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Commit656d1fe

Browse files
committed
data.table threads updated to match input colossus cores
1 parent3ac452e commit656d1fe

38 files changed

+513
-529
lines changed

‎NAMESPACE‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -55,6 +55,7 @@ importFrom(data.table,data.table)
5555
importFrom(data.table,fread)
5656
importFrom(data.table,set)
5757
importFrom(data.table,setDT)
58+
importFrom(data.table,setDTthreads)
5859
importFrom(data.table,setkeyv)
5960
importFrom(data.table,setnames)
6061
importFrom(data.table,setorderv)

‎R/BasicRun.R‎

Lines changed: 133 additions & 17 deletions
Large diffs are not rendered by default.

‎R/CaseControl_Regression.R‎

Lines changed: 1 addition & 41 deletions
Original file line numberDiff line numberDiff line change
@@ -11,53 +11,13 @@
1111
#' @return returns a list of the final results
1212
#' @noRd
1313
#' @family Case Control Wrapper Functions
14-
#' @examples
15-
#' library(data.table)
16-
#' ## basic example code reproduced from the starting-description vignette
17-
#' df <- data.table::data.table(
18-
#' "UserID" = c(112, 114, 213, 214, 115, 116, 117),
19-
#' "Starting_Age" = c(18, 20, 18, 19, 21, 20, 18),
20-
#' "Ending_Age" = c(30, 45, 57, 47, 36, 60, 55),
21-
#' "Cancer_Status" = c(0, 0, 1, 0, 1, 0, 0),
22-
#' "a" = c(0, 1, 1, 0, 1, 0, 1),
23-
#' "b" = c(1, 1.1, 2.1, 2, 0.1, 1, 0.2),
24-
#' "c" = c(10, 11, 10, 11, 12, 9, 11),
25-
#' "d" = c(0, 0, 0, 1, 1, 1, 1),
26-
#' "e" = c(0, 0, 1, 0, 0, 0, 1)
27-
#' )
28-
#' # For the interval case
29-
#' time1 <- "Starting_Age"
30-
#' time2 <- "Ending_Age"
31-
#' event <- "Cancer_Status"
32-
#' names <- c("a", "b", "c", "d")
33-
#' a_n <- list(c(1.1, -0.1, 0.2, 0.5), c(1.6, -0.12, 0.3, 0.4))
34-
#' # used to test at a specific point
35-
#' term_n <- c(0, 1, 1, 2)
36-
#' tform <- c("loglin", "lin", "lin", "plin")
37-
#' modelform <- "M"
38-
#' keep_constant <- c(0, 0, 0, 0)
39-
#' control <- list(
40-
#' "ncores" = 2, "lr" = 0.75, "maxiters" = c(5, 5, 5),
41-
#' "halfmax" = 5, "epsilon" = 1e-3, "deriv_epsilon" = 1e-3,
42-
#' "step_max" = 1.0, "thres_step_max" = 100.0,
43-
#' "verbose" = FALSE,
44-
#' "ties" = "breslow", "double_step" = 1
45-
#' )
46-
#' e <- RunCaseControlRegression_Omnibus(df, time1, time2, event,
47-
#' names, term_n, tform, keep_constant,
48-
#' a_n, modelform, control,
49-
#' model_control = list(
50-
#' "stata" = FALSE,
51-
#' "time_risk" = FALSE
52-
#' )
53-
#' )
5414
#' @importFrom rlang .data
5515
RunCaseControlRegression_Omnibus<-function(df,time1="%trunc%",time2="%trunc%",event0="event",names= c("CONST"),term_n= c(0),tform="loglin",keep_constant= c(0),a_n= c(0),modelform="M",control=list(),strat_col="null",cens_weight="null",model_control=list(),cons_mat= as.matrix(c(0)),cons_vec= c(0)) {
5616
func_t_start<- Sys.time()
5717
if (class(df)[[1]]!="data.table") {
5818
tryCatch(
5919
{
60-
df<-setDT(df)# nocov
20+
setDT(df)# nocov
6121
},
6222
error=function(e) {# nocov
6323
df<- data.table(df)# nocov

