From fbc3a245b2655d1d6ed4f0485c71b1d6eef4f65d Mon Sep 17 00:00:00 2001 From: kauedesousa Date: Tue, 28 Nov 2023 11:54:20 +0100 Subject: [PATCH] v1.1 --- DESCRIPTION | 4 +- NEWS.md | 7 +++ R/AAA-getDataCM.R | 5 -- R/getProjectProgress.R | 1 - R/getProjectsCM.R | 3 -- R/internal_functions.R | 3 -- R/randomize.R | 48 +++++++++++++++++--- README.md | 2 +- codemeta.json | 6 +-- docs/404.html | 2 +- docs/CODE_OF_CONDUCT.html | 2 +- docs/CONTRIBUTING.html | 2 +- docs/LICENSE-text.html | 2 +- docs/articles/Overview.html | 18 ++++---- docs/articles/index.html | 2 +- docs/authors.html | 2 +- docs/index.html | 6 +-- docs/news/index.html | 11 ++++- docs/pkgdown.yml | 2 +- docs/reference/ClimMobTools.html | 6 +-- docs/reference/getDataCM.html | 2 +- docs/reference/getProjectProgress.html | 2 +- docs/reference/getProjectsCM.html | 2 +- docs/reference/getTraitList.html | 2 +- docs/reference/index.html | 2 +- docs/reference/randomize.html | 63 +++++++++++++++++++------- docs/reference/rankTricot.html | 2 +- docs/reference/rmGeoIdentity.html | 2 +- man/ClimMobTools.Rd | 2 +- man/randomize.Rd | 33 +++++++++++++- tests/diagnostic-randomize.R | 37 +++++++++++++++ vignettes/Overview.Rmd | 2 +- 32 files changed, 210 insertions(+), 75 deletions(-) create mode 100644 tests/diagnostic-randomize.R diff --git a/DESCRIPTION b/DESCRIPTION index bcff510..52572f5 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: ClimMobTools Type: Package Title: API Client for the 'ClimMob' Platform -Version: 1.0 +Version: 1.1 Authors@R: c(person("Kauê", "de Sousa", email = "desousa.kaue@gmail.com", role = c("aut", "cre"), @@ -13,7 +13,7 @@ URL: https://agrdatasci.github.io/ClimMobTools/ BugReports: https://github.com/agrdatasci/ClimMobTools/issues Description: API client for 'ClimMob', an open source software for decentralized large-N trials with the 'tricot' approach . - Developed by van Etten et al. (2016) , it turns the + Developed by Quiros et al. (2023) , it turns the research paradigm on its head; instead of a few researchers designing complicated trials to compare several technologies in search of the best solutions for the target environment, it enables many participants to carry out reasonably simple diff --git a/NEWS.md b/NEWS.md index 6dbb09f..4b386c7 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,10 @@ +ClimMobTools 1.1 (2023-11-28) +========================= + +### BUG FIXES + +* Fix an issue in `.smart.round()` to handle `NA` in the `randomize()` function + ClimMobTools 1.0 (2023-11-10) ========================= diff --git a/R/AAA-getDataCM.R b/R/AAA-getDataCM.R index f63a3fb..a1e755f 100644 --- a/R/AAA-getDataCM.R +++ b/R/AAA-getDataCM.R @@ -96,8 +96,3 @@ getDataCM <- function(key, return(cmdata) } - - - - - diff --git a/R/getProjectProgress.R b/R/getProjectProgress.R index da34f4c..b172c80 100644 --- a/R/getProjectProgress.R +++ b/R/getProjectProgress.R @@ -120,4 +120,3 @@ getProjectProgress <- function(key, project, userowner, server = "climmob3"){ return(r) } - diff --git a/R/getProjectsCM.R b/R/getProjectsCM.R index f5a224a..8918fd3 100644 --- a/R/getProjectsCM.R +++ b/R/getProjectsCM.R @@ -120,6 +120,3 @@ getProjectsCM <- function(key, server = "climmob3", ...){ return(dat) } - - - diff --git a/R/internal_functions.R b/R/internal_functions.R index a8f0aa4..f702d60 100644 --- a/R/internal_functions.R +++ b/R/internal_functions.R @@ -234,6 +234,3 @@ return(ranks) } - - - diff --git a/R/randomize.R b/R/randomize.R index cda8ce8..f0f25c6 100644 --- a/R/randomize.R +++ b/R/randomize.R @@ -37,7 +37,38 @@ #' npackages = npackages, #' itemnames = itemnames, #' availability = availability) -#' +#' +#' @examplesIf interactive() +#' # run diagnostics to certify that randomization is balanced +#' # the number of interactions should have the lower sd as possible +#' # this verification may not work well when technologies are +#' # tested in different proportions +#' design = randomize(ncomp = ncomp, +#' npackages = npackages, +#' itemnames = itemnames) +#' +#' design$best = "A" +#' +#' design$worst = "C" +#' +#' # number of times each item is tested in the +#' # trial design +#' ntest = table(unlist(design[,c(1:3)])) +#' +#' ntest +#' +#' # put into the PlackettLuce structure to check +#' # number of interactions between items +#' r = gosset::rank_tricot(design, c(1:3), c(4:5)) +#' +#' bn = gosset::set_binomialfreq(r) +#' +#' bn$interactions = bn$win1 + bn$win2 +#' +#' bn = bn[,c(1,2,5)] +#' +#' bn +#' #' @aliases randomise #' @importFrom Matrix Diagonal #' @importFrom methods as @@ -503,13 +534,16 @@ makeAllocationsMatrix <- function(allocations){ return(t(out)) } -# Rounding values to closest integer while retaining the same sum -# From