GPC_cpp {BuyseTest} | R Documentation |
C++ function performing the pairwise comparison over several endpoints.
Description
GPC_cpp
call for each endpoint and each strata the pairwise comparison function suited to the type of endpoint and store the results.
Usage
GPC_cpp(
endpoint,
status,
indexC,
posC,
indexT,
posT,
threshold,
restriction,
weightEndpoint,
weightObs,
method,
pool,
op,
D,
D_UTTE,
n_strata,
nUTTE_analyzedPeron_M1,
index_endpoint,
index_status,
index_UTTE,
list_survTimeC,
list_survTimeT,
list_survJumpC,
list_survJumpT,
list_lastSurv,
p_C,
p_T,
iid_survJumpC,
iid_survJumpT,
zeroPlus,
correctionUninf,
hierarchical,
hprojection,
neutralAsUninf,
addHalfNeutral,
keepScore,
precompute,
paired,
returnIID,
debug
)
GPC2_cpp(
endpoint,
status,
indexC,
posC,
indexT,
posT,
threshold,
restriction,
weightEndpoint,
weightObs,
method,
pool,
op,
D,
D_UTTE,
n_strata,
nUTTE_analyzedPeron_M1,
index_endpoint,
index_status,
index_UTTE,
list_survTimeC,
list_survTimeT,
list_survJumpC,
list_survJumpT,
list_lastSurv,
p_C,
p_T,
iid_survJumpC,
iid_survJumpT,
zeroPlus,
correctionUninf,
hierarchical,
hprojection,
neutralAsUninf,
addHalfNeutral,
keepScore,
precompute,
paired,
returnIID,
debug
)
Arguments
endpoint |
A matrix containing the values of each endpoint (in columns) for each observation (in rows). |
status |
A matrix containing the values of the status variables relative to each endpoint (in columns) for each observation (in rows). |
indexC |
A list containing, for each strata, which rows of the endpoint and status matrices corresponds to the control observations. Not unique when bootstraping. |
posC |
A list containing, for each strata, the unique identifier of each control observations. |
indexT |
A list containing, for each strata, which rows of the endpoint and status matrices corresponds to the treatment observations. Not unique when bootstraping. |
posT |
A list containing, for each strata, the unique identifier of each treatment observations. |
threshold |
Store the thresholds associated to each endpoint. Must have length D. The threshold is ignored for binary endpoints. |
restriction |
Store the restriction time associated to each endpoint. Must have length D. |
weightEndpoint |
Store the weight associated to each endpoint. Must have length D. |
weightObs |
A vector containing the weight associated to each observation. |
method |
The index of the method used to score the pairs. Must have length D. 1 for binary/continuous, 2 for Gaussian, 3/4 for Gehan (left or right-censoring), and 5/6 for Peron (right-censoring survival or competing risks). |
pool |
The index of the method used to pool results across strata. Can be 0 (weight inversely proportional to the sample size), 1 (Mantel Haenszel weights), 2 (equal weights), 3 (precision weights) |
op |
The index of the operator used to score the pairs. Must have length D. 1 for larger is beter, -1 for smaller is better. |
D |
The number of endpoints. |
D_UTTE |
The number of distinct time to event endpoints. |
n_strata |
The number of strata. |
nUTTE_analyzedPeron_M1 |
The number of unique time-to-event endpoints that have been analyzed the Peron scoring rule before the current endpoint. Must have length D. |
index_endpoint |
The position of the endpoint at each priority in the argument endpoint. Must have length D. |
index_status |
The position of the status at each priority in the argument status. Must have length D. |
index_UTTE |
The position, among all the unique tte endpoints, of the TTE endpoints. Equals -1 for non tte endpoints. Must have length n_TTE. |
list_survTimeC |
A list of matrix containing the survival estimates (-threshold, 0, +threshold ...) for each event of the control group (in rows). |
list_survTimeT |
A list of matrix containing the survival estimates (-threshold, 0, +threshold ...) for each event of the treatment group (in rows). |
list_survJumpC |
A list of matrix containing the survival estimates and survival jumps when the survival for the control arm jumps. |
list_survJumpT |
A list of matrix containing the survival estimates and survival jumps when the survival for the treatment arm jumps. |
list_lastSurv |
A list of matrix containing the last survival estimate in each strata (rows) and treatment group (columns). |
p_C |
Number of nuisance parameter in the survival model for the control group, for each endpoint and strata |
p_T |
Number of nuisance parameter in the survival model for the treatment group, for each endpoint and strata |
iid_survJumpC |
A list of matrix containing the iid of the survival estimates in the control group. |
iid_survJumpT |
A list of matrix containing the iid of the survival estimates in the treatment group. |
zeroPlus |
Value under which doubles are considered 0? |
correctionUninf |
Should the uninformative weight be re-distributed to favorable and unfavorable? |
hierarchical |
Should only the uninformative pairs be analyzed at the lower priority endpoints (hierarchical GPC)? Otherwise all pairs will be compaired for all endpoint (full GPC). |
hprojection |
Order of the H-projection used to compute the variance. |
neutralAsUninf |
Should paired classified as neutral be re-analyzed using endpoints of lower priority? |
addHalfNeutral |
Should half of the neutral score be added to the favorable and unfavorable scores? |
keepScore |
Should the result of each pairwise comparison be kept? |
precompute |
Have the integrals relative to the survival be already computed and stored in list_survTimeC/list_survTimeT and list_survJumpC/list_survJumpT (derivatives) |
paired |
In case of paired data, the variance of the summary statistic across strata will be added to the variance of the pooled statistic. |
returnIID |
Should the iid be computed? Second element: is there any nuisance parameter? |
debug |
Print messages tracing the execution of the function to help debugging. The amount of messages increase with the value of debug (0-5). |
Details
GPC_cpp implements GPC looping first over endpoints and then over pairs. To handle multiple endpoints, it stores some of the results which can be memory demanding when considering large sample - especially when computing the iid decomposition. GPC2_cpp implements GPC looping first over pairs and then over endpoints. It has rather minimal memory requirement but does not handle correction for uninformative pairs.
Author(s)
Brice Ozenne