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R/umx_ICA_report.R
In umx: Structural Equation Modeling and Twin Modeling in R
Defines functions
umx_ICA_report
Documented in
umx_ICA_report
# Editorial clocks for a Scholastica export of Intelligence & Cognitive Abilities.
#' Journal processing report for an ICA Scholastica export
#'
#' @description
#' Read a Scholastica CSV export and open an HTML report of editorial
#' efficiency. Journal time on each version runs from that version hitting the
#' desk to the decision on it. Time the author spends between a decision and
#' the next version is counted on its own. The page gives means and medians
#' for triage, review, the editor after the reviews are in, author revision,
#' and acceptance of a revision, with the ggplot figures embedded in the page.
#'
#' @param dataDir Directory of the Scholastica CSV export. A single string.
#' Default is `~/bin/ica/ICAdata`. The files used are `manuscripts.csv`,
#' `decisions.csv`, `reviewer-invitations.csv`, and `reviews.csv`.
#' @param asOf Date used to age manuscripts that are still in review or still
#' with the author. A `Date`, or something [base::as.Date()] can parse. Default is
#' [Sys.Date()].
#'
#' @details
#' ## Files and keys
#'
#' The export is a set of tables joined by id, one Scholastica submission
#' version per manuscript row.
#'
#' * `manuscripts.csv` has one row per version. `manuscript_id` is unique to
#' that version. `previous_version_id` is the previous version's
#' `manuscript_id` (empty on the first version). `submission_id` is shared by
#' every version of the same paper, so it identifies the paper, but it is not
#' reliably the first or the latest `manuscript_id`. `version_number` is 1,
#' 2, or 3. `created_at` is when that version hit the desk. `workflow_state`
#' is the current state of that version. `decision_created_at` is when the
#' decision on that version was made.
#' * `decisions.csv` has one row per decided version, joined on `manuscript_id`.
#' `decision_type` is `accept`, `reject`, or `revise_and_resubmit`. Its
#' `created_at` matches `manuscripts.csv` `decision_created_at`.
#' * `reviewer-invitations.csv` is joined on the version `manuscript_id`.
#' `created_at` is when the invitation was sent. `accepted_at` is when the
#' reviewer accepted. `workflow_state` is `submitted` (review filed),
#' `accepted` (agreed, review not in), `declined`, `expired`, `revoked`, or
#' `hard_bounced`. `manuscript_version_number` repeats the version.
#' * `reviews.csv` has no `manuscript_id`. It joins to an invitation through
#' `reviewer_invitation_id`. `created_at` is when the review was filed.
#' `publication_recommendation` is Accept, Revise and resubmit, or Reject.
#' * `authors.csv` joins on `manuscript_id`. `articles.csv` is the published
#' article, joined on `manuscript_id`, with `published_at`. `activities.csv`
#' is a prose log of the same events (submitted, invited, accepted an
#' invitation, submitted a review, made a decision). The clocks below use the
#' structured timestamps, not the prose log. `issues.csv` is journal issues.
#' `posts.csv` is empty in the export this function was written against.
#'
#' Trial rows are dropped: `title` beginning with `[EXAMPLE]`, or `editor_tags`
#' containing `trial entries to ignore`.
#'
#' A paper is the chain walked from a version with no `previous_version_id`
#' along `previous_version_id`. Outcomes come from the latest version's
#' `workflow_state`: `ready_to_publish` accepted, `rejected` or `desk_rejected`
#' rejected, `revise_and_resubmit` with no later version still with the author,
#' `reviewers_confirmed` or `reviews_submitted` still in review, and
#' `withdrawn_before_decision` or `withdrawn_after_non_terminal_decision`
#' withdrawn.
#'
#' ## Seconds columns already on manuscripts.csv
#'
#' Scholastica also stores durations. They are not what the report plots,
#' because the total mixes the two clocks, and the editor buckets sometimes
#' overlap.
#'
#' * `time_to_decision_in_seconds` is journal time on that version only
#' (`created_at` to `decision_created_at`). It does not include the author gap.
#' * `time_spent_with_editor_pre_review_in_seconds` is meant to be desk time
#' before review. On many versions it matches the wait until the first
#' reviewer accepts. On others it keeps running after reviews have arrived.
#' * `time_spent_with_editor_post_review_in_seconds` matches last review filed
#' to the decision.
#' * On two versions, pre-review plus post-review exceeds time-to-decision, so
#' those two buckets are not a partition.
#' * `time_spent_with_author_in_seconds` is stored on the new version and
#' matches the gap from the previous decision to this version's `created_at`.
#' * `total_time_to_decision_across_versions_in_seconds` sums version
#' time-to-decision and the author gaps. It is filled on the latest decided
#' version. A paper reviewed in two days, held by the author for a year, and
#' then accepted the next day has a total near a year.
#'
#' ## Clocks the report uses
#'
#' Timestamps are minute resolution (`2015-01-13 10:18PM` style). Durations are
#' in days.
#'
#' * Hits the desk: that version's `created_at`.
#' * Goes out to a reviewer: invitation `created_at`.
#' * Reviewer takes it on: invitation `accepted_at`.
#' * Review comes back: `reviews.csv` `created_at`.
#' * Decision: `decision_created_at`.
#' * Triage, until a reviewer has it: version `created_at` to the first
#' `accepted_at`. Time until the first invitation is sent is reported beside it.
#' * Review window: first `accepted_at` to the last review filed on that version.
#' * Editor after the reviews are in: last review to the decision.
