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#' ezmmek_calibrate_activities
#'
#' @importFrom magrittr "%>%"
#'
#' @description Calibrates enzyme activity data by standard curve
#'
#' @param df Joined dataframes of class 'new_ezmmek_std_group' and 'new_ezmmek_act_group'
#' @param method Enzyme assay protocol. Must define method as 'isc' or 'ibc'
#' @param columns Column names carried from parent functions
########
### Calibrate activities by standard curve data
########
ezmmek_calibrate_activities <- function(df, method, columns) {
if(method == "isc") {
### Calibrates raw activity data by standard curve
std_act_calibrated <- df %>%
tidyr::unnest(act_raw_data_isc) %>%
dplyr::mutate(signal_calibrated = ((signal - std_lm_homo_buffer_intercept) / std_lm_homo_buffer_slope) -
(kill_control - std_lm_homo_buffer_intercept) / std_lm_homo_buffer_slope) %>% #calibrate signal
tidyr::nest(act_calibrated_data = c(time, signal, kill_control, signal_calibrated)) %>% #place calibrated signal back in nested df
dplyr::mutate(activity = purrr::map_dbl(act_calibrated_data, #calculate slope of calibrated data
function(df) coef(lm(signal_calibrated ~ time,
data = df))[2])) %>%
dplyr::group_by_at(dplyr::vars(substrate_conc, substrate_type, intersect(names(.), columns))) %>%
dplyr::mutate(activity_m = mean(activity), #calculate means and sd's of activities
activity_sd = sd(activity)) %>%
tidyr::unnest(act_calibrated_data) %>%
tidyr::nest(act_calibrated_data_isc = c(substrate_conc,
replicate,
time,
signal,
kill_control,
signal_calibrated,
activity,
activity_m,
activity_sd))
}
if(method == "ibc") {
std_act_calibrated <- df %>%
tidyr::unnest(act_raw_data_ibc) %>%
dplyr::mutate(emission_coef = std_lm_homo_slope / std_vol, #emission coefficient
net_signal = (signal - homo_control) / quench_coef - substrate_control, #net signal
activity = (net_signal * buffer_vol) / (emission_coef * homo_vol * time * soil_mass)) %>% #activity
dplyr::group_by(substrate_conc) %>%
dplyr::mutate(activity_m = mean(activity), activity_sd = sd(activity)) %>% #mean and sd of activity
tidyr::nest(act_calibrated_data_ibc = c(substrate_conc,
replicate,
time,
signal,
buffer_vol,
homo_vol,
soil_mass,
std_vol,
homo_control,
substrate_control,
net_signal,
activity,
activity_m,
activity_sd))
}
std_act_calibrated
}
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