 1000, # use reported volume in monodisperse

polydispersity == "polydisperse" ~ mux_polyfnx(a.x = a.m,

x_UL = mass.per.particle.mg.max * 1000,

x_LL = mass.per.particle.mg.min * 1000))) %>%

#calculate polydisperse effect concentration for volume (particles/mL)

mutate(EC_poly_m.particles.mL_ingest = (EC_mono_p.particles.mL_ingest * mu.m.mono)/mu.m.poly_ingest,

EC_poly_m.particles.mL_trans = (EC_mono_p.particles.mL_trans * mu.m.mono)/mu.m.poly_trans) %>%

#calculate environmentally realistic effect threshold

mutate(EC_env_m.particles.mL_trans = EC_poly_m.particles.mL_trans * CF_bio_trans,

EC_env_m.particles.mL_ingest = EC_poly_m.particles.mL_ingest * CF_bio_ingest) %>%

#################################################

############# SPECIFIC SURFACE AREA ERM #########

####################################################

##### specific surface area ERM ####

mutate(mu.ssa.mono = mu.sa.mono/mu.m.mono) %>% #define mu_x_mono for alignment to ERM (um^2/ug)

### translocation-limited ####

#calculate lower translocatable 1/SSA

mutate(x_LL_ssa_trans = SSA.inversefnx(sa = x_LL_sa_trans, #surface area

m = x_LL_m_trans), #mass

x_UL_ssa_trans = SSA.inversefnx(sa = x_UL_sa_trans, #surface area

m = x_UL_m_trans) #mass

) %>%

#calculate mu_x_poly for specific surface area

#note that mu were calcaulted for polydisperse particles before, so not special case needed here

mutate(mu.ssa.inverse.poly_trans = mux_polyfnx(a.ssa, x_UL_ssa_trans, x_LL_ssa_trans)) %>%

#calculate polydisperse effect concentration for specific surface area (particles/mL)

mutate(mu.ssa.poly_trans = 1 / mu.ssa.inverse.poly_trans) %>% #calculate mu_SSA from inverse

mutate(EC_poly_ssa.particles.mL_trans = (EC_mono_p.particles.mL_trans * mu.ssa.mono)/mu.ssa.poly_trans) %>%

#calculate environmentally realistic effect threshold

mutate(EC_env_ssa.particles.mL_trans = EC_poly_ssa.particles.mL_trans * CF_bio_trans) %>%

### Ingestion-limited ####

#calculate lower ingestlocatable 1/SSA

mutate(x_LL_ssa_ingest = SSA.inversefnx(sa = x_LL_sa_ingest, #surface area

m = x_LL_m_ingest), #mass

x_UL_ssa_ingest = SSA.inversefnx(sa = x_UL_sa_ingest, #surface area

m = x_UL_m_ingest) #mass

) %>%

#calculate mu_x_poly for specific surface area

#note that mu were calcaulted for polydisperse particles before, so not special case needed here

mutate(mu.ssa.inverse.poly_ingest = mux_polyfnx(a.ssa, x_UL_ssa_ingest, x_LL_ssa_ingest)) %>%

#calculate polydisperse effect concentration for specific surface area (particles/mL)

mutate(mu.ssa.poly_ingest = 1 / mu.ssa.inverse.poly_ingest) %>% #calculate mu_SSA from inverse

mutate(EC_poly_ssa.particles.mL_ingest = (EC_mono_p.particles.mL_ingest * mu.ssa.mono)/mu.ssa.poly_ingest) %>%

#calculate environmentally realistic effect threshold

mutate(EC_env_ssa.particles.mL_ingest = EC_poly_ssa.particles.mL_ingest * CF_bio_ingest) %>%

##################################################

### Convert to Metrics other than particles/mL ###

#######################################################

## convert all environmentally realistic thresholds to surface area ##

# particle count to surface area #

mutate(EC_env_p.um2.mL_ingest = EC_env_p.particles.mL_ingest * mux_polyfnx(a.x = a.sa, x_UL = x2D_set, x_LL = x1D_set)) %>%

