library(PKbioanalysis)

## Warning in readLines(file, warn = readLines.warn): incomplete final line found
## on '/home/runner/.config/R/PKbioanalysis/config.yaml'

## 
## Attaching package: 'PKbioanalysis'

## The following object is masked from 'package:stats':
## 
##     integrate

library(dplyr)

## 
## Attaching package: 'dplyr'

## The following objects are masked from 'package:stats':
## 
##     filter, lag

## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union

d <- read.csv(system.file("extdata", "GU_1.csv", package = "PKbioanalysis"))

head(d)

##   TYPE  conc stdconc
## 1 LLOQ 0.232     0.2
## 2 LLOQ 0.206     0.2
## 3 LLOQ 0.203     0.2
## 4 LLOQ 0.202     0.2
## 5 LLOQ 0.207     0.2
## 6 LLOQ 0.212     0.2

only_qc <- d |> filter(TYPE %in% c("LLOQ", "LQC", "MQC", "HQC"))

only_qc <- only_qc  |> 
    group_by(TYPE, stdconc) |>
    summarize(
        mean = mean(conc),
        sd = sd(conc),
        cv = sd(conc)/mean(conc)*100,
        n = n()
    )

## `summarise()` has grouped output by 'TYPE'. You can override using the
## `.groups` argument.

only_qc

## # A tibble: 4 × 6
## # Groups:   TYPE [4]
##   TYPE  stdconc    mean     sd    cv     n
##   <chr>   <dbl>   <dbl>  <dbl> <dbl> <int>
## 1 HQC     160   157.    1.37   0.868     6
## 2 LLOQ      0.2   0.210 0.0112 5.32      6
## 3 LQC       0.6   0.613 0.0219 3.57      6
## 4 MQC     100   100.    2.07   2.06      6

plot_var_pattern(only_qc)

fit <- fit_var(d)


formated_print(fit)

Error Type	Estimate	Lower CI	Upper CI	Method	Gradient	SE	RSE%
Constant	0.016	0.008	0.033	nlminb	0.000	0.006	37.6%
Proportional	3.28%	2.45%	4.39%	nlminb	0.000	0.005	15.0%

Estimate LLOQ

estim_lloq(add_err = 0.016, prop_err = 0.032, cv_lloq = 0.1 , cv_lqc = 0.05)

## $lloq
## [1] 0.1688801
## 
## $lqc
## [1] 0.5066402
## 
## $lqc_x2
## [1] 1.01328
## 
## $rsd_lloq
## [1] 0.1
## 
## $rsd_lqc
## [1] 0.04495925
## 
## $rsd_lqc_x2
## [1] 0.0356838
## 
## $add_err
## [1] 0.016
## 
## $prop_err
## [1] 0.032
## 
## $lloq_rsd_contr
## [1] 0.1
## 
## $lqc_rsd_contr
## [1] 0.05

Estimated dilution limit

Divide additive/proportional error

estim_dil_limit(add_err = 0.016, prop_err = 0.032, lloq = 0.2)

## [1] 0.5