From 840ad2391de4ff86160c4f77b0a3609bb9898384 Mon Sep 17 00:00:00 2001 From: Bharath HU Date: Mon, 2 Mar 2020 17:38:17 +0100 Subject: [PATCH] 1. Added license 2. Removed NSE 3. Removed magrittr and %>% pipes --- DESCRIPTION | 1 - LICENSE.md | 595 +++++++++++++++++++++++++++++++ NAMESPACE | 2 - R/compareRhythms_model_compare.R | 51 +-- R/compareRhythms_rain.R | 88 +++-- R/utils-pipe.R | 11 - R/utils.R | 2 +- 7 files changed, 664 insertions(+), 86 deletions(-) create mode 100644 LICENSE.md delete mode 100644 R/utils-pipe.R diff --git a/DESCRIPTION b/DESCRIPTION index 7520424..8d6c086 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -11,7 +11,6 @@ Encoding: UTF-8 LazyData: true RoxygenNote: 7.0.2 Imports: - magrittr (>= 1.5), rain (>= 1.18.0), DODR (>= 0.99.2), limma (>= 3.38.3) diff --git a/LICENSE.md b/LICENSE.md new file mode 100644 index 0000000..ce7a8d4 --- /dev/null +++ b/LICENSE.md @@ -0,0 +1,595 @@ +GNU General Public License +========================== + +_Version 3, 29 June 2007_ +_Copyright © 2007 Free Software Foundation, Inc. <>_ + +Everyone is permitted to copy and distribute verbatim copies of this license +document, but changing it is not allowed. + +## Preamble + +The GNU General Public License is a free, copyleft license for software and other +kinds of works. + +The licenses for most software and other practical works are designed to take away +your freedom to share and change the works. By contrast, the GNU General Public +License is intended to guarantee your freedom to share and change all versions of a +program--to make sure it remains free software for all its users. We, the Free +Software Foundation, use the GNU General Public License for most of our software; it +applies also to any other work released this way by its authors. You can apply it to +your programs, too. + +When we speak of free software, we are referring to freedom, not price. Our General +Public Licenses are designed to make sure that you have the freedom to distribute +copies of free software (and charge for them if you wish), that you receive source +code or can get it if you want it, that you can change the software or use pieces of +it in new free programs, and that you know you can do these things. + +To protect your rights, we need to prevent others from denying you these rights or +asking you to surrender the rights. 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Additional Terms + +“Additional permissions” are terms that supplement the terms of this +License by making exceptions from one or more of its conditions. Additional +permissions that are applicable to the entire Program shall be treated as though they +were included in this License, to the extent that they are valid under applicable +law. If additional permissions apply only to part of the Program, that part may be +used separately under those permissions, but the entire Program remains governed by +this License without regard to the additional permissions. + +When you convey a copy of a covered work, you may at your option remove any +additional permissions from that copy, or from any part of it. (Additional +permissions may be written to require their own removal in certain cases when you +modify the work.) 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If the Program as you received +it, or any part of it, contains a notice stating that it is governed by this License +along with a term that is a further restriction, you may remove that term. If a +license document contains a further restriction but permits relicensing or conveying +under this License, you may add to a covered work material governed by the terms of +that license document, provided that the further restriction does not survive such +relicensing or conveying. + +If you add terms to a covered work in accord with this section, you must place, in +the relevant source files, a statement of the additional terms that apply to those +files, or a notice indicating where to find the applicable terms. + +Additional terms, permissive or non-permissive, may be stated in the form of a +separately written license, or stated as exceptions; the above requirements apply +either way. + +### 8. Termination + +You may not propagate or modify a covered work except as expressly provided under +this License. 