https://stackoverflow.com/questions/32544646/round-vector-of-numerics-to-integer-while-preserving-their-sum +#' Rounding values to closest integer while retaining the same sum +#' https://stackoverflow.com/questions/32544646/round-vector-of-numerics-to-integer-while-preserving-their-sum +#' @examples +#' .smart.round(c(NA, 3.5, 7.8, 9, 10.4)) #' @noRd -.smart.round <- function(x) { - y <- floor(x) - indices <- utils::tail(order(x-y), round(sum(x)) - sum(y)) - y[indices] <- y[indices] + 1 +.smart.round = function(x) { + x[is.na(x)] = 0 + y = floor(x) + indices = utils::tail(order(x - y), round(sum(x)) - sum(y)) + y[indices] = y[indices] + 1 y } diff --git a/README.md b/README.md index 330683b..b0d2897 100644 --- a/README.md +++ b/README.md @@ -13,7 +13,7 @@ ClimMobTools ## Overview -**ClimMobTools** the API Client for the 'ClimMob' platform in R. [ClimMob](https://climmob.net/) is an open source software for decentralized large-N trials with the 'tricot' approach. Developed by [van Etten et al. (2019)](https://doi.org/10.1017/S0014479716000739) 'tricot' turns the research paradigm on its head; instead of a few researchers designing complicated trials to compare several technologies in search of the best solutions, it enables many participants to carry out reasonably simple experiments that taken together can offer even more information. +**ClimMobTools** the API Client for the 'ClimMob' platform in R. [ClimMob](https://climmob.net/) is an open source software for decentralized large-N trials with the 'tricot' approach. Developed by [Quiros et al. (2023)](http://dx.doi.org/10.2139/ssrn.4463406) 'tricot' turns the research paradigm on its head; instead of a few researchers designing complicated trials to compare several technologies in search of the best solutions, it enables many participants to carry out reasonably simple experiments that taken together can offer even more information. ## Package website diff --git a/codemeta.json b/codemeta.json index 70506d2..bd362e2 100644 --- a/codemeta.json +++ b/codemeta.json @@ -2,12 +2,12 @@ "@context": "https://doi.org/10.5063/schema/codemeta-2.0", "@type": "SoftwareSourceCode", "identifier": "ClimMobTools", - "description": "API client for 'ClimMob', an open source software for decentralized large-N trials with the 'tricot' approach . Developed by van Etten et al. (2016) , it turns the research paradigm on its head; instead of a few researchers designing complicated trials to compare several technologies in search of the best solutions for the target environment, it enables many participants to carry out reasonably simple experiments that taken together can offer even more information. 'ClimMobTools' enables project managers to deep explore and analyse their 'ClimMob' data in R.", + "description": "API client for 'ClimMob', an open source software for decentralized large-N trials with the 'tricot' approach . Developed by Quiros et al. (2023) , it turns the research paradigm on its head; instead of a few researchers designing complicated trials to compare several technologies in search of the best solutions for the target environment, it enables many participants to carry out reasonably simple experiments that taken together can offer even more information. 'ClimMobTools' enables project managers to deep explore and analyse their 'ClimMob' data in R.", "name": "ClimMobTools: API Client for the 'ClimMob' Platform", "codeRepository": "https://agrdatasci.github.io/ClimMobTools/", "issueTracker": "https://github.com/agrdatasci/ClimMobTools/issues", "license": "https://spdx.org/licenses/MIT", - "version": "1.0", + "version": "1.1", "programmingLanguage": { "@type": "ComputerLanguage", "name": "R", @@ -232,7 +232,7 @@ }, "SystemRequirements": null }, - "fileSize": "1248.669KB", + "fileSize": "1250.405KB", "citation": [ { "@type": "ScholarlyArticle", diff --git a/docs/404.html b/docs/404.html index df50c42..90508ae 100644 --- a/docs/404.html +++ b/docs/404.html @@ -39,7 +39,7 @@ ClimMobTools - 1.0 + 1.1 diff --git a/docs/CODE_OF_CONDUCT.html b/docs/CODE_OF_CONDUCT.html index 089567b..eefd673 100644 --- a/docs/CODE_OF_CONDUCT.html +++ b/docs/CODE_OF_CONDUCT.html @@ -17,7 +17,7 @@ ClimMobTools - 1.0 + 1.1 diff --git a/docs/CONTRIBUTING.html b/docs/CONTRIBUTING.html index ecbacd0..a8c2bee 100644 --- a/docs/CONTRIBUTING.html +++ b/docs/CONTRIBUTING.html @@ -17,7 +17,7 @@ ClimMobTools - 1.0 + 1.1 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 67edb31..f3732ef 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -17,7 +17,7 @@ ClimMobTools - 1.0 + 1.1 diff --git a/docs/articles/Overview.html b/docs/articles/Overview.html index 670b3b9..0b1102a 100644 --- a/docs/articles/Overview.html +++ b/docs/articles/Overview.html @@ -40,7 +40,7 @@ ClimMobTools - 1.0 + 1.1 @@ -116,14 +116,14 @@