#' * Round-1 journal time: first version `created_at` to its decision. Desk
#' rejects and editorial accepts with no invitation are in this total, and
#' are also reported on their own.
#' * Author revision time: decision on version N to `created_at` of version N+1.
#' Each return is one observation. An open revise-and-resubmit is aged to
#' `asOf` and kept out of the completed mean.
#' * Time to accept a revision: `created_at` to the accept decision on a version
#' whose `decision_type` is `accept` and whose `version_number` is greater
#' than 1.
#' * Journal time for a finished paper: sum over its versions of
#' (decision - arrived). Author gaps are not in that sum.
#' * Calendar time: first version `created_at` to the final decision. This is
#' journal time plus author time.
#'
#' Versions that have not yet been decided are left out of the completed
#' journal means. Their elapsed time is listed under papers still open.
#'
#' @return Invisibly, a list. `htmlFile` is the temporary HTML page that was
#' opened. `papers` is one row per paper. `versions` is one row per version.
#' `authorGaps` is one row per completed author return. `reviewTurns` is one
#' row per filed review. `revisionRounds` is one row per decided version
#' after the first.
#' @export
#' @family Miscellaneous Utility Functions
#' @md
#' @examples
#' \dontrun{
#' umx_ICA_report()
#' umx_ICA_report(dataDir = "~/bin/ica/ICAdata")
#' }
umx_ICA_report <- function(dataDir = "~/bin/ica/ICAdata", asOf = Sys.Date()) {
dataDir = path.expand(dataDir)
asOf = as.Date(asOf)
if (length(dataDir) != 1 || !dir.exists(dataDir)) {
stop("dataDir is not a directory: ", dataDir)
}
asOfClock = as.POSIXct(paste(asOf, "00:00:00"), tz = "UTC")
oldLocale = Sys.getlocale("LC_TIME")
Sys.setlocale("LC_TIME", "C")
on.exit(Sys.setlocale("LC_TIME", oldLocale), add = TRUE)
parseUtc = function(x) {
x = gsub("[[:space:]]+", " ", trimws(as.character(x)))
x[x == "" | x == "NA"] = NA_character_
as.POSIXct(x, format = "%Y-%m-%d %I:%M%p", tz = "UTC")
}
readExport = function(fileName) {
path = file.path(dataDir, fileName)
if (!file.exists(path)) {
stop("Missing export file: ", path)
}
raw = utils::read.csv(path, stringsAsFactors = FALSE, check.names = FALSE, fileEncoding = "UTF-8-BOM")
if (ncol(raw) == 0) {
return(raw)
}
names(raw)[1] = sub("^\ufeff", "", names(raw)[1])
names(raw) = gsub(" \\(in UTC\\)", "", names(raw))
names(raw) = gsub("[^A-Za-z0-9]+", "_", names(raw))
names(raw) = gsub("^_|_$", "", names(raw))
raw
}
idChar = function(x) {
out = rep(NA_character_, length(x))
ok = !is.na(x) & as.character(x) != ""
out[ok] = as.character(x[ok])
out
}
daysBetween = function(a, b) {
as.numeric(difftime(b, a, units = "days"))
}
firstTime = function(x) {
x = x[!is.na(x)]
if (length(x) == 0) {
return(as.POSIXct(NA, tz = "UTC"))
}
min(x)
}
lastTime = function(x) {
x = x[!is.na(x)]
if (length(x) == 0) {
return(as.POSIXct(NA, tz = "UTC"))
}
max(x)
}
fmt = function(x, digits = 1) {
if (length(x) == 0 || all(is.na(x))) {
return("-")
}
format(round(x, digits), nsmall = digits, trim = TRUE)
}
htmlEscape = function(x) {
x = gsub("&", "&", x, fixed = TRUE)
x = gsub("<", "<", x, fixed = TRUE)
x = gsub(">", ">", x, fixed = TRUE)
x = gsub("\"", """, x, fixed = TRUE)
x
}
statRow = function(label, x) {
x = x[!is.na(x)]
cells = if (length(x) == 0) {
c("0", "-", "-", "-", "-")
} else {
qs = stats::quantile(x, c(0.25, 0.75))
c(as.character(length(x)), fmt(mean(x)), fmt(stats::median(x)), fmt(qs[1]), fmt(qs[2]))
}
paste0("<tr><th>", htmlEscape(label), "</th>", paste0("<td>", cells, "</td>", collapse = ""), "</tr>")
}
statTable = function(rows) {
paste0(
"<table><thead><tr><th></th><th>n</th><th>Mean (days)</th><th>Median</th><th>25th</th><th>75th</th></tr></thead><tbody>",
paste(rows, collapse = ""),
"</tbody></table>"
)
}
rawToBase64 = function(x) {
alphabet = c(LETTERS, letters, as.character(0:9), "+", "/")
n = length(x)
pad = (3 - n %% 3) %% 3
if (pad > 0) {
x = c(x, raw(pad))
}
bytes = as.integer(x)
b1 = bytes[seq(1, length(bytes), by = 3)]
b2 = bytes[seq(2, length(bytes), by = 3)]
b3 = bytes[seq(3, length(bytes), by = 3)]
enc = paste0(
alphabet[bitwShiftR(b1, 2) + 1L],
alphabet[bitwOr(bitwShiftL(bitwAnd(b1, 3L), 4L), bitwShiftR(b2, 4L)) + 1L],
alphabet[bitwOr(bitwShiftL(bitwAnd(b2, 15L), 2L), bitwShiftR(b3, 6L)) + 1L],
alphabet[bitwAnd(b3, 63L) + 1L],
collapse = ""
)
if (pad > 0) {
substr(enc, nchar(enc) - pad + 1, nchar(enc)) = strrep("=", pad)
}
enc
}
plotUri = list()
embedPlot = function(name, plot, width, height) {
tmpPng = tempfile(fileext = ".png")
ggplot2::ggsave(tmpPng, plot, width = width, height = height, dpi = 120, bg = "white")
raw = readBin(tmpPng, "raw", n = file.info(tmpPng)$size)
unlink(tmpPng)
plotUri[[name]] <<- paste0("data:image/png;base64,", rawToBase64(raw))
}
shortTitle = function(title, n = 52) {
title = gsub("[[:space:]]+", " ", title)
ifelse(nchar(title) <= n, title, paste0(substr(title, 1, n - 1), "..."))