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You may not convey a covered work if you are a party to an arrangement with +a third party that is in the business of distributing software, under which you make +payment to the third party based on the extent of your activity of conveying the +work, and under which the third party grants, to any of the parties who would receive +the covered work from you, a discriminatory patent license **(a)** in connection with +copies of the covered work conveyed by you (or copies made from those copies), or **(b)** +primarily for and in connection with specific products or compilations that contain +the covered work, unless you entered into that arrangement, or that patent license +was granted, prior to 28 March 2007. + +Nothing in this License shall be construed as excluding or limiting any implied +license or other defenses to infringement that may otherwise be available to you +under applicable patent law. + +### 12. No Surrender of Others' Freedom + +If conditions are imposed on you (whether by court order, agreement or otherwise) +that contradict the conditions of this License, they do not excuse you from the +conditions of this License. If you cannot convey a covered work so as to satisfy +simultaneously your obligations under this License and any other pertinent +obligations, then as a consequence you may not convey it at all. For example, if you +agree to terms that obligate you to collect a royalty for further conveying from +those to whom you convey the Program, the only way you could satisfy both those terms +and this License would be to refrain entirely from conveying the Program. + +### 13. Use with the GNU Affero General Public License + +Notwithstanding any other provision of this License, you have permission to link or +combine any covered work with a work licensed under version 3 of the GNU Affero +General Public License into a single combined work, and to convey the resulting work. +The terms of this License will continue to apply to the part which is the covered +work, but the special requirements of the GNU Affero General Public License, section +13, concerning interaction through a network will apply to the combination as such. + +### 14. Revised Versions of this License + +The Free Software Foundation may publish revised and/or new versions of the GNU +General Public License from time to time. Such new versions will be similar in spirit +to the present version, but may differ in detail to address new problems or concerns. + +Each version is given a distinguishing version number. If the Program specifies that +a certain numbered version of the GNU General Public License “or any later +version” applies to it, you have the option of following the terms and +conditions either of that numbered version or of any later version published by the +Free Software Foundation. If the Program does not specify a version number of the GNU +General Public License, you may choose any version ever published by the Free +Software Foundation. + +If the Program specifies that a proxy can decide which future versions of the GNU +General Public License can be used, that proxy's public statement of acceptance of a +version permanently authorizes you to choose that version for the Program. + +Later license versions may give you additional or different permissions. However, no +additional obligations are imposed on any author or copyright holder as a result of +your choosing to follow a later version. + +### 15. Disclaimer of Warranty + +THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. +EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES +PROVIDE THE PROGRAM “AS IS” WITHOUT WARRANTY OF ANY KIND, EITHER +EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE +QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE +DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. + +### 16. Limitation of Liability + +IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY +COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS +PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, +INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE +PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE +OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE +WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE +POSSIBILITY OF SUCH DAMAGES. + +### 17. Interpretation of Sections 15 and 16 + +If the disclaimer of warranty and limitation of liability provided above cannot be +given local legal effect according to their terms, reviewing courts shall apply local +law that most closely approximates an absolute waiver of all civil liability in +connection with the Program, unless a warranty or assumption of liability accompanies +a copy of the Program in return for a fee. + +_END OF TERMS AND CONDITIONS_ + +## How to Apply These Terms to Your New Programs + +If you develop a new program, and you want it to be of the greatest possible use to +the public, the best way to achieve this is to make it free software which everyone +can redistribute and change under these terms. + +To do so, attach the following notices to the program. It is safest to attach them +to the start of each source file to most effectively state the exclusion of warranty; +and each file should have at least the “copyright” line and a pointer to +where the full notice is found. + + + Copyright (C) 2020 Bharath Ananthasubramaniam + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + +If the program does terminal interaction, make it output a short notice like this +when it starts