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Step3_estimate_Dvalues.R
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Step3_estimate_Dvalues.R
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##### This R script enables to estimate the value of D from all raw kinetics data previously collected
#### Packages ####
library(ggplot2)
#### Load all raw kinetics data ####
load(file="Kinetics_data.RData")
#### Estimation of D ####
##### Function to automatize the procedure #####
f_estimate_Dvalues = function(dk) {
## This function enables to automatized the estimation of D by fitting linear inactivation model for each kinetics
## INTPUT
## dk (data.frame) data frame with at least the following columns
## $ Kinetics_key (factor/character): ID of the kinetics
## $ time_hours (numeric): experimental time points (in hour)
## $ y (numeric): measured of the viral concentration in log10 scale
## OUTPUT
## - output (list)
## $ regplot (list) list of de linear regression plot for each kinetics, e.g.:
## $ K102 (ggplot2 object) regression plot for the kinetics K102
## $ K103 (ggplot2 object) regression plot for the kinetics K103
## ...
## $ Dvalues_tab (dataframe) estimated values of log10(D) for each kinetics
## $ Kinetics_key (character): ID of the kinetics
## $ log10Dvalues (numeric): estimated value of log10(D)
# Total number of kinetics in the data frame dk
nb_kinetics = length(levels(dk$Kinetics_key))
## Initialize the output objects
# Dvalues_tab
Dvalues_tab <- data.frame(Kinetics_key = levels(dk$Kinetics_key),
#y_variable = rep(NA, nb_kinetics),
nb_points = rep(NA, nb_kinetics),
Dvalues = rep(NA, nb_kinetics),
Dvalues_stderr = rep(NA, nb_kinetics),
Dvalues_CV = rep(NA, nb_kinetics))
# regplot
regplot <- list()
# Automatic estimation of D
for (i in 1:nb_kinetics) { # for each kinetics
# extract the kinetics key
Kinetic_i <- levels(dk$Kinetics_key)[i]
# console check
writeLines(paste("kinetics", Kinetic_i))
# extract the data associated with the considered kinetics
tab_Kinetic_i <- subset(dk, Kinetics_key == Kinetic_i)
# total number of available points associated with the considered kinetics
nb_points_i <- sum(!is.na(tab_Kinetic_i$y))
# save the kinetics keys and number of points in the output data frame
Dvalues_tab$Kinetics_key[i] <- Kinetic_i
Dvalues_tab$nb_points[i] <- nb_points_i
# save the regression plot associated with the considered kinetics
regplot[[Kinetic_i]] <- ggplot(data = tab_Kinetic_i,
mapping = aes(x = time_hours, y = y)) +
geom_point(shape = 18, size=3) +
geom_smooth(formula = y~x, method = lm, colour = "black") +
theme(axis.ticks=element_blank(),
axis.title = element_text(face="bold", size=14),
panel.background=element_rect(fill="white"),
panel.grid=element_line(colour="grey")) +
labs(title = paste("Kinetics key:", Kinetic_i)) +
coord_cartesian(xlim = c(min(tab_Kinetic_i$time_hours[!is.na(tab_Kinetic_i$y)]),
max(tab_Kinetic_i$time_hours[!is.na(tab_Kinetic_i$y)]))) +
