Last updated on 2024-12-18 19:49:32 CET.
| Package | NOTE | OK |
|---|---|---|
| MCPModPack | 4 | 9 |
| MedianaDesigner | 12 | 1 |
| rsides | 4 | 9 |
Current CRAN status: NOTE: 4, OK: 9
Version: 0.5
Check: installed package size
Result: NOTE
installed size is 5.9Mb
sub-directories of 1Mb or more:
libs 5.4Mb
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Current CRAN status: NOTE: 12, OK: 1
Version: 0.13
Check: Rd files
Result: NOTE
checkRd: (-1) ADPopSel.Rd:17-23: Lost braces
17 | \item \code{endpoint_type}{: Character value defining the primary endpoint's type. Possible values:
| ^
checkRd: (-1) ADPopSel.Rd:24: Lost braces
24 | \item \code{direction}{: Character value defining the direction of favorable outcome. Possible values: \code{"Higher"} (a higher value of the endpoint indicates a more favorable outcome) and \code{"Lower"} (a lower value of the endpoint indicates a more favorable outcome).}
| ^
checkRd: (-1) ADPopSel.Rd:25: Lost braces
25 | \item \code{sample_size}{: Integer vector with two elements defining the number of enrolled patients in the two trial arms (control and experimental treatment). Each element must be positive.}
| ^
checkRd: (-1) ADPopSel.Rd:26: Lost braces
26 | \item \code{control_mean}{: Numeric value defining the mean of the primary endpoint in the control arm. This parameter is required only with normally distributed endpoints (\code{endpoint_type="Normal"}).}
| ^
checkRd: (-1) ADPopSel.Rd:27: Lost braces
27 | \item \code{control_sd}{: Numeric value defining the standard deviation of the primary endpoint in the control arm. This value must be positive. This parameter is required only with normally distributed endpoints.}
| ^
checkRd: (-1) ADPopSel.Rd:28: Lost braces
28 | \item \code{treatment_mean}{: Numeric value defining the mean of the primary endpoint in the experimental treatment arm. This parameter is required only with normally distributed endpoints.}
| ^
checkRd: (-1) ADPopSel.Rd:29: Lost braces
29 | \item \code{treatment_sd}{: Numeric value defining the standard deviation of the primary endpoint in the experimental treatment arm. This value must be positive. This parameter is required only with normally distributed endpoints.}
| ^
checkRd: (-1) ADPopSel.Rd:30: Lost braces
30 | \item \code{control_rate}{: Numeric value defining the proportion or response rate for the primary endpoint in the control arm. This value must be between 0 and 1. This parameter is required only with binary endpoints \cr (\code{endpoint_type="Binary"}).}
| ^
checkRd: (-1) ADPopSel.Rd:31: Lost braces
31 | \item \code{treatment_rate}{: Numeric value defining the proportion or response rate for the primary endpoint in the experimental treatment arm. This value must be between 0 and 1. This parameter is required only with binary endpoints.}
| ^
checkRd: (-1) ADPopSel.Rd:32: Lost braces
32 | \item \code{control_time}{: Numeric value defining the median time, e.g., the median survival time, for the exponentially distributed primary endpoint in the control arm. This value must be positive. This parameter is required only with time-to-event endpoints (\code{endpoint_type="Time-to-event"}).}
| ^
checkRd: (-1) ADPopSel.Rd:33: Lost braces
33 | \item \code{treatment_time}{: Numeric value defining the median time, e.g., the median survival time, for the exponentially distributed primary endpoint in the experimental treatment arm. This value must be positive. This parameter is required only with time-to-event endpoints.}
| ^
checkRd: (-1) ADPopSel.Rd:34: Lost braces
34 | \item \code{info_frac}{: Numeric vector with three elements defining the information fractions at the first interim analysis, at the second interim analysis and at the final analysis. The first and second elements must be between 0 and 1, and the third element must be 1.}
| ^
checkRd: (-1) ADPopSel.Rd:35: Lost braces
35 | \item \code{event_count}{: Numeric value defining the total number of events at the final analysis. This value must be positive. This parameter is required only with time-to-event endpoints.}
| ^
checkRd: (-1) ADPopSel.Rd:36: Lost braces
36 | \item \code{futility_threshold}{: Numeric value defining the futility threshold for conditional power at the first interim analysis. This value must be positive.}
| ^
checkRd: (-1) ADPopSel.Rd:37: Lost braces
37 | \item \code{influence}{: Numeric value defining the influence threshold for selecting the most promising population or populations at the second interim analysis. This value must be positive.}
| ^
checkRd: (-1) ADPopSel.Rd:38: Lost braces
38 | \item \code{interaction}{: Numeric value defining the interaction threshold for selecting the most promising population or populations at the second interim analysis. This value must be greater than 1.}
| ^
checkRd: (-1) ADPopSel.Rd:39: Lost braces
39 | \item \code{dropout_rate}{: Numeric value defining the patient dropout rate. With normally distributed endpoints and binary endpoints, a uniform patient dropout process is assumed and thus this parameter defines the fraction of patients that will be excluded from the interim and final analyses. With time-to-event endpoints, the time to patient dropout is assumed to follow an exponential distribution and this parameter defines the annual dropout rate. This value must be between 0 and 1.}
| ^
checkRd: (-1) ADPopSel.Rd:40: Lost braces
40 | \item \code{enrollment_period}{: Numeric value defining the length of the patient enrollment period. This value must be positive. This parameter is required only with time-to-event endpoints.}
| ^
checkRd: (-1) ADPopSel.Rd:41: Lost braces
41 | \item \code{enrollment_parameter}{: Numeric value defining the median enrollment time. The patient enrollment process is assumed to be governed by a truncated exponential distribution and this parameter defines the time point by which 50\% of the patients are enrolled into the trial. This value must be between 0 and the length of the patient enrollment period. This parameter is required only with time-to-event endpoints.}.