in an interactive mode: + + compareRhythms Copyright (C) 2020 Bharath Ananthasubramaniam + This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type 'show c' for details. + +The hypothetical commands `show w` and `show c` should show the appropriate parts of +the General Public License. Of course, your program's commands might be different; +for a GUI interface, you would use an “about box”. + +You should also get your employer (if you work as a programmer) or school, if any, to +sign a “copyright disclaimer” for the program, if necessary. For more +information on this, and how to apply and follow the GNU GPL, see +<>. + +The GNU General Public License does not permit incorporating your program into +proprietary programs. If your program is a subroutine library, you may consider it +more useful to permit linking proprietary applications with the library. If this is +what you want to do, use the GNU Lesser General Public License instead of this +License. But first, please read +<>. diff --git a/NAMESPACE b/NAMESPACE index cc1f3c5..da086f1 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,6 +1,4 @@ # Generated by roxygen2: do not edit by hand -export("%>%") export(compareRhythms_model_compare) export(compareRhythms_rain) -importFrom(magrittr,"%>%") diff --git a/R/compareRhythms_model_compare.R b/R/compareRhythms_model_compare.R index 2df9b62..203060b 100644 --- a/R/compareRhythms_model_compare.R +++ b/R/compareRhythms_model_compare.R @@ -30,18 +30,14 @@ compareRhythms_model_compare <- function(y, exp_design, period = 24, group_id <- base::unique(exp_design$group) - exp_design <- exp_design %>% - base::transform(inphase = cos(2 * pi * time / period), - outphase = sin(2 * pi * time / period)) + exp_design <- base::cbind(exp_design, + inphase = cos(2 * pi * exp_design$time / period), + outphase = sin(2 * pi * exp_design$time / period)) design <- stats::model.matrix(~0 + group + group:inphase + group:outphase, - data = exp_design) %>% - magrittr::set_colnames(gsub("group", "", colnames(.))) %>% - magrittr::set_colnames(gsub(":", "_", colnames(.))) - - colnames(design) <- gsub("group", "", colnames(design)) %>% { - gsub(":", "_", .) - } + data = exp_design) + colnames(design) <- gsub("group", "", colnames(design)) + colnames(design) <- gsub(":", "_", colnames(design)) design_DR <- design @@ -52,11 +48,13 @@ compareRhythms_model_compare <- function(y, exp_design, period = 24, colnames(design))] design_ABR <- stats::model.matrix(~0 + group + inphase + outphase, - data = exp_design) %>% - magrittr::set_colnames(gsub("group", "", colnames(.))) + data = exp_design) + + colnames(design_ABR) <- base::gsub("group", "", colnames(design_ABR)) + + design_noR <- stats::model.matrix(~0 + group, data = exp_design) - design_noR <- stats::model.matrix(~0 + group, data = exp_design) %>% - magrittr::set_colnames(gsub("group", "", colnames(.))) + colnames(design_noR) <- gsub("group", "", colnames(design_noR)) design_list <- list(noR = design_noR, AR = design_AR, @@ -66,24 +64,27 @@ compareRhythms_model_compare <- function(y, exp_design, period = 24, model_selection <- limma::selectModel(y, design_list, criterion = criterion) - model_assignment <- with(model_selection, pref[pref != "noR"]) + model_assignment <- model_selection$pref[model_selection$pref != "noR"] - model_circ_params <- lapply(design_list[-1], + model_circ_params <- base::lapply(design_list[-1], compute_model_params, y, group_id) circ_params <- base::vapply(model_assignment, function(m) { model_circ_params[[base::as.character(m)]][names(m), ] }, - FUN.VALUE = double(4)) %>% t() - - results <- data.frame(circ_params) %>% - {base::cbind(symbol = names(model_assignment), - best_model = unname(model_assignment), ., - max_amp = pmax(.[, paste0(group_id[1], "_amp")], - .[, paste0(group_id[2], "_amp")]))} %>% - base::subset(max_amp > amp_cutoff) %>% - base::subset(select = -max_amp) + FUN.VALUE = double(4)) + + results <- data.frame(t(circ_params)) + results <- base::cbind(symbol = names(model_assignment), + best_model = unname(model_assignment), + results) + + results$max_amp <- pmax(results[, paste0(group_id[1], "_amp")], + results[, paste0(group_id[2], "_amp")]) + + results <- results[results$max_amp > amp_cutoff, ] + results$max_amp <- NULL for (i in seq(nrow(results))) { if (results[i, "best_model"] == "DR") { diff --git a/R/compareRhythms_rain.R b/R/compareRhythms_rain.R index e277da9..b96940f 100644 --- a/R/compareRhythms_rain.R +++ b/R/compareRhythms_rain.R @@ -32,47 +32,46 @@ compareRhythms_rain <- function(y, exp_design, period=24, rhythm_fdr = 0.05, group_id <- base::unique(exp_design$group) - exp_design_A <- base::subset(exp_design, group == group_id[1]) + exp_design_A <- exp_design[exp_design$group == group_id[1], ] exp_design_A <- exp_design_A[base::order(exp_design_A$time), ] - exp_design_B <- base::subset(exp_design, group == group_id[2]) + exp_design_B <- exp_design[exp_design$group == group_id[2], ] exp_design_B <- exp_design_B[base::order(exp_design_B$time), ] - deltat_A <- exp_design_A %$% base::unique(time) %>% - diff %>% - min - + deltat_A <- min(diff(base::unique(exp_design_A$time))) time_A <- base::seq(min(exp_design_A$time), max(exp_design_A$time), by = deltat_A) - measure_sequence_A <- base::table(exp_design_A$time) %>% { - base::vapply(time_A, - function(t) ifelse(any(names(.) == t), - .