‎R/Cox_Regression.R‎

Lines changed: 5 additions & 45 deletions
Original file line numberDiff line numberDiff line change
@@ -11,53 +11,13 @@
1111
#' @return returns a list of the final results
1212
#' @noRd
1313
#' @family Cox Wrapper Functions
14-
#' @examples
15-
#' library(data.table)
16-
#' ## basic example code reproduced from the starting-description vignette
17-
#' df <- data.table::data.table(
18-
#' "UserID" = c(112, 114, 213, 214, 115, 116, 117),
19-
#' "Starting_Age" = c(18, 20, 18, 19, 21, 20, 18),
20-
#' "Ending_Age" = c(30, 45, 57, 47, 36, 60, 55),
21-
#' "Cancer_Status" = c(0, 0, 1, 0, 1, 0, 0),
22-
#' "a" = c(0, 1, 1, 0, 1, 0, 1),
23-
#' "b" = c(1, 1.1, 2.1, 2, 0.1, 1, 0.2),
24-
#' "c" = c(10, 11, 10, 11, 12, 9, 11),
25-
#' "d" = c(0, 0, 0, 1, 1, 1, 1),
26-
#' "e" = c(0, 0, 1, 0, 0, 0, 1)
27-
#' )
28-
#' # For the interval case
29-
#' time1 <- "Starting_Age"
30-
#' time2 <- "Ending_Age"
31-
#' event <- "Cancer_Status"
32-
#' names <- c("a", "b", "c", "d")
33-
#' a_n <- list(c(1.1, -0.1, 0.2, 0.5), c(1.6, -0.12, 0.3, 0.4))
34-
#' # used to test at a specific point
35-
#' term_n <- c(0, 1, 1, 2)
36-
#' tform <- c("loglin", "lin", "lin", "plin")
37-
#' modelform <- "M"
38-
#' keep_constant <- c(0, 0, 0, 0)
39-
#' control <- list(
40-
#' "ncores" = 2, "lr" = 0.75, "maxiters" = c(5, 5, 5),
41-
#' "halfmax" = 5, "epsilon" = 1e-3, "deriv_epsilon" = 1e-3,
42-
#' "step_max" = 1.0, "thres_step_max" = 100.0,
43-
#' "verbose" = FALSE,
44-
#' "ties" = "breslow", "double_step" = 1, "guesses" = 2
45-
#' )
46-
#' e <- RunCoxRegression_Omnibus(df, time1, time2, event,
47-
#' names, term_n, tform, keep_constant,
48-
#' a_n, modelform, control,
49-
#' model_control = list(
50-
#' "single" = FALSE,
51-
#' "basic" = FALSE, "cr" = FALSE, "null" = FALSE
52-
#' )
53-
#' )
5414
#' @importFrom rlang .data
5515
RunCoxRegression_Omnibus<-function(df,time1="%trunc%",time2="%trunc%",event0="event",names= c("CONST"),term_n= c(0),tform="loglin",keep_constant= c(0),a_n= c(0),modelform="M",control=list(),strat_col="null",cens_weight="null",model_control=list(),cons_mat= as.matrix(c(0)),cons_vec= c(0)) {
5616
func_t_start<- Sys.time()
5717
if (class(df)[[1]]!="data.table") {
5818
tryCatch(
5919
{
60-
df<-setDT(df)# nocov
20+
setDT(df)# nocov
6121
},
6222
error=function(e) {# nocov
6323
df<- data.table(df)# nocov
@@ -290,7 +250,7 @@ Cox_Relative_Risk <- function(df, time1 = "%trunc%", time2 = "%trunc%", event0 =
290250
if (class(df)[[1]]!="data.table") {
291251
tryCatch(
292252
{
293-
df<-setDT(df)# nocov
253+
setDT(df)# nocov
294254
},
295255
error=function(e) {# nocov
296256
df<- data.table(df)# nocov
@@ -338,7 +298,7 @@ RunCoxPlots <- function(df, time1 = "%trunc%", time2 = "%trunc%", event0 = "even
338298
if (class(df)[[1]]!="data.table") {
339299
tryCatch(
340300
{
341-
df<-setDT(df)# nocov
301+
setDT(df)# nocov
342302
},
343303
error=function(e) {# nocov
344304
df<- data.table(df)# nocov
@@ -621,7 +581,7 @@ RunCoxRegression_Omnibus_Multidose <- function(df, time1 = "%trunc%", time2 = "%
621581
if (class(df)[[1]]!="data.table") {
622582
tryCatch(
623583
{
624-
df<-setDT(df)# nocov
584+
setDT(df)# nocov
625585
},
626586
error=function(e) {# nocov
627587
df<- data.table(df)# nocov
@@ -798,7 +758,7 @@ CoxCurveSolver <- function(df, time1 = "%trunc%", time2 = "%trunc%", event0 = "e
798758
if (class(df)[[1]]!="data.table") {
799759
tryCatch(
800760
{
801-
df<-setDT(df)# nocov
761+
setDT(df)# nocov
802762
},
803763
error=function(e) {# nocov
804764
df<- data.table(df)# nocov