| ^
checkRd: (-1) ADPopSel.Rd:42: Lost braces
42 | \item \code{alpha}{: Numeric value defining the overall one-sided Type I error rate. The default value is 0.025.}
| ^
checkRd: (-1) ADPopSel.Rd:43: Lost braces
43 | \item \code{random_seed}{: Integer value defining the random number generator seed. The default value is 49283.}
| ^
checkRd: (-1) ADPopSel.Rd:44: Lost braces
44 | \item \code{nsims}{: Integer value defining the number of simulation runs.}
| ^
checkRd: (-1) ADPopSel.Rd:45: Lost braces
45 | \item \code{ncores}{: Integer value defining the number of cores for parallel calculations. The number of cores cannot exceed the maximum available number of cores. The default value is 1.}
| ^
checkRd: (-1) ADRand.Rd:19-23: Lost braces
19 | \item \code{endpoint_type}{: Character value defining the primary endpoint's type. Possible values:
| ^
checkRd: (-1) ADRand.Rd:24: Lost braces
24 | \item \code{direction}{: Character value defining the direction of favorable outcome. Possible values: \code{"Higher"} (a higher value of the endpoint indicates a more favorable outcome) and \code{"Lower"} (a lower value of the endpoint indicates a more favorable outcome).}
| ^
checkRd: (-1) ADRand.Rd:25: Lost braces
25 | \item \code{dose_levels}{: Integer vector defining the dose levels in the trial (0 corresponds to the placebo group). Each element must be non-negative.}
| ^
checkRd: (-1) ADRand.Rd:26: Lost braces
26 | \item \code{stage_sample_size}{: Integer vector defining the total number of patients enrolled in each stage. Each element must be positive.}
| ^
checkRd: (-1) ADRand.Rd:27: Lost braces
27 | \item \code{control_mean}{: Numeric value defining the mean of the primary endpoint in the placebo arm. }
| ^
checkRd: (-1) ADRand.Rd:28: Lost braces
28 | \item \code{control_sd}{: Numeric value defining the standard deviation of the primary endpoint in the placebo arm. This value must be positive. }
| ^
checkRd: (-1) ADRand.Rd:29: Lost braces
29 | \item \code{treatment_mean}{: Numeric vector defining the mean of the primary endpoint in each dosing arm.}
| ^
checkRd: (-1) ADRand.Rd:30: Lost braces
30 | \item \code{treatment_sd}{: Numeric vector defining the standard deviation of the primary endpoint in each dosing arm.}
| ^
checkRd: (-1) ADRand.Rd:31: Lost braces
31 | \item \code{treatment_period}{: Numeric value defining the length of the treatment period in the trial.}
| ^
checkRd: (-1) ADRand.Rd:32: Lost braces
32 | \item \code{ratio_placebo}{: Numeric value defining the fixed randomization ratio in the placebo arm. This value must be between 0 and 1.}
| ^
checkRd: (-1) ADRand.Rd:33: Lost braces
33 | \item \code{balance}{: Numeric value defining the degree of balance for adaptive randomization. This value must be between 0 and 3.}
| ^
checkRd: (-1) ADRand.Rd:34: Lost braces
34 | \item \code{delta}{: Numeric value defining the threshold for a clinically meaningful improvement over placebo.}
| ^
checkRd: (-1) ADRand.Rd:35: Lost braces
35 | \item \code{exponential_model_parameter}{: Numeric value defining the non-linear parameter (delta) for the exponential dose-response model used in the MCPMod method. This value must be positive.}
| ^
checkRd: (-1) ADRand.Rd:36: Lost braces
36 | \item \code{emax_model_parameter}{: Numeric value defining the non-linear parameter (ED50) for the Emax dose-response model used in the MCPMod method. This value must be positive.}
| ^
checkRd: (-1) ADRand.Rd:37: Lost braces
37 | \item \code{logistic_model_parameters}{: Numeric vector with two elements defining the non-linear parameters (ED50 and delta) for the logistic dose-response model used in the MCPMod method. The values must be positive.}
| ^
checkRd: (-1) ADRand.Rd:38: Lost braces
38 | \item \code{enrollment_period}{: Numeric value defining the length of the patient enrollment period. This value must be positive. }
| ^
checkRd: (-1) ADRand.Rd:39: Lost braces
39 | \item \code{enrollment_parameter}{: Numeric value defining the median enrollment time. The patient enrollment process is assumed to be governed by a truncated exponential distribution and this parameter defines the time point by which 50\% of the patients are enrolled into the trial. This value must be between 0 and the length of the patient enrollment period.}
| ^
checkRd: (-1) ADRand.Rd:40: Lost braces
40 | \item \code{dropout_rate}{: Numeric value defining the patient dropout rate. A uniform patient dropout process is assumed and thus this parameter defines the fraction of patients that will be excluded from the interim and final analyses. This value must be between 0 and 1.}
| ^
checkRd: (-1) ADRand.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ADRand.Rd:42: Lost braces
42 | \item \code{random_seed}{: Integer value defining the random number generator seed. The default value is 49283.}
| ^
checkRd: (-1) ADRand.Rd:43: Lost braces
43 | \item \code{nsims}{: Integer value defining the number of simulation runs.}
| ^
checkRd: (-1) ADRand.Rd:44: Lost braces
44 | \item \code{ncores}{: Integer value defining the number of cores for parallel calculations. The number of cores cannot exceed the maximum available number of cores. The default value is 1.}
| ^
checkRd: (-1) ADSSMod.Rd:17-23: Lost braces
17 | \item \code{endpoint_type}{: Character value defining the primary endpoint's type. Possible values:
| ^
checkRd: (-1) ADSSMod.Rd:24: Lost braces
24 | \item \code{direction}{: Character value defining the direction of favorable outcome. Possible values: \code{"Higher"} (a higher value of the endpoint indicates a more favorable outcome) and \code{"Lower"} (a lower value of the endpoint indicates a more favorable outcome).}
| ^
checkRd: (-1) ADSSMod.Rd:25: Lost braces
25 | \item \code{sample_size}{: Integer vector with two elements defining the number of enrolled patients in the two trial arms (control and experimental treatment). Each element must be positive.}
| ^
checkRd: (-1) ADSSMod.Rd:26: Lost braces
26 | \item \code{control_mean}{: Numeric value defining the mean of the primary endpoint in the control arm. This parameter is required only with normally distributed endpoints (\code{endpoint_type="Normal"}).}
| ^
checkRd: (-1) ADSSMod.Rd:27: Lost braces
27 | \item \code{control_sd}{: Numeric value defining the standard deviation of the primary endpoint in the control arm. This value must be positive. This parameter is required only with normally distributed endpoints.}
| ^
checkRd: (-1) ADSSMod.Rd:28: Lost braces
28 | \item \code{treatment_mean}{: Numeric value defining the mean of the primary endpoint in the experimental treatment arm. This parameter is required only with normally distributed endpoints.}
| ^
checkRd: (-1) ADSSMod.Rd:29: Lost braces
29 | \item \code{treatment_sd}{: Numeric value defining the standard deviation of the primary endpoint in the experimental treatment arm. This value must be positive. This parameter is required only with normally distributed endpoints.}
| ^
checkRd: (-1) ADSSMod.Rd:30: Lost braces
30 | \item \code{control_rate}{: Numeric value defining the proportion or response rate for the primary endpoint in the control arm. This value must be between 0 and 1. This parameter is required only with binary endpoints \cr (\code{endpoint_type="Binary"}).}
| ^
checkRd: (-1) ADSSMod.Rd:31: Lost braces
31 | \item \code{treatment_rate}{: Numeric value defining the proportion or response rate for the primary endpoint in the experimental treatment arm. This value must be between 0 and 1. This parameter is required only with binary endpoints.}
| ^
checkRd: (-1) ADSSMod.Rd:32: Lost braces
32 | \item \code{control_time}{: Numeric value defining the median time, e.g., the median survival time, for the exponentially distributed primary endpoint in the control arm. This value must be positive. This parameter is required only with time-to-event endpoints (\code{endpoint_type="Time-to-event"}).}
| ^
checkRd: (-1) ADSSMod.Rd:33: Lost braces
33 | \item \code{treatment_time}{: Numeric value defining the median time, e.g., the median survival time, for the exponentially distributed primary endpoint in the experimental treatment arm. This value must be positive. This parameter is required only with time-to-event endpoints.}
| ^
checkRd: (-1) ADSSMod.Rd:34: Lost braces
34 | \item \code{info_frac}{: Numeric vector with four elements defining the information fractions at the first interim analysis, at the second interim analysis, at the final analysis before sample size/event count adjustment and at the final analysis after sample size/event count adjustment adjustment. The first and second elements must be between 0 and 1, the third element must be 1 and the fourth element must be greater than 1.}
| ^
checkRd: (-1) ADSSMod.Rd:35: Lost braces
35 | \item \code{event_count}{: Numeric value defining the total number of events at the final analysis before event count adjustment. This value must be positive. This parameter is required only with time-to-event endpoints.}
| ^
checkRd: (-1) ADSSMod.Rd:36: Lost braces
36 | \item \code{futility_threshold}{: Numeric value defining the futility threshold for conditional power at the first interim analysis. This value must be positive.}
| ^
checkRd: (-1) ADSSMod.Rd:37: Lost braces
37 | \item \code{promising_interval}{: Numeric vector with two elements defining the promising interval for conditional power at the second interim analysis. Each element must be between 0 and 1.}
| ^
checkRd: (-1) ADSSMod.Rd:38: Lost braces
38 | \item \code{target_power}{: Numeric value defining the target conditional power for increasing the number of patients or events at the second interim analysis. This value must be between 0 and 1.}
| ^
checkRd: (-1) ADSSMod.Rd:39: Lost braces
39 | \item \code{dropout_rate}{: Numeric value defining the patient dropout rate. With normally distributed endpoints and binary endpoints, a uniform patient dropout process is assumed and thus this parameter defines the fraction of patients that will be excluded from the interim and final analyses. With time-to-event endpoints, the time to patient dropout is assumed to follow an exponential distribution and this parameter defines the annual dropout rate. This value must be between 0 and 1.}
| ^
checkRd: (-1) ADSSMod.Rd:40: Lost braces
40 | \item \code{enrollment_period}{: Numeric value defining the length of the patient enrollment period. This value must be positive. This parameter is required only with time-to-event endpoints.}
| ^
checkRd: (-1) ADSSMod.Rd:41: Lost braces