}
ms = readExport("manuscripts.csv")
dec = readExport("decisions.csv")
inv = readExport("reviewer-invitations.csv")
rev = readExport("reviews.csv")
trial = startsWith(ms$title, "[EXAMPLE]") | grepl("trial entries to ignore", ms$editor_tags, fixed = TRUE)
ms = ms[!trial, , drop = FALSE]
versions = data.frame(
submissionId = idChar(ms$submission_id),
manuscriptId = idChar(ms$manuscript_id),
versionNumber = as.integer(ms$version_number),
title = ms$title,
previousVersionId = idChar(ms$previous_version_id),
workflowState = ms$workflow_state,
createdAt = parseUtc(ms$created_at),
decidedAt = parseUtc(ms$decision_created_at),
stringsAsFactors = FALSE
)
decisionType = rep(NA_character_, nrow(versions))
decMid = idChar(dec$manuscript_id)
decWhen = parseUtc(dec$created_at)
for (i in seq_len(nrow(versions))) {
hit = which(decMid == versions$manuscriptId[i])
if (length(hit) == 0) {
next
}
pick = hit[which.max(decWhen[hit])]
decisionType[i] = dec$decision_type[pick]
}
versions$decisionType = decisionType
invMid = idChar(inv$manuscript_id)
invId = idChar(inv$id)
invSent = parseUtc(inv$created_at)
invAccepted = parseUtc(inv$accepted_at)
revInvId = idChar(rev$reviewer_invitation_id)
revFiled = parseUtc(rev$created_at)
nInvite = integer(nrow(versions))
nAccept = integer(nrow(versions))
nReview = integer(nrow(versions))
firstInviteAt = rep(as.POSIXct(NA, tz = "UTC"), nrow(versions))
firstAcceptAt = rep(as.POSIXct(NA, tz = "UTC"), nrow(versions))
lastReviewAt = rep(as.POSIXct(NA, tz = "UTC"), nrow(versions))
for (i in seq_len(nrow(versions))) {
hit = which(invMid == versions$manuscriptId[i])
nInvite[i] = length(hit)
if (length(hit) == 0) {
next
}
firstInviteAt[i] = firstTime(invSent[hit])
firstAcceptAt[i] = firstTime(invAccepted[hit])
nAccept[i] = sum(!is.na(invAccepted[hit]))
filed = revFiled[revInvId %in% invId[hit]]
nReview[i] = length(filed)
lastReviewAt[i] = lastTime(filed)
}
versions$nInvite = nInvite
versions$nAccept = nAccept
versions$nReview = nReview
versions$firstInviteAt = firstInviteAt
versions$firstAcceptAt = firstAcceptAt
versions$lastReviewAt = lastReviewAt
versions$journalDays = daysBetween(versions$createdAt, versions$decidedAt)
versions$triageToInviteDays = daysBetween(versions$createdAt, versions$firstInviteAt)
versions$triageToAcceptDays = daysBetween(versions$createdAt, versions$firstAcceptAt)
versions$reviewWindowDays = daysBetween(versions$firstAcceptAt, versions$lastReviewAt)
versions$editorAfterDays = daysBetween(versions$lastReviewAt, versions$decidedAt)
reviewTurns = data.frame(
invitationId = character(0),
manuscriptId = character(0),
versionNumber = integer(0),
fromInviteDays = numeric(0),
fromAcceptDays = numeric(0),
stringsAsFactors = FALSE
)
for (i in seq_len(nrow(inv))) {
filedHit = which(revInvId == invId[i])
if (length(filedHit) == 0) {
next
}
verHit = which(versions$manuscriptId == invMid[i])
versionNumber = NA_integer_
if (length(verHit) == 1) {
versionNumber = versions$versionNumber[verHit]
}
reviewTurns = rbind(reviewTurns, data.frame(
invitationId = invId[i],
manuscriptId = invMid[i],
versionNumber = versionNumber,
fromInviteDays = daysBetween(invSent[i], revFiled[filedHit[1]]),
fromAcceptDays = daysBetween(invAccepted[i], revFiled[filedHit[1]]),
stringsAsFactors = FALSE
))
}
childOf = list()
for (i in seq_len(nrow(versions))) {
parent = versions$previousVersionId[i]
if (!is.na(parent)) {
childOf[[parent]] = c(childOf[[parent]], versions$manuscriptId[i])
}
}
for (parent in names(childOf)) {
if (length(childOf[[parent]]) > 1) {
stop("Version ", parent, " has more than one resubmission: ", paste(childOf[[parent]], collapse = ", "))
}
}
rootRows = which(is.na(versions$previousVersionId))
papers = data.frame(
submissionId = character(0),
rootId = character(0),
latestId = character(0),
title = character(0),
nRounds = integer(0),
outcome = character(0),
workflowState = character(0),
firstCreated = as.POSIXct(character(0), tz = "UTC"),
lastDecided = as.POSIXct(character(0), tz = "UTC"),
round1Journal = numeric(0),
laterJournal = numeric(0),
journalDays = numeric(0),
authorDays = numeric(0),
calendarDays = numeric(0),
round1Reviewed = logical(0),
stringsAsFactors = FALSE