xlab("time (hours)") +
ylab(unique(dk$y_variable[dk$Kinetics_key == Kinetic_i]))
## Estimation of D for each kinetics by fitting log-linear regression model on data
skip_to_next <- FALSE
tryCatch({
model_i <- nls(data = tab_Kinetic_i,
formula = y ~ b - (time_hours/D_value),
start = list(b = tab_Kinetic_i$y[1],
D_value = -1/lm(data = tab_Kinetic_i,
formula = y ~ time_hours)$coefficients[2]),
algorithm = "port")
# extract the estimated values of D and its standard error
Dvalues_i <- summary(model_i)$coefficients[2,1]
Dvalues_stderr_i <- summary(model_i)$coefficients[2,2]
# save estimated values in the output data frame Dvalues_tab
Dvalues_tab$Dvalues[i] <- abs(Dvalues_i)
Dvalues_tab$Dvalues_stderr[i] <- Dvalues_stderr_i
Dvalues_tab$Dvalues_CV[i] <- Dvalues_stderr_i / abs(Dvalues_i)
}, error = function(e) { skip_to_next <<- TRUE})
if(skip_to_next) { next }
}
## Prepare the output object (regression plots and data frame of estimated values)
output <- list("regplot" = regplot,
"Dvalues_tab" = Dvalues_tab)
return(output)
}
##### Estimation of D: automatic run #####
D <- f_estimate_Dvalues(dk)
##### Processing non-convergence cases #####
###### K009 #####
key <- "K009"
row_id <- which(D$Dvalues_tab$Kinetics_key == key)
d <- subset(dk, Kinetics_key==key)
#D$regplot$K009
#-1/lm(data = d, formula = y ~ time_hours)$coefficients[2]
model_nls <- nls(data = d, formula = y ~ b - (time_hours/D_value),
start = list(b = d$y[1],
D_value = 10),
algorithm = "port")
D$Dvalues_tab[row_id,]$Dvalues <- summary(model_nls)$coefficients[2,1]
D$Dvalues_tab[row_id,]$Dvalues_stderr <- summary(model_nls)$coefficients[2,2]
D$Dvalues_tab[row_id,]$Dvalues_CV <- summary(model_nls)$coefficients[2,2] / abs(summary(model_nls)$coefficients[2,1])
##### K013 #####
key <- "K013"
row_id <- which(D$Dvalues_tab$Kinetics_key == key)
d <- subset(dk, Kinetics_key==key)
#D$regplot$K013
#-1/lm(data = d, formula = y ~ time_hours)$coefficients[2]
model_nls <- nls(data = d, formula = y ~ b - (time_hours/D_value),
start = list(b = 0,
D_value = 5),
algorithm = "port")
#summary(model_nls)
D$Dvalues_tab[row_id,]$Dvalues <- summary(model_nls)$coefficients[2,1]
D$Dvalues_tab[row_id,]$Dvalues_stderr <- summary(model_nls)$coefficients[2,2]
D$Dvalues_tab[row_id,]$Dvalues_CV <- summary(model_nls)$coefficients[2,2] / abs(summary(model_nls)$coefficients[2,1])
#### K016 ####
key <- "K016"
row_id <- which(D$Dvalues_tab$Kinetics_key == key)
d <- subset(dk, Kinetics_key==key)
#D$regplot$K016
#-1/lm(data = d, formula = y ~ time_hours)$coefficients[2]
model_nls <- nls(data = d, formula = y ~ b - (time_hours/D_value),
start = list(b = 0,
D_value = 5),
algorithm = "port")
#summary(model_nls)
D$Dvalues_tab[row_id,]$Dvalues <- summary(model_nls)$coefficients[2,1]
D$Dvalues_tab[row_id,]$Dvalues_stderr <- summary(model_nls)$coefficients[2,2]
D$Dvalues_tab[row_id,]$Dvalues_CV <- summary(model_nls)$coefficients[2,2] / abs(summary(model_nls)$coefficients[2,1])