41 | \item \code{enrollment_parameter}{: Numeric value defining the median enrollment time. The patient enrollment process is assumed to be governed by a truncated exponential distribution and this parameter defines the time point by which 50\% of the patients are enrolled into the trial. This value must be between 0 and the length of the patient enrollment period. This parameter is required only with time-to-event endpoints.}.
| ^
checkRd: (-1) ADSSMod.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ADSSMod.Rd:43: Lost braces
43 | \item \code{random_seed}{: Integer value defining the random number generator seed. The default value is 49283.}
| ^
checkRd: (-1) ADSSMod.Rd:44: Lost braces
44 | \item \code{nsims}{: Integer value defining the number of simulation runs.}
| ^
checkRd: (-1) ADSSMod.Rd:45: Lost braces
45 | \item \code{ncores}{: Integer value defining the number of cores for parallel calculations. The number of cores cannot exceed the maximum available number of cores. The default value is 1.}
| ^
checkRd: (-1) ADTreatSel.Rd:17-23: Lost braces
17 | \item \code{endpoint_type}{: Character value defining the primary endpoint's type. Possible values:
| ^
checkRd: (-1) ADTreatSel.Rd:24: Lost braces
24 | \item \code{direction}{: Character value defining the direction of favorable outcome. Possible values: \code{"Higher"} (a higher value of the endpoint indicates a more favorable outcome) and \code{"Lower"} (a lower value of the endpoint indicates a more favorable outcome).}
| ^
checkRd: (-1) ADTreatSel.Rd:25: Lost braces
25 | \item \code{sample_size}{: Integer vector defining the number of enrolled patients in the trial arms (control and multiple experimental treatments). Each element must be positive.}
| ^
checkRd: (-1) ADTreatSel.Rd:26: Lost braces
26 | \item \code{control_mean}{: Numeric value defining the mean of the primary endpoint in the control arm. This parameter is required only with normally distributed endpoints (\code{endpoint_type="Normal"}).}
| ^
checkRd: (-1) ADTreatSel.Rd:27: Lost braces
27 | \item \code{control_sd}{: Numeric value defining the standard deviation of the primary endpoint in the control arm. This value must be positive. This parameter is required only with normally distributed endpoints.}
| ^
checkRd: (-1) ADTreatSel.Rd:28: Lost braces
28 | \item \code{treatment_mean}{: Numeric vector defining the means of the primary endpoint in the experimental treatment arms. This parameter is required only with normally distributed endpoints.}
| ^
checkRd: (-1) ADTreatSel.Rd:29: Lost braces
29 | \item \code{treatment_sd}{: Numeric vector defining the standard deviations of the primary endpoint in the experimental treatment arms. Each element must be positive. This parameter is required only with normally distributed endpoints.}
| ^
checkRd: (-1) ADTreatSel.Rd:30: Lost braces
30 | \item \code{control_rate}{: Numeric value defining the proportion or response rate for the primary endpoint in the control arm. This value must be between 0 and 1. This parameter is required only with binary endpoints \cr (\code{endpoint_type="Binary"}).}
| ^
checkRd: (-1) ADTreatSel.Rd:31: Lost braces
31 | \item \code{treatment_rate}{: Numeric vector defining the proportions or response rates for the primary endpoint in the experimental treatment arms. Each element must be between 0 and 1. This parameter is required only with binary endpoints.}
| ^
checkRd: (-1) ADTreatSel.Rd:32: Lost braces
32 | \item \code{control_time}{: Numeric value defining the median time, e.g., the median survival time, for the exponentially distributed primary endpoint in the control arm. This value must be positive. This parameter is required only with time-to-event endpoints (\code{endpoint_type="Time-to-event"}).}
| ^
checkRd: (-1) ADTreatSel.Rd:33: Lost braces
33 | \item \code{treatment_time}{: Numeric vector defining the median times, e.g., the median survival times, for the exponentially distributed primary endpoint in the experimental treatment arms. Each element must be positive. This parameter is required only with time-to-event endpoints.}
| ^
checkRd: (-1) ADTreatSel.Rd:34: Lost braces
34 | \item \code{info_frac}{: Numeric vector with three elements defining the information fractions at the first interim analysis, at the second interim analysis and at the final analysis. The first and second elements must be between 0 and 1, and the third element must be 1.}
| ^
checkRd: (-1) ADTreatSel.Rd:35: Lost braces
35 | \item \code{event_count}{: Numeric value defining the total number of events at the final analysis. This value must be positive. This parameter is required only with time-to-event endpoints.}
| ^
checkRd: (-1) ADTreatSel.Rd:36: Lost braces
36 | \item \code{futility_threshold}{: Numeric value defining the futility threshold for conditional power at the first interim analysis. This value must be positive.}
| ^
checkRd: (-1) ADTreatSel.Rd:37: Lost braces
37 | \item \code{dropout_rate}{: Numeric value defining the patient dropout rate. With normally distributed endpoints and binary endpoints, a uniform patient dropout process is assumed and thus this parameter defines the fraction of patients that will be excluded from the interim and final analyses. With time-to-event endpoints, the time to patient dropout is assumed to follow an exponential distribution and this parameter defines the annual dropout rate. This value must be between 0 and 1.}