)
authorGaps = data.frame(
rootId = character(0),
title = character(0),
fromVersion = integer(0),
days = numeric(0),
decidedAt = as.POSIXct(character(0), tz = "UTC"),
returnedAt = as.POSIXct(character(0), tz = "UTC"),
stringsAsFactors = FALSE
)
revisionRounds = data.frame(
manuscriptId = character(0),
title = character(0),
versionNumber = integer(0),
decisionType = character(0),
journalDays = numeric(0),
nReview = integer(0),
stringsAsFactors = FALSE
)
openRows = list()
for (r in rootRows) {
chain = versions$manuscriptId[r]
guard = 0
repeat {
kids = childOf[[chain[length(chain)]]]
if (is.null(kids)) {
break
}
chain = c(chain, kids)
guard = guard + 1
if (guard > 20) {
stop("Version chain did not end, starting at ", versions$manuscriptId[r])
}
}
idx = match(chain, versions$manuscriptId)
latest = versions[idx[length(idx)], ]
state = latest$workflowState
if (state == "ready_to_publish") {
outcome = "accepted"
} else if (state %in% c("rejected", "desk_rejected")) {
outcome = "rejected"
} else if (startsWith(state, "withdrawn")) {
outcome = "withdrawn"
} else if (state == "revise_and_resubmit") {
outcome = "with_author"
} else {
outcome = "in_review"
}
round1 = versions[idx[1], ]
round1Journal = round1$journalDays
laterJournal = 0
authorSum = 0
if (length(idx) > 1) {
later = versions$journalDays[idx[-1]]
later = later[!is.na(later)]
if (length(later) > 0) {
laterJournal = sum(later)
}
}
for (k in seq_len(length(idx) - 1)) {
gap = daysBetween(versions$decidedAt[idx[k]], versions$createdAt[idx[k + 1]])
authorSum = authorSum + gap
authorGaps = rbind(authorGaps, data.frame(
rootId = versions$manuscriptId[idx[1]],
title = versions$title[idx[length(idx)]],
fromVersion = versions$versionNumber[idx[k]],
days = gap,
decidedAt = versions$decidedAt[idx[k]],
returnedAt = versions$createdAt[idx[k + 1]],
stringsAsFactors = FALSE
))
}
for (k in idx[-1]) {
if (is.na(versions$journalDays[k])) {
next
}
revisionRounds = rbind(revisionRounds, data.frame(
manuscriptId = versions$manuscriptId[k],
title = versions$title[k],
versionNumber = versions$versionNumber[k],
decisionType = versions$decisionType[k],
journalDays = versions$journalDays[k],
nReview = versions$nReview[k],
stringsAsFactors = FALSE
))
}
journalDays = NA_real_
calendarDays = NA_real_
decidedIdx = idx[!is.na(versions$decidedAt[idx])]
if (outcome %in% c("accepted", "rejected") && length(decidedIdx) == length(idx)) {
journalDays = sum(versions$journalDays[idx])
calendarDays = daysBetween(versions$createdAt[idx[1]], versions$decidedAt[idx[length(idx)]])
}
papers = rbind(papers, data.frame(
submissionId = versions$submissionId[idx[1]],
rootId = versions$manuscriptId[idx[1]],
latestId = latest$manuscriptId,
title = latest$title,
nRounds = length(idx),
outcome = outcome,
workflowState = state,
firstCreated = versions$createdAt[idx[1]],
lastDecided = if (is.na(latest$decidedAt)) as.POSIXct(NA, tz = "UTC") else latest$decidedAt,
round1Journal = round1Journal,
laterJournal = laterJournal,
journalDays = journalDays,
authorDays = if (outcome %in% c("accepted", "rejected")) authorSum else NA_real_,
calendarDays = calendarDays,
round1Reviewed = round1$nReview > 0,
stringsAsFactors = FALSE
))
if (outcome == "in_review") {
openRows[[length(openRows) + 1]] = data.frame(
title = latest$title,
workflowState = state,
versionNumber = latest$versionNumber,
elapsedDays = daysBetween(latest$createdAt, asOfClock),
stringsAsFactors = FALSE
)
}
if (outcome == "with_author") {
openRows[[length(openRows) + 1]] = data.frame(
title = latest$title,
workflowState = "with author since revise and resubmit",
versionNumber = latest$versionNumber,
elapsedDays = daysBetween(latest$decidedAt, asOfClock),
stringsAsFactors = FALSE
)
}
}
accepted = papers[papers$outcome == "accepted", , drop = FALSE]
round1 = versions[is.na(versions$previousVersionId), , drop = FALSE]
round1Decided = round1[!is.na(round1$journalDays), , drop = FALSE]
round1Reviewed = round1[round1$nReview > 0, , drop = FALSE]
deskOnly = round1Decided[round1Decided$nInvite == 0, , drop = FALSE]
acceptRounds = revisionRounds[!is.na(revisionRounds$decisionType) & revisionRounds$decisionType == "accept", , drop = FALSE]