# surface area to surface area #

mutate(EC_env_sa.um2.mL_ingest = EC_env_sa.particles.mL_ingest * mux_polyfnx(a.x = a.sa, x_UL = x2D_set, x_LL = x1D_set)) %>%

# volume to surface area #

mutate(EC_env_v.um2.mL_ingest = EC_env_v.particles.mL_ingest * mux_polyfnx(a.x = a.sa, x_UL = x2D_set, x_LL = x1D_set)) %>%

# mass to surface area #

mutate(EC_env_m.um2.mL_ingest = EC_env_m.particles.mL_ingest * mux_polyfnx(a.x = a.sa, x_UL = x2D_set, x_LL = x1D_set)) %>%

# specific surface area to surface area #

mutate(EC_env_ssa.um2.mL_ingest = EC_env_ssa.particles.mL_ingest * mux_polyfnx(a.x = a.sa, x_UL = x2D_set, x_LL = x1D_set)) %>%

## convert all environmentally realistic thresholds to volume ##

# particle count to volume #

mutate(EC_env_p.um3.mL_ingest = EC_env_p.particles.mL_ingest * mux_polyfnx(a.x = a.v, x_UL = x2D_set, x_LL = x1D_set)) %>%

# surface area to volume #

mutate(EC_env_sa.um3.mL_ingest = EC_env_sa.particles.mL_ingest * mux_polyfnx(a.x = a.v, x_UL = x2D_set, x_LL = x1D_set)) %>%

# volume to volume #

mutate(EC_env_v.um3.mL_ingest = EC_env_v.particles.mL_ingest * mux_polyfnx(a.x = a.v, x_UL = x2D_set, x_LL = x1D_set)) %>%

# mass to volume #

mutate(EC_env_m.um3.mL_ingest = EC_env_m.particles.mL_ingest * mux_polyfnx(a.x = a.v, x_UL = x2D_set, x_LL = x1D_set)) %>%

# specific surface area to volume #

mutate(EC_env_ssa.um3.mL_ingest = EC_env_ssa.particles.mL_ingest * mux_polyfnx(a.x = a.v, x_UL = x2D_set, x_LL = x1D_set)) %>%

## convert all environmentally realistic thresholds to mass ##

# particle count to mass #

mutate(EC_env_p.ug.mL_ingest = EC_env_p.particles.mL_ingest * mux_polyfnx(a.x = a.m, x_UL = x2D_set, x_LL = x1D_set)) %>%

# surface area to mass #

mutate(EC_env_sa.ug.mL_ingest = EC_env_sa.particles.mL_ingest * mux_polyfnx(a.x = a.m, x_UL = x2D_set, x_LL = x1D_set)) %>%

# volume to mass #

mutate(EC_env_v.ug.mL_ingest = EC_env_v.particles.mL_ingest * mux_polyfnx(a.x = a.m, x_UL = x2D_set, x_LL = x1D_set)) %>%

# mass to mass #

mutate(EC_env_m.ug.mL_ingest = EC_env_m.particles.mL_ingest * mux_polyfnx(a.x = a.m, x_UL = x2D_set, x_LL = x1D_set)) %>%

# specific surface area to mass #

mutate(EC_env_ssa.ug.mL_ingest = EC_env_ssa.particles.mL_ingest * mux_polyfnx(a.x = a.m, x_UL = x2D_set, x_LL = x1D_set)) %>%

## convert all environmentally realistic thresholds to specific surface area ##

# particle count to specific surface area #

mutate(EC_env_p.um2.ug.mL_ingest = EC_env_p.particles.mL_ingest * mux_polyfnx(a.x = a.ssa, x_UL = x2D_set, x_LL = x1D_set)) %>%

# surface area to specific surface area #

mutate(EC_env_sa.um2.ug.mL_ingest = EC_env_sa.particles.mL_ingest * mux_polyfnx(a.x = a.ssa, x_UL = x2D_set, x_LL = x1D_set)) %>%

# volume to specific surface area #

mutate(EC_env_v.um2.ug.mL_ingest = EC_env_v.particles.mL_ingest * mux_polyfnx(a.x = a.ssa, x_UL = x2D_set, x_LL = x1D_set)) %>%