| ^
checkRd: (-1) ADTreatSel.Rd:38: Lost braces
38 | \item \code{enrollment_period}{: Numeric value defining the length of the patient enrollment period. This value must be positive. This parameter is required only with time-to-event endpoints.}
| ^
checkRd: (-1) ADTreatSel.Rd:39: Lost braces
39 | \item \code{enrollment_parameter}{: Numeric value defining the median enrollment time. The patient enrollment process is assumed to be governed by a truncated exponential distribution and this parameter defines the time point by which 50\% of the patients are enrolled into the trial. This value must be between 0 and the length of the patient enrollment period. This parameter is required only with time-to-event endpoints.}.
| ^
checkRd: (-1) ADTreatSel.Rd:40: Lost braces
40 | \item \code{treatment_count}{: Integer value defining the number of treatments to be selected at the second interim analysis. This value must range between 1 and the total number of treatments in the trial.}
| ^
checkRd: (-1) ADTreatSel.Rd:41-51: Lost braces
41 | \item \code{mult_test}{: Character value defining the multiple testing procedure to be used in the trial. Possible values:
| ^
checkRd: (-1) ADTreatSel.Rd:47: Lost braces
47 | \item \code{alpha}{: Numeric value defining the overall one-sided Type I error rate. The default value is 0.025.}
| ^
checkRd: (-1) ADTreatSel.Rd:48: Lost braces
48 | \item \code{random_seed}{: Integer value defining the random number generator seed. The default value is 49283.}
| ^
checkRd: (-1) ADTreatSel.Rd:49: Lost braces
49 | \item \code{nsims}{: Integer value defining the number of simulation runs.}
| ^
checkRd: (-1) ADTreatSel.Rd:50: Lost braces
50 | \item \code{ncores}{: Integer value defining the number of cores for parallel calculations. The number of cores cannot exceed the maximum available number of cores. The default value is 1.}
| ^
checkRd: (-1) ClustRand.Rd:20-25: Lost braces
20 | \item \code{endpoint_type}{: Character value defining the primary endpoint's type. Possible values:
| ^
checkRd: (-1) ClustRand.Rd:26: Lost braces
26 | \item \code{direction}{: Character value defining the direction of favorable outcome. Possible values: \code{"Higher"} (a higher value of the endpoint indicates a more favorable outcome) and \code{"Lower"} (a lower value of the endpoint indicates a more favorable outcome).}
| ^
checkRd: (-1) ClustRand.Rd:27: Lost braces
27 | \item \code{sample_size}{: Integer vector defining the number of completers in the trial arms (control arm and several treatment arms). Completers are defined as patients who complete the trial and are included in the final analysis. Each element must be positive.}
| ^
checkRd: (-1) ClustRand.Rd:28-33: Lost braces
28 | \item \code{method_type}{: Character value defining the data analysis method. Possible values:
| ^
checkRd: (-1) ClustRand.Rd:34-39: Lost braces
34 | \item \code{cluster_scheme}{: Character value defining the cluster scheme. Possible values:
| ^
checkRd: (-1) ClustRand.Rd:40: Lost braces
40 | \item \code{control_cluster_size}{: Numeric vector defining the number of cluster sizes in the control arm. This parameter is required only if the cluster sizes are pre-defined (\code{cluster_scheme="Fixed"}).}
| ^
checkRd: (-1) ClustRand.Rd:41: Lost braces
41 | \item \code{treatment_cluster_size}{: Numeric matrix defining the number of cluster sizes in the treatment arms (each row corresponds to a treatment arm). This parameter is required only if the cluster sizes are pre-defined.}
| ^
checkRd: (-1) ClustRand.Rd:42: Lost braces
42 | \item \code{control_cluster_proportion}{: Numeric vector of relative cluster sizes in the control arm. The cluster membership is determined using a generalized Bernoulli distribution based on the relative cluster sizes. Each element must be between 0 and 1. This parameter is required only if the cluster sizes are random (\code{cluster_scheme="Random"}).}
| ^
checkRd: (-1) ClustRand.Rd:43: Lost braces
43 | \item \code{treatment_cluster_proportion}{: Numeric matrix of relative cluster sizes in the treatment arms (each row corresponds to a treatment arm). The cluster membership in each treatment arm is determined using a generalized Bernoulli distribution based on the relative cluster sizes. Each element must be between 0 and 1. This parameter is required only if the cluster sizes are random.}
| ^
checkRd: (-1) ClustRand.Rd:44: Lost braces
44 | \item \code{control_mean}{: Numeric value defining the mean of the primary endpoint in the control arm. This parameter is required only with normally distributed endpoints (\code{endpoint_type="Normal"}).}
| ^
checkRd: (-1) ClustRand.Rd:45: Lost braces
45 | \item \code{treatment_mean}{: Numeric vector defining the means of the primary endpoint in the treatment arms. This parameter is required only with normally distributed endpoints.}
| ^
checkRd: (-1) ClustRand.Rd:46: Lost braces
46 | \item \code{control_rate}{: Numeric value defining the proportion or response rate for the primary endpoint in the control arm. This value must be between 0 and 1. This parameter is required only with binary endpoints \cr (\code{endpoint_type="Binary"}).}
| ^
checkRd: (-1) ClustRand.Rd:47: Lost braces