# Figures. ggplot objects are built and saved. They are not printed.
journalBlue = "#1B4F72"
journalLight = "#5DADE2"
authorGold = "#B9770E"
if (nrow(accepted) > 0) {
stack = accepted
stack$label = shortTitle(stack$title)
if (any(duplicated(stack$label))) {
stack$label = paste0(stack$label, " [", stack$latestId, "]")
}
stack = stack[order(stack$calendarDays, stack$label), , drop = FALSE]
long = data.frame(
label = rep(stack$label, 3),
piece = rep(c("Round 1 with the journal", "Later rounds with the journal", "With the author"), each = nrow(stack)),
days = c(stack$round1Journal, stack$laterJournal, stack$authorDays),
stringsAsFactors = FALSE
)
long$label = factor(long$label, levels = stack$label)
long$piece = factor(long$piece, levels = c("Round 1 with the journal", "Later rounds with the journal", "With the author"))
pAccepted = ggplot2::ggplot(long, ggplot2::aes(x = .data$days, y = .data$label, fill = .data$piece))
# reverse = TRUE puts the first factor level at the axis, so the bar reads left to right: round 1, later rounds, author.
pAccepted = pAccepted + ggplot2::geom_col(width = 0.72, position = ggplot2::position_stack(reverse = TRUE))
pAccepted = pAccepted + ggplot2::scale_fill_manual(values = c("Round 1 with the journal" = journalBlue, "Later rounds with the journal" = journalLight, "With the author" = authorGold))
pAccepted = pAccepted + ggplot2::labs(x = "Days from first submission to acceptance", y = NULL, fill = NULL, title = "Accepted papers: journal time and author time")
pAccepted = pAccepted + ggplot2::theme_bw(base_size = 11)
pAccepted = pAccepted + ggplot2::theme(legend.position = "bottom", panel.grid.major.y = ggplot2::element_blank())
embedPlot("accepted", pAccepted, width = 10, height = max(6, 0.32 * nrow(stack) + 1.6))
}
stage = data.frame(
stage = c(
rep("To first acceptance", sum(!is.na(round1$triageToAcceptDays))),
rep("Review window", sum(!is.na(round1Reviewed$reviewWindowDays))),
rep("Editor after reviews", sum(!is.na(round1Reviewed$editorAfterDays)))
),
days = c(
round1$triageToAcceptDays[!is.na(round1$triageToAcceptDays)],
round1Reviewed$reviewWindowDays[!is.na(round1Reviewed$reviewWindowDays)],
round1Reviewed$editorAfterDays[!is.na(round1Reviewed$editorAfterDays)]
),
stringsAsFactors = FALSE
)
stage$stage = factor(stage$stage, levels = c("To first acceptance", "Review window", "Editor after reviews"))
pStages = ggplot2::ggplot(stage, ggplot2::aes(x = .data$stage, y = .data$days))
pStages = pStages + ggplot2::geom_boxplot(fill = journalBlue, alpha = 0.25, width = 0.55, outlier.shape = NA)
pStages = pStages + ggplot2::geom_jitter(width = 0.12, height = 0, size = 1.6, alpha = 0.55, colour = journalBlue)
pStages = pStages + ggplot2::labs(x = NULL, y = "Days", title = "First version, once a reviewer is involved", subtitle = "Triage, then the review window, then the editor.")
pStages = pStages + ggplot2::theme_bw(base_size = 12)
pStages = pStages + ggplot2::theme(panel.grid.major.x = ggplot2::element_blank())
embedPlot("stages", pStages, width = 8, height = 5.2)
if (nrow(reviewTurns) > 0) {
turnMed = stats::median(reviewTurns$fromAcceptDays, na.rm = TRUE)
pReviews = ggplot2::ggplot(reviewTurns, ggplot2::aes(x = .data$fromAcceptDays))
pReviews = pReviews + ggplot2::geom_histogram(binwidth = 5, fill = journalBlue, colour = "white", boundary = 0)
pReviews = pReviews + ggplot2::geom_vline(xintercept = turnMed, linetype = 2, colour = authorGold, linewidth = 0.6)
pReviews = pReviews + ggplot2::labs(x = "Days from accepting the invitation to filing the review", y = "Reviews", title = "Reviewer turnaround", subtitle = paste0("n = ", sum(!is.na(reviewTurns$fromAcceptDays)), ". Dashed line is the median, ", fmt(turnMed), " days."))
pReviews = pReviews + ggplot2::theme_bw(base_size = 12)
embedPlot("reviews", pReviews, width = 8, height = 4.6)
}
if (nrow(authorGaps) > 0) {
authorMed = stats::median(authorGaps$days)
pAuthor = ggplot2::ggplot(authorGaps, ggplot2::aes(x = .data$days))
pAuthor = pAuthor + ggplot2::geom_histogram(binwidth = 14, fill = authorGold, colour = "white", boundary = 0)
pAuthor = pAuthor + ggplot2::geom_vline(xintercept = authorMed, linetype = 2, colour = journalBlue, linewidth = 0.6)
pAuthor = pAuthor + ggplot2::labs(x = "Days from the decision to the next version arriving", y = "Revision returns", title = "Time with the author", subtitle = paste0("n = ", nrow(authorGaps), " completed returns. Dashed line is the median, ", fmt(authorMed), " days."))