#### K018 ####
key <- "K018"
row_id <- which(D$Dvalues_tab$Kinetics_key == key)
d <- subset(dk, Kinetics_key==key)
#D$regplot$K018
#-1/lm(data = d, formula = y ~ time_hours)$coefficients[2]
model_nls <- nls(data = d, formula = y ~ b - (time_hours/D_value),
start = list(b = 0,
D_value = 5),
algorithm = "port")
#summary(model_nls)
D$Dvalues_tab[row_id,]$Dvalues <- summary(model_nls)$coefficients[2,1]
D$Dvalues_tab[row_id,]$Dvalues_stderr <- summary(model_nls)$coefficients[2,2]
D$Dvalues_tab[row_id,]$Dvalues_CV <- summary(model_nls)$coefficients[2,2] / abs(summary(model_nls)$coefficients[2,1])
#### K019 ####
key <- "K019"
row_id <- which(D$Dvalues_tab$Kinetics_key == key)
d <- subset(dk, Kinetics_key==key)
#D$regplot$K019
#-1/lm(data = d, formula = y ~ time_hours)$coefficients[2]
model_nls <- nls(data = d, formula = y ~ b - (time_hours/D_value),
start = list(b = 0,
D_value = 5),
algorithm = "port")
#summary(model_nls)
D$Dvalues_tab[row_id,]$Dvalues <- summary(model_nls)$coefficients[2,1]
D$Dvalues_tab[row_id,]$Dvalues_stderr <- summary(model_nls)$coefficients[2,2]
D$Dvalues_tab[row_id,]$Dvalues_CV <- summary(model_nls)$coefficients[2,2] / abs(summary(model_nls)$coefficients[2,1])
#### K029 ####
key <- "K029"
row_id <- which(D$Dvalues_tab$Kinetics_key == key)
d <- subset(dk, Kinetics_key==key)
#D$regplot$K029
#-1/lm(data = d, formula = y ~ time_hours)$coefficients[2]
model_nls <- nls(data = d, formula = y ~ b - (time_hours/D_value),
start = list(b = 0,
D_value = 5),
algorithm = "port")
#summary(model_nls)
D$Dvalues_tab[row_id,]$Dvalues <- summary(model_nls)$coefficients[2,1]
D$Dvalues_tab[row_id,]$Dvalues_stderr <- summary(model_nls)$coefficients[2,2]
D$Dvalues_tab[row_id,]$Dvalues_CV <- summary(model_nls)$coefficients[2,2] / abs(summary(model_nls)$coefficients[2,1])
#### K037 ####
key <- "K037"
row_id <- which(D$Dvalues_tab$Kinetics_key == key)
d <- subset(dk, Kinetics_key==key)
#D$regplot$K037
#-1/lm(data = d, formula = y ~ time_hours)$coefficients[2]
model_nls <- nls(data = d, formula = y ~ b - (time_hours/D_value),
start = list(b = 0,
D_value = 5),
algorithm = "port")
summary(model_nls)
D$Dvalues_tab[row_id,]$Dvalues <- summary(model_nls)$coefficients[2,1]
D$Dvalues_tab[row_id,]$Dvalues_stderr <- summary(model_nls)$coefficients[2,2]
D$Dvalues_tab[row_id,]$Dvalues_CV <- summary(model_nls)$coefficients[2,2] / abs(summary(model_nls)$coefficients[2,1])
#### K039 ####
key <- "K039"
row_id <- which(D$Dvalues_tab$Kinetics_key == key)
d <- subset(dk, Kinetics_key==key)
#D$regplot$K039
#-1/lm(data = d, formula = y ~ time_hours)$coefficients[2]
model_nls <- nls(data = d, formula = y ~ b - (time_hours/D_value),
start = list(b = 0,
D_value = 5),
algorithm = "port")
summary(model_nls)
D$Dvalues_tab[row_id,]$Dvalues <- summary(model_nls)$coefficients[2,1]
D$Dvalues_tab[row_id,]$Dvalues_stderr <- summary(model_nls)$coefficients[2,2]