47 | \item \code{treatment_rate}{: Numeric vector defining the proportion or response rate for the primary endpoint in the treatment arms. Each element must be between 0 and 1. This parameter is required only with binary endpoints.}
| ^
checkRd: (-1) ClustRand.Rd:48: Lost braces
48 | \item \code{control_icc}{: Numeric value defining the intra-cluster correlation coefficient in the control arm. This value must be between 0 and 1.}
| ^
checkRd: (-1) ClustRand.Rd:49: Lost braces
49 | \item \code{control_between_cluster_sd}{: Numeric value defining the between-cluster standard deviation in the control arm. This value must be positive. This parameter is required only with normally distributed endpoints.}
| ^
checkRd: (-1) ClustRand.Rd:50: Lost braces
50 | \item \code{treatment_icc}{: Numeric vector defining the intra-cluster correlation coefficients in the treatment arms. Each element must be between 0 and 1.}
| ^
checkRd: (-1) ClustRand.Rd:51: Lost braces
51 | \item \code{treatment_between_cluster_sd}{: Numeric vector defining the between-cluster standard deviation in the treatment arms. Each element must be positive. This parameter is required only with normally distributed endpoints.}
| ^
checkRd: (-1) ClustRand.Rd:52: Lost braces
52 | \item \code{descriptive_statistics}{: Logical value requesting the computation of descriptive statistics (arm-specific effects and cluster sizes if the cluster sizes are random) from each simulation run. The default value is FALSE.}
| ^
checkRd: (-1) ClustRand.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ClustRand.Rd:54: Lost braces
54 | \item \code{random_seed}{: Integer value defining the random number generator seed. The default value is 49283.}
| ^
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55 | \item \code{nsims}{: Integer value defining the number of simulation runs.}
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56 | \item \code{ncores}{: Integer value defining the number of cores for parallel calculations. The number of cores cannot exceed the maximum available number of cores. The default value is 1.}
| ^
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18 | \item \code{data_set}{: Data frame that contains blinded patient enrollment, event and dropout data at the interim analysis with a single record per patient. The following :
| ^
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20 | \item \code{enrollment}{: Time of the patient's enrollment.}
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21 | \item \code{time}{: Time of the patient's death or last contact if the event is censored relative to the patient's enrollment.}
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22 | \item \code{event}{: Event indicator (1 if the patient died and 0 otherwise).}
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23 | \item \code{dropout}{: Patient dropout indicator (1 if the patient dropped out of the trial/was lost to follow up and 0 otherwise).}
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27 | \item \code{time_points}{: Numeric vector defining the future time points for computing event predictions. Each elements must be greater than the latest time point in the \code{data_set}.}
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28 | \item \code{event_prior_distribution}{: Numeric vector with two elements defining the shape and rate parameters of the prior gamma distribution for the event hazard rate. Each element must be positive. The parameters could be computed using the \code{\link{EventPredPriorDistribution}} function.}
| ^
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29 | \item \code{dropout_prior_distribution}{: Numeric vector with two elements defining the shape and rate parameters of the prior gamma distribution for the patient dropout hazard rate. Each element must be positive. The parameters could be computed using the \code{\link{EventPredPriorDistribution}} function.}
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30 | \item \code{enrollment_prior_distribution}{: Numeric vector with two elements defining the shape and rate parameters of the prior gamma distribution for the patient enrollment rate. Each element must be positive. The parameters could be computed using the \code{\link{EventPredPriorDistribution}} function.}
| ^
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31 | \item \code{random_seed}{: Integer value defining the random number generator seed. The default value is 49283.}
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32 | \item \code{nsims}{: Integer value defining the number of simulation runs.}
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33 | \item \code{ncores}{: Integer value defining the number of cores for parallel calculations. The number of cores cannot exceed the maximum available number of cores. The default value is 1.}
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17 | \item \code{endpoint_type}{: Character value defining the primary endpoint's type. Possible values:
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24 | \item \code{direction}{: Character value defining the direction of favorable outcome. Possible values: \code{"Higher"} (a higher value of the endpoint indicates a more favorable outcome) and \code{"Lower"} (a lower value of the endpoint indicates a more favorable outcome).}