pAuthor = pAuthor + ggplot2::theme_bw(base_size = 12)
embedPlot("author", pAuthor, width = 8, height = 4.6)
}
if (nrow(revisionRounds) > 0) {
revisionRounds$decisionLabel = revisionRounds$decisionType
revisionRounds$decisionLabel[revisionRounds$decisionLabel == "accept"] = "Accept"
revisionRounds$decisionLabel[revisionRounds$decisionLabel == "reject"] = "Reject"
revisionRounds$decisionLabel[revisionRounds$decisionLabel == "revise_and_resubmit"] = "Revise and resubmit"
revisionRounds$decisionLabel[is.na(revisionRounds$decisionLabel)] = "Undecided label"
pRevision = ggplot2::ggplot(revisionRounds, ggplot2::aes(x = .data$decisionLabel, y = .data$journalDays))
pRevision = pRevision + ggplot2::geom_boxplot(fill = journalLight, alpha = 0.35, width = 0.5, outlier.shape = NA)
pRevision = pRevision + ggplot2::geom_jitter(width = 0.12, height = 0, size = 1.8, alpha = 0.65, colour = journalBlue)
pRevision = pRevision + ggplot2::labs(x = NULL, y = "Days from resubmission to the decision", title = "Journal time on a revision", subtitle = "Version 2 and later. An accept with no new reviews sits near zero.")
pRevision = pRevision + ggplot2::theme_bw(base_size = 12)
pRevision = pRevision + ggplot2::theme(panel.grid.major.x = ggplot2::element_blank())
embedPlot("revision", pRevision, width = 8, height = 5)
}
createdSpan = range(versions$createdAt, na.rm = TRUE)
nAccepted = sum(papers$outcome == "accepted")
nRejected = sum(papers$outcome == "rejected")
nWithdrawn = sum(papers$outcome == "withdrawn")
nWithAuthor = sum(papers$outcome == "with_author")
nInReview = sum(papers$outcome == "in_review")
direct = accepted[accepted$nRounds == 1, , drop = FALSE]
via = accepted[accepted$nRounds > 1, , drop = FALSE]
fig = function(name, alt) {
src = plotUri[[name]]
if (is.null(src)) {
return("")
}
paste0("<figure><img alt=\"", htmlEscape(alt), "\" src=\"", src, "\"></figure>")
}
page = c(
"<!DOCTYPE html>",
"<html lang=\"en\"><head><meta charset=\"utf-8\">",
"<title>ICA editorial efficiency</title>",
"<style>",
"body { font: 16px/1.45 -apple-system, BlinkMacSystemFont, sans-serif; color: #1c2833; max-width: 920px; margin: 2rem auto; padding: 0 1.2rem 3rem; }",
"h1 { font-size: 1.6rem; margin-bottom: 0.3rem; } h2 { font-size: 1.2rem; margin: 1.8rem 0 0.4rem; }",
"p { margin: 0.45rem 0 0.7rem; } p.lead { margin: 0.15rem 0; } p.note { margin: 0.6rem 0 0.8rem; } figure { margin: 0.4rem 0 1rem; }",
"img { width: 100%; height: auto; }",
"table { border-collapse: collapse; width: 100%; margin: 0.4rem 0 0.8rem; }",
"th, td { text-align: right; padding: 0.28rem 0.5rem; border-bottom: 1px solid #d5d8dc; vertical-align: top; }",
"th:first-child, td:first-child { text-align: left; }",
"thead th { border-bottom: 2px solid #1b4f72; }",
"</style></head><body>",
"<h1>ICA editorial efficiency</h1>",
paste0("<p class=\"lead\">Report written ", htmlEscape(format(Sys.time(), "%Y-%m-%d %H:%M %Z")), "</p>"),
paste0("<p class=\"lead\">We have handled ", nrow(papers), " papers, ", nrow(versions), " versions (trial submissions dropped).</p>"),
paste0("<p class=\"lead\">Latest state: ", nAccepted, " accepted, ", nRejected, " rejected, ", nInReview, " in review, ", nWithAuthor, " with the author, ", nWithdrawn, " withdrawn.</p>"),
"<h2>Accepted papers</h2>",
statTable(c(
statRow("Calendar, first submission to acceptance", accepted$calendarDays),
statRow("With the journal", accepted$journalDays),
statRow("With the author", accepted$authorDays),
statRow("Accepted with no revision, journal time", direct$journalDays),
statRow("Revised then accepted, journal time", via$journalDays),
statRow("Revised then accepted, author time", via$authorDays),
statRow("Revised then accepted, round 1 with the journal", via$round1Journal),
statRow("Revised then accepted, later rounds with the journal", via$laterJournal)
)),
paste0("<p class=\"note\">Note: Calendar days run from the first submission to the final decision; Journal days sum, over each version, the time from that version arriving to its decision; Author days are the gaps between a decision and the next version. First submission ", format(createdSpan[1], "%Y-%m-%d"), ", most recent ", format(createdSpan[2], "%Y-%m-%d"), ".</p>"),
fig("accepted", "Accepted papers, journal time and author time"),
paste0("<p>", nrow(direct), " papers were accepted on the first version. ", nrow(via), " went out and came back at least once. On those, later rounds with the journal are much shorter than round 1, because most accepting rounds did not go out for a new review.</p>"),
"<h2>First submission</h2>",
statTable(c(
statRow("Submit to first reviewer invited", round1$triageToInviteDays),
statRow("Submit to first reviewer accepts", round1$triageToAcceptDays),
statRow("First acceptance to last review", round1Reviewed$reviewWindowDays),
statRow("Last review to the decision", round1Reviewed$editorAfterDays),
statRow("Submit to first decision, all decided first versions", round1Decided$journalDays),
statRow("No reviewer invited, submit to decision", deskOnly$journalDays)
)),
fig("stages", "First-version stage times"),