‎R/LogitRegression.R‎

Lines changed: 1 addition & 36 deletions
Original file line numberDiff line numberDiff line change
@@ -9,48 +9,13 @@
99
#' @return returns a list of the final results
1010
#' @noRd
1111
#' @family Logistic Wrapper Functions
12-
#' @examples
13-
#' library(data.table)
14-
#' ## basic example code reproduced from the starting-description vignette
15-
#' df <- data.table::data.table(
16-
#' "Trials" = c(30, 45, 57, 47, 36, 60, 55),
17-
#' "Cancer_Status" = c(0, 0, 1, 0, 1, 0, 0),
18-
#' "a" = c(0, 1, 1, 0, 1, 0, 1),
19-
#' "b" = c(1, 1.1, 2.1, 2, 0.1, 1, 0.2),
20-
#' "c" = c(10, 11, 10, 11, 12, 9, 11),
21-
#' "d" = c(0, 0, 0, 1, 1, 1, 1),
22-
#' "e" = c(0, 0, 1, 0, 0, 0, 1)
23-
#' )
24-
#' # For the interval case
25-
#' trial <- "Trials"
26-
#' event <- "Cancer_Status"
27-
#' names <- c("a", "b", "c", "d")
28-
#' a_n <- c(1.1, -0.1, 0.2, 0.5) # used to test at a specific point
29-
#' term_n <- c(0, 1, 1, 2)
30-
#' tform <- c("loglin", "lin", "lin", "plin")
31-
#' modelform <- "M"
32-
#' keep_constant <- c(0, 0, 0, 0)
33-
#' control <- list(
34-
#' "ncores" = 2, "lr" = 0.75, "maxiter" = 5,
35-
#' "halfmax" = 5, "epsilon" = 1e-3,
36-
#' "deriv_epsilon" = 1e-3, "step_max" = 1.0,
37-
#' "thres_step_max" = 100.0, "verbose" = FALSE, "ties" = "breslow",
38-
#' "double_step" = 1
39-
#' )
40-
#' strat_col <- "e"
41-
#' e <- RunLogisticRegression_Omnibus(
42-
#' df, trial, event, names, term_n,
43-
#' tform, keep_constant,
44-
#' a_n, modelform,
45-
#' control
46-
#' )
4712
#' @importFrom rlang .data
4813
RunLogisticRegression_Omnibus<-function(df,trial0="CONST",event0="event",names= c("CONST"),term_n= c(0),tform="loglin",keep_constant= c(0),a_n= c(0),modelform="M",control=list(),model_control=list(),cons_mat= as.matrix(c(0)),cons_vec= c(0)) {
4914
func_t_start<- Sys.time()
5015
if (class(df)[[1]]!="data.table") {
5116
tryCatch(
5217
{
53-
df<-setDT(df)# nocov
18+
setDT(df)# nocov
5419
},
5520
error=function(e) {# nocov
5621
df<- data.table(df)# nocov

