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| function(beta, X, y, offset, theta, lambda, S, fact = c(1,1)){ | |
| n <- dim(X)[1] | |
| eta <- offset + X%*%beta | |
| mu <- exp(eta) | |
| aux1 <- theta + y | |
| aux2 <- theta + mu | |
| ## pull the log inside to use gamma and factorial in log space due to | |
| ## possibly very high numbers | |
| l <- sum(lgamma(aux1) - (lfactorial(y) + lgamma(theta))) + t(y) %*% eta + n*theta*log(theta) - t(aux1) %*% log(aux2) | |
| pen <- t(beta) %*% S %*% beta | |
| return((-1/fact[1] * l[1]) + (1/fact[2] * lambda*pen[1,1])) | |
| } |
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| > resetProfiler() | |
| > | |
| > do.call(f, fargs) | |
| [1] 13436.764099638114 | |
| > | |
| > Completed in 0.0 minutes | |
| TOP-LEVEL FUNCTION CALLS | |
| ================== | |
| Function Count Time Own Time % kb Alloc | |
| R do.call 1 337 27 8% 201.0 kb | |
| R print 1 0 0 0% | |
| B resetProfiler 1 0 0 0% | |
| FUNCTION CALLS BY OWN TIME | |
| ========================== | |
| Function Count Time Own Time % kb Alloc | |
| R selectMethod 7 98 97 29% 1.3 mb | |
| C Csparse_dense_prod 1 49 48 14% 173.4 kb | |
| C dgeMatrix_matrix_mm 3 29 28 8% 848.5 kb | |
| R do.call 1 337 27 8% 201.0 kb | |
| R .M.vectorSub 1 21 20 6% | |
| B return 600 44 17 5% 95.1 kb | |
| B .Call 443 122 6 2% 11.7 kb | |
| B length 305 5 5 2% 39.3 kb | |
| C Csparse_dense_crossprod 2 5 4 1% 18.8 kb | |
| B exp 2 5 4 1% 10.3 kb | |
| R identical 851 27 3 1% | |
| B dim 3 3 3 1% 12.8 kb | |
| B standardGeneric 22 418 3 1% 2.8 kb | |
| R eval 15 9 3 1% | |
| R .findInheritedMethods 1 13 3 1% 15.2 kb | |
| R t.default 8 3 3 1% | |
| B lgamma 3 2 2 1% | |
| B names 209 2 2 1% 24.8 kb | |
| R deparse 5 3 2 1% | |
| R topenv 95 8 2 1% | |
| R getClassDef 211 15 2 1% | |
| B as.character 356 2 2 1% 6.5 kb | |
| B @<- 44 10 1 1% | |
| B dimnames 2 1 1 0% 9.2 kb | |
| R .requirePackage 87 3 1 0% | |
| B log 5 3 1 0% | |
| B c 93 19 1 0% 2.8 kb | |
| B sum 6 4 1 0% | |
| R match 181 2 1 0% | |
| B UseMethod 42 7 1 0% | |
| R el 89 1 1 0% | |
| R exists 144 1 0 0% 1.1 kb | |
| R is 63 13 0 0% | |
| R mget 1 0 0 0% | |
| R callGeneric 10 11 0 0% | |
| R possibleExtends 46 2 0 0% 9.8 kb | |
| R print.default 1 0 0 0% | |
| B attr 245 0 0 0% | |
| R get 51 0 0 0% | |
| R .identC 300 2 0 0% | |
| R options 97 0 0 0% | |
| R as 17 115 0 0% | |
| R nchar 99 0 0 0% 19.7 kb | |
| R getOption 97 1 0 0% | |
| R getClass 88 5 0 0% | |
| R nzchar 99 1 0 0% | |
| R structure 6 2 0 0% 1.3 kb | |
| R .asCoerceMethod 5 15 0 0% | |
| R .mergeAttrs 11 1 0 0% | |
| R parent.frame 133 0 0 0% | |
| R .classEnv 37 3 0 0% | |
| R callNextMethod 1 158 0 0% | |
| B @ 339 0 0 0% | |
| R .findNextFromTable 1 136 0 0% | |
| R .makeAsMethod 4 4 0 0% | |
| B is.na 187 0 0 0% 1.6 kb | |
| R packageSlot 244 1 0 0% | |
| R checkAtAssignment 44 4 0 0% | |
| R validObject 2 20 0 0% | |
| R as<- 1 14 0 0% | |
| R .getClassFromCache 88 1 0 0% | |
| B is.null 500 0 0 0% | |
| B is.character 345 0 0 0% | |
| R paste 20 0 0 0% | |
| R asS4 12 2 0 0% | |
| R as.list.default 10 0 0 0% | |
| R elNamed 66 2 0 0% | |
| B getNamespace 87 0 0 0% | |
| B missing 220 0 0 0% | |
| R getGenericFromCall 10 0 0 0% | |
| B attributes 220 2 0 0% | |
| B class 173 0 0 0% | |
| R parent.env 95 0 0 0% | |
| R sys.call 31 0 0 0% | |
| B attributes<- 19 0 0 0% | |
| B isNamespace 190 0 0 0% | |
| R .getGeneric 9 1 0 0% | |
| R seq.default 8 0 0 0% | |
| B is.environment 103 0 0 0% | |
| R .getMethodsTable 25 0 0 0% | |
| R %in% 25 0 0 0% | |
| R environment 51 0 0 0% | |
| R .dataSlot 11 0 0 0% | |
| R sys.parent 21 0 0 0% | |
| B list 70 0 0 0% | |
| B names<- 17 0 0 0% | |