"<p>The boxplots are first versions that reached a reviewer. Desk rejects and editorial accepts with no invitation are in the row with no reviewer invited, and inside the all-decided first-decision row.</p>",
"<h2>Reviewers</h2>",
statTable(c(
statRow("Invitation sent to review filed", reviewTurns$fromInviteDays),
statRow("Invitation accepted to review filed", reviewTurns$fromAcceptDays)
)),
fig("reviews", "Reviewer turnaround"),
"<p>Each filed review is one count. The manuscript-level review window above runs from the first acceptance to the last review on that version, so it is longer than a typical single review when two reviewers are out together or the second is found late.</p>",
"<h2>Author revision</h2>",
statTable(statRow("Decision to the next version", authorGaps$days)),
fig("author", "Time with the author")
)
if (nrow(authorGaps) > 0) {
slow = authorGaps[which.max(authorGaps$days), ]
page = c(page, paste0("<p>The longest completed return is ", fmt(slow$days), " days, on “", htmlEscape(slow$title), "”, decision ", format(slow$decidedAt, "%Y-%m-%d"), ", revision in on ", format(slow$returnedAt, "%Y-%m-%d"), ".</p>"))
}
page = c(page,
"<h2>Accepting a revision</h2>",
statTable(c(
statRow("Any decided revision round", revisionRounds$journalDays),
statRow("The round that accepted", acceptRounds$journalDays),
statRow("Accepting round with a new review", acceptRounds$journalDays[acceptRounds$nReview > 0]),
statRow("Accepting round with no new review", acceptRounds$journalDays[acceptRounds$nReview == 0])
)),
fig("revision", "Journal time on a revision"),
"<h2>Still open</h2>"
)
if (length(openRows) == 0) {
page = c(page, "<p>No manuscript is in review or waiting on an author.</p>")
} else {
openHtml = paste0("<p>Elapsed days use ", format(asOf), " as the clock. These papers are not in the means above.</p>")
openHtml = paste0(openHtml, "<table><thead><tr><th>Manuscript</th><th>State</th><th>Version</th><th>Days elapsed</th></tr></thead><tbody>")
for (i in seq_along(openRows)) {
row = openRows[[i]]
openHtml = paste0(openHtml, "<tr><td>", htmlEscape(row$title), "</td><td>", htmlEscape(row$workflowState), "</td><td>", row$versionNumber, "</td><td>", fmt(row$elapsedDays), "</td></tr>")
}
page = c(page, paste0(openHtml, "</tbody></table>"))
}
acceptedHtml = "<h2>Accepted papers, one row each</h2><table><thead><tr><th>Manuscript</th><th>Rounds</th><th>Journal</th><th>Author</th><th>Calendar</th></tr></thead><tbody>"
if (nrow(accepted) > 0) {
show = accepted[order(-accepted$calendarDays), , drop = FALSE]
for (i in seq_len(nrow(show))) {
acceptedHtml = paste0(acceptedHtml, "<tr><td>", htmlEscape(show$title[i]), "</td><td>", show$nRounds[i], "</td><td>", fmt(show$journalDays[i]), "</td><td>", fmt(show$authorDays[i]), "</td><td>", fmt(show$calendarDays[i]), "</td></tr>")
}
}
page = c(page, paste0(acceptedHtml, "</tbody></table></body></html>"))
htmlFile = tempfile(pattern = "ica_report_", fileext = ".html")
writeLines(page, htmlFile)
umx_open(htmlFile)
invisible(list(
htmlFile = htmlFile,
papers = papers,
versions = versions,
authorGaps = authorGaps,
reviewTurns = reviewTurns,
revisionRounds = revisionRounds
))
}
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Defines functions umx_ICA_report
Documented in umx_ICA_report
# Editorial clocks for a Scholastica export of Intelligence & Cognitive Abilities.
#' Journal processing report for an ICA Scholastica export
#'
#' @description
#' Read a Scholastica CSV export and open an HTML report of editorial
#' efficiency. Journal time on each version runs from that version hitting the
#' desk to the decision on it. Time the author spends between a decision and
#' the next version is counted on its own. The page gives means and medians
#' for triage, review, the editor after the reviews are in, author revision,
#' and acceptance of a revision, with the ggplot figures embedded in the page.
#'
#' @param dataDir Directory of the Scholastica CSV export. A single string.
#' Default is `~/bin/ica/ICAdata`. The files used are `manuscripts.csv`,
#' `decisions.csv`, `reviewer-invitations.csv`, and `reviews.csv`.
#' @param asOf Date used to age manuscripts that are still in review or still
#' with the author. A `Date`, or something [base::as.Date()] can parse. Default is
#' [Sys.Date()].
#'
#' @details
#' ## Files and keys
#'
#' The export is a set of tables joined by id, one Scholastica submission
#' version per manuscript row.
#'
#' * `manuscripts.csv` has one row per version. `manuscript_id` is unique to
#' that version. `previous_version_id` is the previous version's
#' `manuscript_id` (empty on the first version). `submission_id` is shared by
#' every version of the same paper, so it identifies the paper, but it is not
#' reliably the first or the latest `manuscript_id`. `version_number` is 1,
#' 2, or 3. `created_at` is when that version hit the desk. `workflow_state`
#' is the current state of that version. `decision_created_at` is when the
#' decision on that version was made.
#' * `decisions.csv` has one row per decided version, joined on `manuscript_id`.