‎R/Poisson_Regression.R‎

Lines changed: 5 additions & 79 deletions
Original file line numberDiff line numberDiff line change
@@ -9,50 +9,13 @@
99
#' @return returns a list of the final results
1010
#' @noRd
1111
#' @family Poisson Wrapper Functions
12-
#' @examples
13-
#' library(data.table)
14-
#' ## basic example code reproduced from the starting-description vignette
15-
#' df <- data.table::data.table(
16-
#' "UserID" = c(112, 114, 213, 214, 115, 116, 117),
17-
#' "Starting_Age" = c(18, 20, 18, 19, 21, 20, 18),
18-
#' "Ending_Age" = c(30, 45, 57, 47, 36, 60, 55),
19-
#' "Cancer_Status" = c(0, 0, 1, 0, 1, 0, 0),
20-
#' "a" = c(0, 1, 1, 0, 1, 0, 1),
21-
#' "b" = c(1, 1.1, 2.1, 2, 0.1, 1, 0.2),
22-
#' "c" = c(10, 11, 10, 11, 12, 9, 11),
23-
#' "d" = c(0, 0, 0, 1, 1, 1, 1),
24-
#' "e" = c(0, 0, 1, 0, 0, 0, 1)
25-
#' )
26-
#' # For the interval case
27-
#' pyr <- "Ending_Age"
28-
#' event <- "Cancer_Status"
29-
#' names <- c("a", "b", "c", "d")
30-
#' a_n <- c(1.1, -0.1, 0.2, 0.5) # used to test at a specific point
31-
#' term_n <- c(0, 1, 1, 2)
32-
#' tform <- c("loglin", "lin", "lin", "plin")
33-
#' modelform <- "M"
34-
#' keep_constant <- c(0, 0, 0, 0)
35-
#' control <- list(
36-
#' "ncores" = 2, "lr" = 0.75, "maxiter" = 5,
37-
#' "halfmax" = 5, "epsilon" = 1e-3,
38-
#' "deriv_epsilon" = 1e-3, "step_max" = 1.0,
39-
#' "thres_step_max" = 100.0, "verbose" = FALSE, "ties" = "breslow",
40-
#' "double_step" = 1
41-
#' )
42-
#' strat_col <- "e"
43-
#' e <- RunPoissonRegression_Omnibus(
44-
#' df, pyr, event, names, term_n,
45-
#' tform, keep_constant,
46-
#' a_n, modelform,
47-
#' control, strat_col
48-
#' )
4912
#' @importFrom rlang .data
5013
RunPoissonRegression_Omnibus<-function(df,pyr0="pyr",event0="event",names= c("CONST"),term_n= c(0),tform="loglin",keep_constant= c(0),a_n= c(0),modelform="M",control=list(),strat_col="null",model_control=list(),cons_mat= as.matrix(c(0)),cons_vec= c(0)) {
5114
func_t_start<- Sys.time()
5215
if (class(df)[[1]]!="data.table") {
5316
tryCatch(
5417
{
55-
df<-setDT(df)# nocov
18+
setDT(df)# nocov
5619
},
5720
error=function(e) {# nocov
5821
df<- data.table(df)# nocov
@@ -181,7 +144,7 @@ RunPoissonEventAssignment <- function(df, pyr0 = "pyr", event0 = "event", names
181144
if (class(df)[[1]]!="data.table") {
182145
tryCatch(
183146
{
184-
df<-setDT(df)# nocov
147+
setDT(df)# nocov
185148
},
186149
error=function(e) {# nocov
187150
df<- data.table(df)# nocov
@@ -266,49 +229,12 @@ RunPoissonEventAssignment <- function(df, pyr0 = "pyr", event0 = "event", names
266229
#' @return returns a list of the final results
267230
#' @noRd
268231
#' @family Poisson Wrapper Functions
269-
#' @examples
270-
#' library(data.table)
271-
#' ## basic example code reproduced from the starting-description vignette
272-
#' df <- data.table::data.table(
273-
#' "UserID" = c(112, 114, 213, 214, 115, 116, 117),
