Display the diagnostic curves for BMR estimation
It turns out for the percent_mortality_96 endpoint, the shape is not in the right form (as the percent_affected_96 endpoint).
zfishdev a subset of data from a 32-compound screen using zebrafish developmental assays. Our goal is to decide whether a compound is active in a particular toxicity endpoint. The active is determined by if the responses is monotonic (as the increase of concentration). In addition, the maximum response has to be larger than a certain response threshold.
# More details of the dataset can be found ?zfishdev.
data(zfishdev)
str(zfishdev)
#> tibble [96 × 5] (S3: tbl_df/tbl/data.frame)
#> $ endpoint: chr [1:96] "percent_affected_48" "percent_affected_48" "percent_affected_48" "percent_affected_48" ...
#> $ chemical: chr [1:96] "Caffeine|58-08-2" "Caffeine|58-08-2" "Caffeine|58-08-2" "Caffeine|58-08-2" ...
#> $ conc : num [1:96] -4 -3.82 -3.52 -3.3 -3.12 -3 -2.82 -2.7 -7 -6.52 ...
#> $ n_in : int [1:96] 0 2 5 15 15 15 15 15 0 2 ...
#> $ N : int [1:96] 15 15 15 15 15 15 15 15 15 15 ...The Rcurvep is a tool to decide whether responses are monotonic (as the increase of concentration) based on a set of pre-defined parameters. The default setting of those parameters can be obtained through curvep_defaults(). The TRSH is the threshold parameter, below which, all responses are considered as noise. This threshold is particularly important for toxicologists, since the point-of-departure (POD) can be defined as the concentration at which response equivalent to this threshold. The threshold can also be called as benchmark response (BMR).
Since zfishdev does not contain a column with responses, create_dataset() can be used to generate the responses for this particular type of data. However, this function is already incorporated.
If there is a preferred BMR, you can run the dataset using the threshold. The act_set in the result contains potency and efficacy information of the concentration-response data (aka curve).
out <- combi_run_rcurvep(
zfishdev,
TRSH = 25, # BMR = 25
RNGE = 1000000 # increasing direction
)
out
#>
#> 4 endpoint(s) and 3 chemical(s)
#> Components in the list: result, config
#> Components in the result: act_set, resp_set, fp_set
#>
out$config
#>
#> curvep configuration parameters
#> TRSH: [25]
#> RNGE: [1e+06]
#> MXDV: [5]
#> CARR: [0]
#> BSFT: [3]
#> USHP: [4]
#> TrustHi: [TRUE]
#> StrictImp: [TRUE]
#> DUMV: [-999]
#> TLOG: [-24]
#> seed: [NA]
#> The results of the summary is saved in the tibble, act_summary.
The confidence interval is calculated using simulated datasets created by bootstrapping the original responses. By setting the parameter, n_samples, number of curves are simulated. The same summarize_rcurvep_output() can be used to summarize the results.
set.seed(300)
out <- combi_run_rcurvep(
zfishdev,
n_samples = 10, # often 1000 samples are preferred
TRSH = 25,
RNGE = 1000000,
keep_sets = "act_set"
)
sum_out <- summarize_rcurvep_output(out)
sum_out
#>
#> 4 endpoint(s) and 3 chemical(s)
#> Components in the list: result, config, act_summary
#> Components in the result: act_set
#> The optimal BMR may be defined as the threshold at which the potency estimation is more accurate. The concept can be translated as the lowest threshold (which gives the highest potency), at which a decrease of variance in potency estimation is stabilized. By using the simulated datasets, the pooled variance across chemicals at a certain threshold can be estimated.
# The combi_run_rcurvep() can be used for a combination of Curvep parameters.
# finishing the code will take some time.
set.seed(300)
data(zfishdev_all)
zfishdev_act <- combi_run_rcurvep(
zfishdev_all,
n_samples = 100,
keep_sets = c("act_set"),
TRSH = seq(5, 95, by = 5), # test all candidates, 5 to 95
RNGE = 1000000,
CARR = 20
)For the two endpoints, BMR = 25 (in bmr_ori column) is suggested for the percent_affected_96 endpoint with an OK comment but for the percent_mortality_96 endpoint, check is noted.
data(zfishdev_act)
bmr_out <- estimate_dataset_bmr(zfishdev_act, plot = FALSE)
bmr_out$outcome
#> # A tibble: 2 × 12
#> RNGE CARR endpoint bmr_ori p1_ori p2_ori bmr_exp p1_exp p2_exp cor_exp_fit
#> <dbl> <dbl> <chr> <dbl> <int> <int> <dbl> <int> <int> <dbl>
#> 1 1000000 20 percent… 25 1 19 20 1 19 0.994
#> 2 1000000 20 percent… 55 6 19 50 1 19 0.789
#> # ℹ 2 more variables: cor_lm_fit <dbl>, qc <chr>It turns out for the percent_mortality_96 endpoint, the shape is not in the right form (as the percent_affected_96 endpoint).
Since zfishdev does not contain a column with responses, create_dataset() needs to be used to generate the responses for this particular type of data. Unlike combi_run_rcurvep(), create_dataset() has to be called explicitly.
# set the preferred direction as increasing hill_pdir = 1
# this is to use the 3-parameter hill
fitd1 <- run_fit(create_dataset(zfishdev), hill_pdir = 1, modls = "hill")
fitd1
#>
#> 4 endpoint(s) and 3 chemical(s)
#> Components in the list: result, result_nested
#> Components in the result: fit_set, resp_set
#>
# can also use the curve class2 4-parameter hill with classification SD as 5%
# please ?fit_cc2_modl to understand curve classification
fitd2 <- run_fit(create_dataset(zfishdev), cc2_classSD = 5, modls = "cc2")
fitd2
#>
#> 4 endpoint(s) and 3 chemical(s)
#> Components in the list: result, result_nested
#> Components in the result: fit_set, resp_set
#> The results of the summary is saved in the tibble, act_summary.
# thr_resp will get BMC10% and perc_resp will get EC20%
# hill with 3-parameter
fitd_sum_out1 <- summarize_fit_output(fitd1, thr_resp = 10, perc_resp = 20, extract_only = TRUE)
# cc2 (hill with 4-parameter + curve classification)
fitd_sum_out2 <- summarize_fit_output(fitd2, thr_resp = 10, perc_resp = 20, extract_only = TRUE)#EC20% concordance (when both methods provide values)
cor(fitd_sum_out1$result$act_set$ECxx, fitd_sum_out2$result$act_set$ECxx, use = "pairwise.complete.obs")
#> [1] 0.9941618
#BMC10% (when both methods provide values)
cor(fitd_sum_out1$result$act_set$POD, fitd_sum_out2$result$act_set$POD, use = "pairwise.complete.obs")
#> [1] 0.9888046
#EC50 (when both methods provide values)
cor(fitd_sum_out1$result$act_set$EC50, fitd_sum_out2$result$act_set$EC50, use = "pairwise.complete.obs")
#> [1] 0.9994521
# check number of curves consider as active by both
sum(fitd_sum_out1$result$act_set$hit == 0) # no fit
#> [1] 7
sum(fitd_sum_out2$result$act_set$hit == 4) # cc2 = 4 (inactive)
#> [1] 7