D$Dvalues_tab[row_id,]$Dvalues_CV <- summary(model_nls)$coefficients[2,2] / abs(summary(model_nls)$coefficients[2,1])
#### K089 ####
key <- "K089"
row_id <- which(D$Dvalues_tab$Kinetics_key == key)
d <- subset(dk, Kinetics_key==key)
#D$regplot$K089
#-1/lm(data = d, formula = y ~ time_hours)$coefficients[2]
model_nls <- nls(data = d, formula = y ~ b - (time_hours/D_value),
start = list(b = 0,
D_value = 5),
algorithm = "port")
summary(model_nls)
D$Dvalues_tab[row_id,]$Dvalues <- summary(model_nls)$coefficients[2,1]
D$Dvalues_tab[row_id,]$Dvalues_stderr <- summary(model_nls)$coefficients[2,2]
D$Dvalues_tab[row_id,]$Dvalues_CV <- summary(model_nls)$coefficients[2,2] / abs(summary(model_nls)$coefficients[2,1])
#### K128 ####
key <- "K128"
row_id <- which(D$Dvalues_tab$Kinetics_key == key)
d <- subset(dk, Kinetics_key==key)
#D$regplot$K128 ## 1 point ! --> Dvalue not estimated
#### K148 ####
key <- "K148"
row_id <- which(D$Dvalues_tab$Kinetics_key == key)
d <- subset(dk, Kinetics_key==key)
#D$regplot$K148 ## 1 point ! --> Dvalue not estimated
#### K185 ####
key <- "K185"
row_id <- which(D$Dvalues_tab$Kinetics_key == key)
d <- subset(dk, Kinetics_key==key)
#D$regplot$K185 ## 1 point --> Dvalue not estimated
#### K238 ####
key <- "K238"
row_id <- which(D$Dvalues_tab$Kinetics_key == key)
d <- subset(dk, Kinetics_key==key)
#D$regplot$K238 ## 3 points en "horizontal" ! --> Dvalue not estimated
#### K267 ####
key <- "K267"
row_id <- which(D$Dvalues_tab$Kinetics_key == key)
d <- subset(dk, Kinetics_key==key)
#D$regplot$K267
-1/lm(data = d, formula = y ~ time_hours)$coefficients[2]
model_nls <- nls(data = d, formula = y ~ b - (time_hours/D_value),
start = list(b = 2,
D_value = -10),
algorithm = "port")
#summary(model_nls)
D$Dvalues_tab[row_id,]$Dvalues <- abs(summary(model_nls)$coefficients[2,1])
D$Dvalues_tab[row_id,]$Dvalues_stderr <- summary(model_nls)$coefficients[2,2]
D$Dvalues_tab[row_id,]$Dvalues_CV <- summary(model_nls)$coefficients[2,2] / abs(summary(model_nls)$coefficients[2,1])
#### K274 ####
key <- "K274"
row_id <- which(D$Dvalues_tab$Kinetics_key == key)
d <- subset(dk, Kinetics_key==key)
#D$regplot$K274
-1/lm(data = d, formula = y ~ time_hours)$coefficients[2]
model_nls <- nls(data = d, formula = y ~ b - (time_hours/D_value),
start = list(b = 2,
D_value = -10),
algorithm = "port")
summary(model_nls)
D$Dvalues_tab[row_id,]$Dvalues <- abs(summary(model_nls)$coefficients[2,1])
D$Dvalues_tab[row_id,]$Dvalues_stderr <- summary(model_nls)$coefficients[2,2]
D$Dvalues_tab[row_id,]$Dvalues_CV <- summary(model_nls)$coefficients[2,2] / abs(summary(model_nls)$coefficients[2,1])
#### K275 ####
key <- "K275"
row_id <- which(D$Dvalues_tab$Kinetics_key == key)
d <- subset(dk, Kinetics_key==key)
#D$regplot$K275
-1/lm(data = d, formula = y ~ time_hours)$coefficients[2]
model_nls <- nls(data = d, formula = y ~ b - (time_hours/D_value),
start = list(b = 2,
D_value = -10),
algorithm = "port")
summary(model_nls)