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25 | \item \code{sample_size}{: Integer vector defining the number of enrolled patients in the trial arms (control and multiple experimental treatments). Each element must be positive.}
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26 | \item \code{control_mean}{: Numeric value defining the mean of the primary endpoint in the control arm. This parameter is required only with normally distributed endpoints (\code{endpoint_type="Normal"}).}
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27 | \item \code{control_sd}{: Numeric value defining the standard deviation of the primary endpoint in the control arm. This value must be positive. This parameter is required only with normally distributed endpoints.}
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28 | \item \code{treatment_mean}{: Numeric vector defining the means of the primary endpoint in the experimental treatment arms. This parameter is required only with normally distributed endpoints.}
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29 | \item \code{treatment_sd}{: Numeric vector defining the standard deviations of the primary endpoint in the experimental treatment arms. Each element must be positive. This parameter is required only with normally distributed endpoints.}
| ^
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30 | \item \code{control_rate}{: Numeric value defining the proportion or response rate for the primary endpoint in the control arm. This value must be between 0 and 1. This parameter is required only with binary endpoints \cr (\code{endpoint_type="Binary"}).}
| ^
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31 | \item \code{treatment_rate}{: Numeric vector defining the proportions or response rates for the primary endpoint in the experimental treatment arms. Each element must be between 0 and 1. This parameter is required only with binary endpoints.}
| ^
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32 | \item \code{control_time}{: Numeric value defining the median time, e.g., the median survival time, for the exponentially distributed primary endpoint in the control arm. This value must be positive. This parameter is required only with time-to-event endpoints (\code{endpoint_type="Time-to-event"}).}
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33 | \item \code{treatment_time}{: Numeric vector defining the median times, e.g., the median survival times, for the exponentially distributed primary endpoint in the experimental treatment arms. Each element must be positive. This parameter is required only with time-to-event endpoints.}
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34 | \item \code{info_frac}{: Numeric value defining the information fraction at the interim analysis. This value must be between 0 and 1.}
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35 | \item \code{event_count}{: Numeric value defining the total number of events at the final analysis. This value must be positive. This parameter is required only with time-to-event endpoints.}
| ^
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36 | \item \code{dropout_rate}{: Numeric value defining the patient dropout rate. With normally distributed endpoints and binary endpoints, a uniform patient dropout process is assumed and thus this parameter defines the fraction of patients that will be excluded from the interim and final analyses. With time-to-event endpoints, the time to patient dropout is assumed to follow an exponential distribution and this parameter defines the annual dropout rate. This value must be between 0 and 1.}
| ^
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37 | \item \code{enrollment_period}{: Numeric value defining the length of the patient enrollment period. This value must be positive. This parameter is required only with time-to-event endpoints.}
| ^
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38 | \item \code{enrollment_parameter}{: Numeric value defining the median enrollment time. The patient enrollment process is assumed to be governed by a truncated exponential distribution and this parameter defines the time point by which 50\% of the patients are enrolled into the trial. This value must be between 0 and the length of the patient enrollment period. This parameter is required only with time-to-event endpoints.}.
| ^
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39 | \item \code{alpha}{: Numeric value defining the overall one-sided Type I error rate. The default value is 0.025.}
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40 | \item \code{random_seed}{: Integer value defining the random number generator seed. The default value is 49283.}
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41 | \item \code{nsims}{: Integer value defining the number of simulation runs.}
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42 | \item \code{ncores}{: Integer value defining the number of cores for parallel calculations. The number of cores cannot exceed the maximum available number of cores. The default value is 1.}
| ^
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103 | Hayes, R.J., Moulton, L.H. (2009). emph{Cluster Randomised Trials: A Practical Approach}. Chapman and Hall/CRC.