274-
#' "Starting_Age" = c(18, 20, 18, 19, 21, 20, 18),
275-
#' "Ending_Age" = c(30, 45, 57, 47, 36, 60, 55),
276-
#' "Cancer_Status" = c(0, 0, 1, 0, 1, 0, 0),
277-
#' "a" = c(0, 1, 1, 0, 1, 0, 1),
278-
#' "b" = c(1, 1.1, 2.1, 2, 0.1, 1, 0.2),
279-
#' "c" = c(10, 11, 10, 11, 12, 9, 11),
280-
#' "d" = c(0, 0, 0, 1, 1, 1, 1),
281-
#' "e" = c(0, 0, 1, 0, 0, 0, 1)
282-
#' )
283-
#' # For the interval case
284-
#' pyr <- "Ending_Age"
285-
#' event <- "Cancer_Status"
286-
#' names <- c("a", "b", "c", "d")
287-
#' a_n <- c(1.1, -0.1, 0.2, 0.5) # used to test at a specific point
288-
#' term_n <- c(0, 1, 1, 2)
289-
#' tform <- c("loglin", "lin", "lin", "plin")
290-
#' modelform <- "M"
291-
#' keep_constant <- c(0, 0, 0, 0)
292-
#' control <- list(
293-
#' "ncores" = 2, "lr" = 0.75, "maxiter" = 5,
294-
#' "halfmax" = 5, "epsilon" = 1e-3,
295-
#' "deriv_epsilon" = 1e-3, "step_max" = 1.0,
296-
#' "thres_step_max" = 100.0, "verbose" = FALSE, "ties" = "breslow",
297-
#' "double_step" = 1
298-
#' )
299-
#' strat_col <- "e"
300-
#' e <- RunPoissonRegression_Residual(
301-
#' df, pyr, event, names, term_n,
302-
#' tform, keep_constant,
303-
#' a_n, modelform,
304-
#' control, strat_col
305-
#' )
306232
#' @importFrom rlang .data
307233
RunPoissonRegression_Residual<-function(df,pyr0="pyr",event0="event",names= c("CONST"),term_n= c(0),tform="loglin",keep_constant= c(0),a_n= c(0),modelform="M",control=list(),strat_col="null",model_control=list()) {
308234
if (class(df)[[1]]!="data.table") {
309235
tryCatch(
310236
{
311-
df<-setDT(df)# nocov
237+
setDT(df)# nocov
312238
},
313239
error=function(e) {# nocov
314240
df<- data.table(df)# nocov
@@ -399,7 +325,7 @@ PoissonCurveSolver <- function(df, pyr0 = "pyr", event0 = "event", names = c("CO
399325
if (class(df)[[1]]!="data.table") {
400326
tryCatch(
401327
{
402-
df<-setDT(df)# nocov
328+
setDT(df)# nocov
403329
},
404330
error=function(e) {# nocov
405331
df<- data.table(df)# nocov
@@ -511,7 +437,7 @@ RunPoisRegression_Omnibus_Multidose <- function(df, pyr0 = "pyr", event0 = "even
511437
if (class(df)[[1]]!="data.table") {
512438
tryCatch(
513439
{
514-
df<-setDT(df)# nocov
440+
setDT(df)# nocov
515441
},
516442
error=function(e) {# nocov
517443
df<- data.table(df)# nocov

‎R/SurvTypes.R‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -12,7 +12,7 @@ get_form_joint <- function(formula_list, df) {
1212
if (class(df)[[1]]!="data.table") {
1313
tryCatch(
1414
{
15-
df<-setDT(df)# nocov
15+
setDT(df)# nocov
1616
},
1717
error=function(e) {# nocov
1818
df<- data.table(df)# nocov
@@ -263,7 +263,7 @@ get_form_list <- function(surv_obj, model_obj, df) {
263263
if (class(df)[[1]]!="data.table") {
264264
tryCatch(
265265
{
266-
df<-setDT(df)
266+
setDT(df)
267267
},
268268
error=function(e) {
269269
df<- data.table(df)

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