D$Dvalues_tab[row_id,]$Dvalues <- abs(summary(model_nls)$coefficients[2,1])
D$Dvalues_tab[row_id,]$Dvalues_stderr <- summary(model_nls)$coefficients[2,2]
D$Dvalues_tab[row_id,]$Dvalues_CV <- summary(model_nls)$coefficients[2,2] / abs(summary(model_nls)$coefficients[2,1])
#### K276 ####
key <- "K276"
row_id <- which(D$Dvalues_tab$Kinetics_key == key)
d <- subset(dk, Kinetics_key==key)
#D$regplot$K276
-1/lm(data = d, formula = y ~ time_hours)$coefficients[2]
model_nls <- nls(data = d, formula = y ~ b - (time_hours/D_value),
start = list(b = 2,
D_value = -10),
algorithm = "port")
summary(model_nls)
D$Dvalues_tab[row_id,]$Dvalues <- abs(summary(model_nls)$coefficients[2,1])
D$Dvalues_tab[row_id,]$Dvalues_stderr <- summary(model_nls)$coefficients[2,2]
D$Dvalues_tab[row_id,]$Dvalues_CV <- summary(model_nls)$coefficients[2,2] / abs(summary(model_nls)$coefficients[2,1])
#### K279 ####
key <- "K279"
row_id <- which(D$Dvalues_tab$Kinetics_key == key)
d <- subset(dk, Kinetics_key==key)
#D$regplot$K279
-1/lm(data = d, formula = y ~ time_hours)$coefficients[2]
model_nls <- nls(data = d, formula = y ~ b - (time_hours/D_value),
start = list(b = 2,
D_value = -10),
algorithm = "port")
summary(model_nls)
D$Dvalues_tab[row_id,]$Dvalues <- abs(summary(model_nls)$coefficients[2,1])
D$Dvalues_tab[row_id,]$Dvalues_stderr <- summary(model_nls)$coefficients[2,2]
D$Dvalues_tab[row_id,]$Dvalues_CV <- summary(model_nls)$coefficients[2,2] / abs(summary(model_nls)$coefficients[2,1])
#### K418 ####
key <- "K418"
row_id <- which(D$Dvalues_tab$Kinetics_key == key)
d <- subset(dk, Kinetics_key==key)
#D$regplot$K418
-1/lm(data = d, formula = y ~ time_hours)$coefficients[2]
model_nls <- nls(data = d, formula = y ~ b - (time_hours/D_value),
start = list(b = 2,
D_value = 100),
algorithm = "port")
#summary(model_nls)
D$Dvalues_tab[row_id,]$Dvalues <- summary(model_nls)$coefficients[2,1]
D$Dvalues_tab[row_id,]$Dvalues_stderr <- summary(model_nls)$coefficients[2,2]
D$Dvalues_tab[row_id,]$Dvalues_CV <- summary(model_nls)$coefficients[2,2] / summary(model_nls)$coefficients[2,1]
#### K460 ####
key <- "K460"
row_id <- which(D$Dvalues_tab$Kinetics_key == key)
d <- subset(dk, Kinetics_key==key)
#D$regplot$K460 ## regression plots
-1/lm(data = d, formula = y ~ time_hours)$coefficients[2]
model_nls <- nls(data = d, formula = y ~ b - (time_hours/D_value),
start = list(b = 2,
D_value = 200),
algorithm = "port")
#summary(model_nls)
D$Dvalues_tab[row_id,]$Dvalues <- summary(model_nls)$coefficients[2,1]
D$Dvalues_tab[row_id,]$Dvalues_stderr <- summary(model_nls)$coefficients[2,2]
D$Dvalues_tab[row_id,]$Dvalues_CV <- summary(model_nls)$coefficients[2,2] / summary(model_nls)$coefficients[2,1]
#### Calculate log10(D) ####
D$Dvalues_tab <- mutate(D$Dvalues_tab, log10D = log10(Dvalues))
# Clear the environment #
rm(d, model_nls, key, row_id, f_estimate_Dvalues)
# Save data with estimated values of D
save.image("Dvalues_data.RData")