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23 | \item \code{endpoint_type}{: Character value defining the common type of trial endpoints. Possible values:
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29 | \item \code{direction}{: Character value defining the common direction of favorable outcome for all endpoints. Possible values: \code{"Higher"} (a higher value of each endpoint indicates a more favorable outcome) and \code{"Lower"} (a lower value of each endpoint indicates a more favorable outcome).}
| ^
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30 | \item \code{n_comparisons}{: Integer value defining the number of dose-control comparisons in the trial. This value must be positive.}
| ^
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31 | \item \code{n_endpoints}{: Integer value defining the number of endpoints in the trial. This value must be positive. Either \code{n_comparisons} or \code{n_endpoints} must be greater than 1.}
| ^
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32 | \item \code{sample_size}{: Integer vector defining the number of enrolled patients in each trial arm (control and experimental treatments). Each element must be positive.}
| ^
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33 | \item \code{control_mean}{: Numeric vector defining the mean of each endpoint in the control arm. This parameter is required only with normally distributed endpoints (\code{endpoint_type="Normal"}).}
| ^
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34 | \item \code{control_sd}{: Numeric vector defining the standard deviation of each endpoint in the control arm. Each element must be positive. This parameter is required only with normally distributed endpoints.}
| ^
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35 | \item \code{treatment_mean}{: Numeric vector or matrix defining the mean of each endpoint in each experimental treatment arm. In clinical trials with several endpoints and several dose-placebo comparisons, the rows corresponds to the endpoints and the columns corresponds to the treatment-control comparisons. This parameter is required only with normally distributed endpoints.}
| ^
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36 | \item \code{treatment_sd}{: Numeric vector or matrix defining the standard deviation of each endpoint in each experimental treatment arm. In clinical trials with several endpoints and several dose-placebo comparisons, the rows corresponds to the endpoints and the columns corresponds to the treatment-control comparisons. Each element must be positive. This parameter is required only with normally distributed endpoints.}
| ^
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37 | \item \code{control_rate}{: Numeric vector defining the proportion or response rate for each endpoint in the control arm. Each element must be between 0 and 1. This parameter is required only with binary endpoints (\code{endpoint_type=} \code{"Binary"}).}
| ^
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38 | \item \code{treatment_rate}{: Numeric vector or matrix defining the proportion or response rate for each endpoint in each experimental treatment arm. In clinical trials with several endpoints and several dose-placebo comparisons, the rows corresponds to the endpoints and the columns corresponds to the treatment-control comparisons. Each element must be between 0 and 1. This parameter is required only with binary endpoints.}
| ^
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39 | \item \code{endpoint_correlation}{: Numeric matrix defining the pairwise correlations among the endpoint-specific test statistics. Each element must be between 0 and 1 and the matrix must be positive definite. This parameter is required only in trials with multiple endpoints.}
| ^
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40 | \item \code{mult_test}{: Character value defining the multiple testing procedure, global testing procedure or gatekeeping procedure. Possible values:
| ^
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52 | \item \code{weights}{: Numeric vector defining the initial hypothesis weights. Each element must be between 0 and 1. This parameter is required only with multiple testing procedures.}
| ^
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53 | \item \code{transition}{: Numeric matrix defining the hypothesis transition parameters. Each element must be between 0 and 1 and the sum of elements in each row must be less than or equal to 1. This parameter is required only with the chain multiple testing procedure.}
| ^
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54 | \item \code{sequence}{: Integer vector defining the hypothesis testing sequence. This parameter is required only with the fixed-sequence multiple testing procedures.}
| ^
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55 | \item \code{mult_method}{: Character value defining the mixture method for the gatekeeping procedure. Possible values:
| ^
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63 | \item \code{mult_test_gamma}{: Numeric vector defining the truncation parameter for each endpoint-specific family of hypotheses. The vector's length must be equal to the number of endpoints. Each element must be between 0 and 1, the last element may be equal to 1 whereas the other elements must be strictly less than 1. This parameter is required only with gatekeeping procedures.}
| ^
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64 | \item \code{dropout_rate}{: Numeric value defining the patient dropout rate. A uniform patient dropout process is assumed and thus this parameter defines the fraction of patients that will be excluded from the analysis. This value must be between 0 and 1.}
| ^
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66 | \item \code{random_seed}{: Integer value defining the random number generator seed. The default value is 49283.}
| ^
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67 | \item \code{nsims}{: Integer value defining the number of simulation runs.}
| ^
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68 | \item \code{ncores}{: Integer value defining the number of cores for parallel calculations. The number of cores cannot exceed the maximum available number of cores. The default value is 1.}
| ^
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64
Version: 0.13
Check: installed package size
Result: NOTE
installed size is 19.0Mb
sub-directories of 1Mb or more:
libs 18.0Mb
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 0.13
Check: R code for possible problems
Result: NOTE
ADPopSel: no visible global function definition for ‘%dorng%’
ADRand: no visible global function definition for ‘%dorng%’
ADSSMod: no visible global function definition for ‘%dorng%’
ADTreatSel: no visible global function definition for ‘%dorng%’
ClustRand: no visible global function definition for ‘%dorng%’
EventPred: no visible global function definition for ‘%dorng%’
FutRuleNCores: no visible global function definition for ‘%dorng%’
MultAdj1NCores: no visible global function definition for ‘%dorng%’
MultAdj2NCores: no visible global function definition for ‘%dorng%’
MultAdj3NCores: no visible global function definition for ‘%dorng%’
Undefined global functions or variables:
%dorng%
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Current CRAN status: NOTE: 4, OK: 9
Version: 0.1
Check: installed package size
Result: NOTE
installed size is 23.8Mb
sub-directories of 1Mb or more:
libs 23.6Mb
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64