[names(.) == t], - 0), - integer(1) - ) - } + unique_times_A <- base::table(exp_design_A$time) + + measure_sequence_A <- base::vapply(time_A, + function(t) { + ifelse(any(names(unique_times_A) == t), + unique_times_A[names(unique_times_A) == t], + 0) + }, + integer(1)) - deltat_B <- exp_design_B %$% base::unique(time) %>% - diff %>% - min + deltat_B <- min(diff(base::unique(exp_design_B$time))) time_B <- base::seq(min(exp_design_B$time), max(exp_design_B$time), by = deltat_B) - measure_sequence_B <- base::table(exp_design_B$time) %>% { - base::vapply(time_B, - function(t) ifelse(any(names(.) == t), - .[names(.) == t], 0), + unique_times_B <- base::table(exp_design_B$time) + + measure_sequence_B <- base::vapply(time_B, + function(t) { + ifelse(any(names(unique_times_B) == t), + unique_times_B[names(unique_times_B) == t], + 0) + }, integer(1)) - } y_A <- y[, exp_design_A$col_number] @@ -84,10 +83,9 @@ compareRhythms_rain <- function(y, exp_design, period=24, rhythm_fdr = 0.05, rain_B <- rain::rain(t(y_B), deltat_B, period, measure.sequence = measure_sequence_B) - rain_results <- data.frame(p_val_adjust_A = p.adjust(rain_A[, "pVal"], - method = "BH"), - p_val_adjust_B = p.adjust(rain_B[, "pVal"], - method = "BH")) + rain_results <- data.frame(stats::p.adjust(rain_A[, "pVal"], method = "BH"), + stats::p.adjust(rain_B[, "pVal"], method = "BH")) + colnames(rain_results) <- c("p_val_adjust_A", "p_val_adjust_B") circ_params_A <- compute_circ_params(y_A, exp_design_A$time, period = period) @@ -95,10 +93,10 @@ compareRhythms_rain <- function(y, exp_design, period=24, rhythm_fdr = 0.05, circ_params_B <- compute_circ_params(y_B, exp_design_B$time, period = period) rhythmic_in_A <- (rain_results$p_val_adjust_A < rhythm_fdr) & - (circ_params_A[, "amps"] > amp_cutoff) + (circ_params_A[, "amps"] > amp_cutoff) rhythmic_in_B <- (rain_results$p_val_adjust_B < rhythm_fdr) & - (circ_params_B[, "amps"] > amp_cutoff) + (circ_params_B[, "amps"] > amp_cutoff) rhythmic_in_either <- rhythmic_in_A | rhythmic_in_B @@ -107,31 +105,29 @@ compareRhythms_rain <- function(y, exp_design, period=24, rhythm_fdr = 0.05, } dodr_results <- DODR::robustDODR(t(y_A[rhythmic_in_either, ]), - t(y_B[rhythmic_in_either, ]), - times1 = exp_design_A$time, - times2 = exp_design_B$time, - norm = TRUE, - period = period) %>% - base::transform(p_val_adjust = p.adjust(p.value, - method = "BH")) + t(y_B[rhythmic_in_either, ]), + times1 = exp_design_A$time, + times2 = exp_design_B$time, + norm = TRUE, + period = period) + dodr_results$p_val_adjust = stats::p.adjust(dodr_results$p.value, method = "BH") results <- data.frame(symbol = rownames(y_A)[rhythmic_in_either], rhythmic_in_A = rhythmic_in_A[rhythmic_in_either], rhythmic_in_B = rhythmic_in_B[rhythmic_in_either], - diff_rhythmic = dodr_results$p_val_adjust < compare_fdr) %>% - magrittr::set_rownames(NULL) + diff_rhythmic = dodr_results$p_val_adjust < compare_fdr) + rownames(results) <- NULL if (include_pvals) { - results <- transform(results, - p_val_adjust_A = p_val_adjust_A[rhythmic_in_either], - p_val_adjust_B = p_val_adjust_B[rhythmic_in_either], - p_val_adjust_dodr = dodr_results$p_value_adjust, - amp_A = circ_params_A[rhythmic_in_either, "amps"], - amp_B = circ_params_B[rhythmic_in_either, "amps"], - phase_A = circ_params_A[rhythmic_in_either, "phases"], - phase_B = circ_params_B[rhythmic_in_either, "phases"]) + results$p_val_adjust_A = p_val_adjust_A[rhythmic_in_either] + results$p_val_adjust_B = p_val_adjust_B[rhythmic_in_either] + results$p_val_adjust_dodr = dodr_results$p_value_adjust + results$amp_A = circ_params_A[rhythmic_in_either, "amps"] + results$amp_B = circ_params_B[rhythmic_in_either, "amps"] + results$phase_A = circ_params_A[rhythmic_in_either, "phases"] + results$phase_B = circ_params_B[rhythmic_in_either, "phases"] } - return(results) + return(results) } diff --git a/R/utils-pipe.R b/R/utils-pipe.R deleted file mode 100644 index e79f3d8..0000000 --- a/R/utils-pipe.R +++ /dev/null @@ -1,11 +0,0 @@ -#' Pipe operator -#' -#' See \code{magrittr::\link[magrittr:pipe]{\%>\%}} for details. -#' -#' @name %>% -#' @rdname pipe -#' @keywords internal -#' @export -#' @importFrom magrittr %>% -#' @usage lhs \%>\% rhs -NULL diff --git a/R/utils.R b/R/utils.R index b106fd2..ebb10ba 100644 --- a/R/utils.R +++ b/R/utils.R @@ -5,7 +5,7 @@ compute_circ_params <- function(y, t, period) { X <- stats::model.matrix(~inphase + outphase) - fit <- lm.fit(X, t(y)) + fit <- stats::lm.fit(X, t(y)) amps <- 2 * sqrt(base::colSums(fit$coefficients[-1, ]^2))