# mass to specific surface area #

mutate(EC_env_m.um2.ug.mL_ingest = EC_env_m.particles.mL_ingest * mux_polyfnx(a.x = a.ssa, x_UL = x2D_set, x_LL = x1D_set)) %>%

# specific surface area to specific surface area #

mutate(EC_env_ssa.um2.ug.mL_ingest = EC_env_ssa.particles.mL_ingest * mux_polyfnx(a.x = a.ssa, x_UL = x2D_set, x_LL = x1D_set)) %>%

#### TRANSLOCATION ####

# particle count to surface area #

mutate(EC_env_p.um2.mL_trans = EC_env_p.particles.mL_trans * mux_polyfnx(a.x = a.sa, x_UL = x2D_set, x_LL = x1D_set)) %>%

# surface area to surface area #

mutate(EC_env_sa.um2.mL_trans = EC_env_sa.particles.mL_trans * mux_polyfnx(a.x = a.sa, x_UL = x2D_set, x_LL = x1D_set)) %>%

# volume to surface area #

mutate(EC_env_v.um2.mL_trans = EC_env_v.particles.mL_trans * mux_polyfnx(a.x = a.sa, x_UL = x2D_set, x_LL = x1D_set)) %>%

# mass to surface area #

mutate(EC_env_m.um2.mL_trans = EC_env_m.particles.mL_trans * mux_polyfnx(a.x = a.sa, x_UL = x2D_set, x_LL = x1D_set)) %>%

# specific surface area to surface area #

mutate(EC_env_ssa.um2.mL_trans = EC_env_ssa.particles.mL_trans * mux_polyfnx(a.x = a.sa, x_UL = x2D_set, x_LL = x1D_set)) %>%

## convert all environmentally realistic thresholds to volume ##

# particle count to volume #

mutate(EC_env_p.um3.mL_trans = EC_env_p.particles.mL_trans * mux_polyfnx(a.x = a.v, x_UL = x2D_set, x_LL = x1D_set)) %>%

# surface area to volume #

mutate(EC_env_sa.um3.mL_trans = EC_env_sa.particles.mL_trans * mux_polyfnx(a.x = a.v, x_UL = x2D_set, x_LL = x1D_set)) %>%

# volume to volume #

mutate(EC_env_v.um3.mL_trans = EC_env_v.particles.mL_trans * mux_polyfnx(a.x = a.v, x_UL = x2D_set, x_LL = x1D_set)) %>%

# mass to volume #

mutate(EC_env_m.um3.mL_trans = EC_env_m.particles.mL_trans * mux_polyfnx(a.x = a.v, x_UL = x2D_set, x_LL = x1D_set)) %>%

# specific surface area to volume #

mutate(EC_env_ssa.um3.mL_trans = EC_env_ssa.particles.mL_trans * mux_polyfnx(a.x = a.v, x_UL = x2D_set, x_LL = x1D_set)) %>%

## convert all environmentally realistic thresholds to mass ##

# particle count to mass #

mutate(EC_env_p.ug.mL_trans = EC_env_p.particles.mL_trans * mux_polyfnx(a.x = a.m, x_UL = x2D_set, x_LL = x1D_set)) %>%

# surface area to mass #

mutate(EC_env_sa.ug.mL_trans = EC_env_sa.particles.mL_trans * mux_polyfnx(a.x = a.m, x_UL = x2D_set, x_LL = x1D_set)) %>%

# volume to mass #

mutate(EC_env_v.ug.mL_trans = EC_env_v.particles.mL_trans * mux_polyfnx(a.x = a.m, x_UL = x2D_set, x_LL = x1D_set)) %>%

# mass to mass #

mutate(EC_env_m.ug.mL_trans = EC_env_m.particles.mL_trans * mux_polyfnx(a.x = a.m, x_UL = x2D_set, x_LL = x1D_set)) %>%

# specific surface area to mass #

mutate(EC_env_ssa.ug.mL_trans = EC_env_ssa.particles.mL_trans * mux_polyfnx(a.x = a.m, x_UL = x2D_set, x_LL = x1D_set)) %>%