| R setDataPart 11 4 0 0% | |
| B any 16 0 0 0% | |
| R typeof 36 0 0 0% | |
| R .matchSigLength 11 0 0 0% | |
| B is.object 64 0 0 0% | |
| R initialize 12 278 0 0% | |
| R inherits 14 0 0 0% | |
| B rep 2 0 0 0% | |
| R extends 3 1 0 0% | |
| R mode 13 0 0 0% | |
| R tryCatch 10 0 0 0% | |
| R as.function.default 9 0 0 0% | |
| B dim<- 3 0 0 0% | |
| R seq_along 8 0 0 0% | |
| C Dim_validate 1 0 0 0% | |
| B dimnames<- 2 0 0 0% | |
| R .classDefEnv 63 2 0 0% | |
| R .nextMethod 1 19 0 0% | |
| B attr<- 16 0 0 0% | |
| B nargs 37 0 0 0% | |
| R .ChangeFormals 4 1 0 0% | |
| R .class1 19 0 0 0% | |
| R pmatch 5 0 0 0% 1.0 kb | |
| R array 2 0 0 0% | |
| R doTryCatch 10 0 0 0% | |
| B resetProfiler 1 0 0 0% | |
| R .cacheMethodInTable 11 1 0 0% | |
| B is.numeric 1 4 0 0% | |
| B substitute 2 0 0 0% | |
| B prod 2 0 0 0% | |
| R new 12 279 0 0% | |
| B min 1 0 0 0% | |
| R as.name 11 0 0 0% | |
| R formals 21 0 0 0% | |
| B is.list 108 0 0 0% | |
| B is.logical 48 0 0 0% | |
| B baseenv 205 0 0 0% | |
| R as.vector 6 0 0 0% | |
| R character 7 0 0 0% | |
| C dgeMatrix_validate 1 0 0 0% | |
| R unique.default 1 0 0 0% | |
| R packageSlot<- 11 0 0 0% | |
| R getGeneric 9 2 0 0% | |
| R assign 13 0 0 0% | |
| R .sigLabel 20 0 0 0% | |
| R rev.default 3 0 0 0% | |
| R .local 5 0 0 0% | |
| R vapply 1 0 0 0% | |
| R getSlots 11 2 0 0% | |
| B is.function 28 0 0 0% | |
| R .eligibleSuperClasses 1 0 0 0% | |
| R tryCatchList 10 0 0 0% | |
| B is.expression 22 0 0 0% | |
| R .quickCoerceSelect 7 2 0 0% | |
| R body 14 0 0 0% | |
| R .duplicateClassesExist 12 0 0 0% | |
| C dMatrix_validate 1 0 0 0% | |
| R anyDuplicated.default 2 0 0 0% | |
| R .findMethodInTable 7 2 0 0% | |
| R cacheMethod 6 1 0 0% | |
| B emptyenv 190 0 0 0% | |
| R .inheritedArgsExpression 1 3 0 0% | |
| R .getGenericSigLength 11 0 0 0% | |
| R tryCatchOne 10 0 0 0% | |
| R .asS4 12 2 0 0% | |
| R slot<- 9 0 0 0% | |
| R .methodPackageSlots 11 0 0 0% | |
| R as.function 9 1 0 0% | |
| R seq 8 0 0 0% | |
| R asMethod 7 1 0 0% | |
| R getDataPart 2 0 0 0% | |
| B as.logical 1 0 0 0% | |
| B isS4 31 0 0 0% | |
| C dimNames_validate 1 0 0 0% | |
| R checkSlotAssignment 4 0 0 0% | |
| R body<- 9 2 0 0% | |
| R as.list 10 0 0 0% | |
| B is.pairlist 15 0 0 0% | |
| R .deparseOpts 5 0 0 0% | |
| B as.integer 2 0 0 0% | |
| R t 8 3 0 0% | |
| R dimNamesCheck 1 1 0 0% | |
| B quote 29 0 0 0% | |
| R Matrix.msg 2 0 0 0% | |
| R .getGenericFromCacheTable 2 0 0 0% | |
| R slot 14 0 0 0% | |
| R getMethodsForDispatch 7 0 0 0% | |
| R fromNextMethod 10 0 0 0% | |
| R .newSignature 1 2 0 0% | |
| R ncol 1 0 0 0% | |
| R try 10 0 0 0% | |
| B as.environment 7 0 0 0% | |
| R anyStrings 4 14 0 0% | |
| R .allowPrimitiveMethods 2 0 0 0% | |
| R .getGenericFromCache 2 0 0 0% | |
| R match.call 1 0 0 0% | |
| B is.name 13 0 0 0% | |
| R validityMethod 4 14 0 0% | |
| R is.vector 1 0 0 0% | |
| R formalArgs 12 0 0 0% | |
| R isClassDef 11 2 0 0% | |
| R vector 1 0 0 0% | |
| B is.call 13 0 0 0% | |
| R unique 1 0 0 0% | |
| B on.exit 1 0 0 0% | |
| R .fixupDimnames 1 0 0 0% | |
| R is.factor 1 0 0 0% | |
| R match.fun 1 0 0 0% | |
| R print 1 0 0 0% | |
| R addNextMethod 1 137 0 0% | |
| R anyDuplicated 2 0 0 0% | |
| R lfactorial 1 0 0 0% | |
| B seq_len 1 0 0 0% | |
| R sys.function 1 0 0 0% | |
| R allNames 2 0 0 0% | |
| R .simpleInheritanceGeneric 1 0 0 0% | |
| R rev 3 0 0 0% | |
| R isTRUE 1 4 0 0% | |
| LONG RUNNING LOOPS | |
| ================== | |
| Function Iterations Time | |
| VECTOR PIPELINER | |
| ================ | |
| Materialization count: 0 | |
| Materialization time (ms): 0 |
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