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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,82 @@ | ||
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| #' @include Grid.R | ||
| #' @include generics.R | ||
| NULL | ||
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| #' @rdname Grid-Dev | ||
| .GridEven <- setClass( | ||
| "GridEven", | ||
| contains = "Grid", | ||
| slots = c( | ||
| "subjects" = "character", | ||
| "length.out" = "numeric" | ||
| ) | ||
| ) | ||
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| #' @rdname Grid-Functions | ||
| #' @export | ||
| GridEven <- function(subjects = NULL, length.out = 30) { | ||
| .GridEven( | ||
| subjects = subjects, | ||
| length.out = length.out | ||
| ) | ||
| } | ||
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| setValidity( | ||
| "GridEven", | ||
| function(object) { | ||
| if (length(object@length.out) != 1 || all(object@length.out <= 0)) { | ||
| return("The `length.out` argument must be a positive integer") | ||
| } | ||
| } | ||
| ) | ||
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| #' @rdname Quant-Dev | ||
| #' @export | ||
| as.QuantityGenerator.GridEven <- function(object, data, ...) { | ||
| assert_class(data, "DataJoint") | ||
| data_list <- as.list(data) | ||
| subjects <- unlist(as.list(object, data = data), use.names = FALSE) | ||
| assert_that( | ||
| all(subjects %in% names(data_list$subject_to_index)), | ||
| msg = "All subject names must be in the `DataSubject` object" | ||
| ) | ||
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| spec <- lapply( | ||
| subjects, | ||
| \(sub) { | ||
| subject_index <- data_list$subject_to_index[[sub]] | ||
| time_index <- data_list$subject_tumour_index == subject_index | ||
| subject_times <- data_list$tumour_time[time_index] | ||
| seq(min(subject_times), max(subject_times), length.out = object@length.out) | ||
| } | ||
| ) | ||
| names(spec) <- subjects | ||
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| as.QuantityGenerator( | ||
| GridManual(spec), | ||
| data = data | ||
| ) | ||
| } | ||
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| #' @rdname Quant-Dev | ||
| #' @export | ||
| as.QuantityCollapser.GridEven <- function(object, data, ...) { | ||
| generator <- as.QuantityGenerator(object, data) | ||
| QuantityCollapser( | ||
| times = generator@times, | ||
| groups = generator@subjects, | ||
| indexes = as.list(seq_along(generator@times)) | ||
| ) | ||
| } | ||
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| #' @export | ||
| as.list.GridEven <- function(x, data, ...) { | ||
| subjects_to_list(x@subjects, data) | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,81 @@ | ||
|
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||
| #' @include Grid.R | ||
| #' @include generics.R | ||
| NULL | ||
|
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||
|
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| #' @rdname Grid-Dev | ||
| .GridManual <- setClass( | ||
| "GridManual", | ||
| contains = "Grid", | ||
| slots = c( | ||
| "spec" = "list" | ||
| ) | ||
| ) | ||
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| #' @rdname Grid-Functions | ||
| #' @export | ||
| GridManual <- function(spec) { | ||
| .GridManual( | ||
| spec = spec | ||
| ) | ||
| } | ||
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| setValidity( | ||
| "GridManual", | ||
| function(object) { | ||
| subject_names <- names(object@spec) | ||
| subject_names_valid <- subject_names[!is.na(subject_names) & subject_names != ""] | ||
| if (length(subject_names_valid) != length(object@spec)) { | ||
| return("Each element of `subjects` must be named") | ||
| } | ||
| for (times in object@spec) { | ||
| if (!is.numeric(times)) { | ||
| return("Each element of `spec` must be a numeric vector") | ||
| } | ||
| if (length(times) != length(unique(times))) { | ||
| return("Each time vector per subject must be unique") | ||
| } | ||
| } | ||
| return(TRUE) | ||
| } | ||
| ) | ||
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| #' @rdname Quant-Dev | ||
| #' @export | ||
| as.QuantityGenerator.GridManual <- function(object, data, ...) { | ||
| assert_class(data, "DataJoint") | ||
| data_list <- as.list(data) | ||
| assert_that( | ||
| all(names(object@spec) %in% names(data_list$subject_to_index)), | ||
| msg = "All subject names must be in the `DataSubject` object" | ||
| ) | ||
| lens <- vapply(object@spec, length, numeric(1)) | ||
| .QuantityGenerator( | ||
| times = unlist(object@spec, use.names = FALSE), | ||
| subjects = rep(names(object@spec), lens) | ||
| ) | ||
| } | ||
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| #' @rdname Quant-Dev | ||
| #' @export | ||
| as.QuantityCollapser.GridManual <- function(object, data, ...) { | ||
| generator <- as.QuantityGenerator(object, data) | ||
| QuantityCollapser( | ||
| times = generator@times, | ||
| groups = generator@subjects, | ||
| indexes = as.list(seq_along(generator@times)) | ||
| ) | ||
| } | ||
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| #' @export | ||
| as.list.GridManual <- function(x, data, ...) { | ||
| subs <- as.list(names(x@spec)) | ||
| names(subs) <- names(x@spec) | ||
| subs | ||
| } |
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