Overview

ClimMobTools the API Client for the ‘ClimMob’ platform in R. ClimMob is an open -source software for crowdsourcing citizen science in agriculture under -the tricot approach1. The -approach aims the rapid assessment of technologies in the target -environment. Tricot turns the research paradigm on its head; instead of -a few researchers designing complicated trials to compare several -technologies in search of the best solutions, it enables many -participants to carry out reasonably simple experiments that taken -together can offer even more information.

+source software for for decentralized large-N trials with the ‘tricot’ +approach1. The approach aims +the rapid assessment of technologies in the target environment. Tricot +turns the research paradigm on its head; instead of a few researchers +designing complicated trials to compare several technologies in search +of the best solutions, it enables many participants to carry out +reasonably simple experiments that taken together can offer even more +information.

Usage diff --git a/docs/articles/index.html b/docs/articles/index.html index 3b79d7e..e8a8402 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -17,7 +17,7 @@ ClimMobTools - 1.0 + 1.1

diff --git a/docs/authors.html b/docs/authors.html index 3d71fa6..2f88d6d 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ ClimMobTools - 1.0 + 1.1 diff --git a/docs/index.html b/docs/index.html index 452cef2..1f6ebb3 100644 --- a/docs/index.html +++ b/docs/index.html @@ -20,7 +20,7 @@ ClimMobTools - 1.0 + 1.1 @@ -105,7 +105,7 @@

Overview

-

ClimMobTools the API Client for the ‘ClimMob’ platform in R. ClimMob is an open source software for decentralized large-N trials with the ‘tricot’ approach. Developed by van Etten et al. (2019) ‘tricot’ turns the research paradigm on its head; instead of a few researchers designing complicated trials to compare several technologies in search of the best solutions, it enables many participants to carry out reasonably simple experiments that taken together can offer even more information.

+

ClimMobTools the API Client for the ‘ClimMob’ platform in R. ClimMob is an open source software for decentralized large-N trials with the ‘tricot’ approach. Developed by Quiros et al. (2023) ‘tricot’ turns the research paradigm on its head; instead of a few researchers designing complicated trials to compare several technologies in search of the best solutions, it enables many participants to carry out reasonably simple experiments that taken together can offer even more information.

Package website diff --git a/docs/news/index.html b/docs/news/index.html index caa23e6..2ac9acd 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -17,7 +17,7 @@ ClimMobTools - 1.0 + 1.1

@@ -58,7 +58,14 @@

Changelog

-

ClimMobTools 1.0 (2023-11-09)

+

ClimMobTools 1.1 (2023-11-28)

+
+

BUG FIXES

+
  • Fix an issue in .smart.round() to handle NA in the randomize() function
    • +
+
+
+

ClimMobTools 1.0 (2023-11-10)2023-11-09

BUG FIXES

  • Fix an issue in randomize() to allocate blocks
    • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 5db94b0..055cf6d 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -3,5 +3,5 @@ pkgdown: 2.0.6 pkgdown_sha: ~ articles: Overview: Overview.html -last_built: 2023-11-09T19:32Z +last_built: 2023-11-28T10:52Z diff --git a/docs/reference/ClimMobTools.html b/docs/reference/ClimMobTools.html index 4aa5a88..88241f6 100644 --- a/docs/reference/ClimMobTools.html +++ b/docs/reference/ClimMobTools.html @@ -1,6 +1,6 @@ API Client for the 'ClimMob' platform in R — ClimMobTools • ClimMobTools