## convert all environmentally realistic thresholds to specific surface area ##

# particle count to specific surface area #

mutate(EC_env_p.um2.ug.mL_trans = EC_env_p.particles.mL_trans * mux_polyfnx(a.x = a.ssa, x_UL = x2D_set, x_LL = x1D_set)) %>%

# surface area to specific surface area #

mutate(EC_env_sa.um2.ug.mL_trans = EC_env_sa.particles.mL_trans * mux_polyfnx(a.x = a.ssa, x_UL = x2D_set, x_LL = x1D_set)) %>%

# volume to specific surface area #

mutate(EC_env_v.um2.ug.mL_trans = EC_env_v.particles.mL_trans * mux_polyfnx(a.x = a.ssa, x_UL = x2D_set, x_LL = x1D_set)) %>%

# mass to specific surface area #

mutate(EC_env_m.um2.ug.mL_trans = EC_env_m.particles.mL_trans * mux_polyfnx(a.x = a.ssa, x_UL = x2D_set, x_LL = x1D_set)) %>%

# specific surface area to specific surface area #

mutate(EC_env_ssa.um2.ug.mL_trans = EC_env_ssa.particles.mL_trans * mux_polyfnx(a.x = a.ssa, x_UL = x2D_set, x_LL = x1D_set)) %>%

#annotate aligned ERM of interest for user interpretability

mutate("Surface-Area Aligned, Ingestion-Limited, Exposure Concentration (particles/mL)" = EC_env_sa.particles.mL_ingest,

"Volume Aligned, Ingestion-Limited, Exposure Concentration (particles/mL)" = EC_env_v.particles.mL_ingest,

"Mass Aligned, Ingestion-Limited, Exposure Concentration (particles/mL)" = EC_env_m.particles.mL_ingest,

"Specific Surface Area Aligned, Ingestion-Limited, Exposure Concentration (particles/mL)" = EC_env_ssa.particles.mL_ingest,

"Surface-Area Aligned, Translocation-Limited, Exposure Concentration (particles/mL)" = EC_env_sa.particles.mL_trans,

"Volume Aligned, Translocation-Limited, Exposure Concentration (particles/mL)" = EC_env_v.particles.mL_trans,

"Mass Aligned, Translocation-Limited, Exposure Concentration (particles/mL)" = EC_env_m.particles.mL_trans,

"Specific Surface Area Aligned, Translocation-Limited, Exposure Concentration (particles/mL)" = EC_env_ssa.particles.mL_trans

) %>%

#nudge to front

dplyr::relocate("Surface-Area Aligned, Ingestion-Limited, Exposure Concentration (particles/mL)",

"Volume Aligned, Ingestion-Limited, Exposure Concentration (particles/mL)",

"Mass Aligned, Ingestion-Limited, Exposure Concentration (particles/mL)",

"Specific Surface Area Aligned, Ingestion-Limited, Exposure Concentration (particles/mL)",

"Surface-Area Aligned, Translocation-Limited, Exposure Concentration (particles/mL)",

"Volume Aligned, Translocation-Limited, Exposure Concentration (particles/mL)",

"Mass Aligned, Translocation-Limited, Exposure Concentration (particles/mL)",

"Specific Surface Area Aligned, Translocation-Limited, Exposure Concentration (particles/mL)"

)

return(df_aligned)

}

cat("Alignment function and dependencies loaded!")

#### EXAMPLE APPLICATION ####

# aoc_z <- readRDS("data/input/aoc_z_tomex2.RDS")

#

# # step 1: prepare data for alignment

# aoc_prepared <- preparation_fxn(aoc_z)

# # step 2: align data

# aoc_aligned <- alignment_fxn(aoc_prepared)

#

# #inspect

# aoc_aligned %>%

# select(Group, Species, size.length.um.used.for.conversions, shape_f, dose.particles.mL.master, `Volume Aligned, Ingestion-Limited, Exposure Concentration (particles/mL)`,

# `Surface-Area Aligned, Translocation-Limited, Exposure Concentration (particles/mL)`) %>%

# head() %>%

# t()