#' `decision_type` is `accept`, `reject`, or `revise_and_resubmit`. Its
#' `created_at` matches `manuscripts.csv` `decision_created_at`.
#' * `reviewer-invitations.csv` is joined on the version `manuscript_id`.
#' `created_at` is when the invitation was sent. `accepted_at` is when the
#' reviewer accepted. `workflow_state` is `submitted` (review filed),
#' `accepted` (agreed, review not in), `declined`, `expired`, `revoked`, or
#' `hard_bounced`. `manuscript_version_number` repeats the version.
#' * `reviews.csv` has no `manuscript_id`. It joins to an invitation through
#' `reviewer_invitation_id`. `created_at` is when the review was filed.
#' `publication_recommendation` is Accept, Revise and resubmit, or Reject.
#' * `authors.csv` joins on `manuscript_id`. `articles.csv` is the published
#' article, joined on `manuscript_id`, with `published_at`. `activities.csv`
#' is a prose log of the same events (submitted, invited, accepted an
#' invitation, submitted a review, made a decision). The clocks below use the
#' structured timestamps, not the prose log. `issues.csv` is journal issues.
#' `posts.csv` is empty in the export this function was written against.
#'
#' Trial rows are dropped: `title` beginning with `[EXAMPLE]`, or `editor_tags`
#' containing `trial entries to ignore`.
#'
#' A paper is the chain walked from a version with no `previous_version_id`
#' along `previous_version_id`. Outcomes come from the latest version's
#' `workflow_state`: `ready_to_publish` accepted, `rejected` or `desk_rejected`
#' rejected, `revise_and_resubmit` with no later version still with the author,
#' `reviewers_confirmed` or `reviews_submitted` still in review, and
#' `withdrawn_before_decision` or `withdrawn_after_non_terminal_decision`
#' withdrawn.
#'
#' ## Seconds columns already on manuscripts.csv
#'
#' Scholastica also stores durations. They are not what the report plots,
#' because the total mixes the two clocks, and the editor buckets sometimes
#' overlap.
#'
#' * `time_to_decision_in_seconds` is journal time on that version only
#' (`created_at` to `decision_created_at`). It does not include the author gap.
#' * `time_spent_with_editor_pre_review_in_seconds` is meant to be desk time
#' before review. On many versions it matches the wait until the first
#' reviewer accepts. On others it keeps running after reviews have arrived.
#' * `time_spent_with_editor_post_review_in_seconds` matches last review filed
#' to the decision.
#' * On two versions, pre-review plus post-review exceeds time-to-decision, so
#' those two buckets are not a partition.
#' * `time_spent_with_author_in_seconds` is stored on the new version and
#' matches the gap from the previous decision to this version's `created_at`.
#' * `total_time_to_decision_across_versions_in_seconds` sums version
#' time-to-decision and the author gaps. It is filled on the latest decided
#' version. A paper reviewed in two days, held by the author for a year, and
#' then accepted the next day has a total near a year.
#'
#' ## Clocks the report uses
#'
#' Timestamps are minute resolution (`2015-01-13 10:18PM` style). Durations are
#' in days.
#'
#' * Hits the desk: that version's `created_at`.
#' * Goes out to a reviewer: invitation `created_at`.
#' * Reviewer takes it on: invitation `accepted_at`.
#' * Review comes back: `reviews.csv` `created_at`.
#' * Decision: `decision_created_at`.
#' * Triage, until a reviewer has it: version `created_at` to the first
#' `accepted_at`. Time until the first invitation is sent is reported beside it.
#' * Review window: first `accepted_at` to the last review filed on that version.
#' * Editor after the reviews are in: last review to the decision.
#' * Round-1 journal time: first version `created_at` to its decision. Desk
#' rejects and editorial accepts with no invitation are in this total, and
#' are also reported on their own.
#' * Author revision time: decision on version N to `created_at` of version N+1.
#' Each return is one observation. An open revise-and-resubmit is aged to
#' `asOf` and kept out of the completed mean.
#' * Time to accept a revision: `created_at` to the accept decision on a version
#' whose `decision_type` is `accept` and whose `version_number` is greater
#' than 1.
#' * Journal time for a finished paper: sum over its versions of
#' (decision - arrived). Author gaps are not in that sum.
#' * Calendar time: first version `created_at` to the final decision. This is
#' journal time plus author time.
#'
#' Versions that have not yet been decided are left out of the completed
#' journal means. Their elapsed time is listed under papers still open.
#'
#' @return Invisibly, a list. `htmlFile` is the temporary HTML page that was
#' opened. `papers` is one row per paper. `versions` is one row per version.
#' `authorGaps` is one row per completed author return. `reviewTurns` is one
#' row per filed review. `revisionRounds` is one row per decided version
#' after the first.
#' @export
#' @family Miscellaneous Utility Functions
#' @md
#' @examples
#' \dontrun{
#' umx_ICA_report()
#' umx_ICA_report(dataDir = "~/bin/ica/ICAdata")
#' }
umx_ICA_report <- function(dataDir = "~/bin/ica/ICAdata", asOf = Sys.Date()) {
dataDir = path.expand(dataDir)
asOf = as.Date(asOf)
if (length(dataDir) != 1 || !dir.exists(dataDir)) {
stop("dataDir is not a directory: ", dataDir)
}
asOfClock = as.POSIXct(paste(asOf, "00:00:00"), tz = "UTC")
oldLocale = Sys.getlocale("LC_TIME")
Sys.setlocale("LC_TIME", "C")
on.exit(Sys.setlocale("LC_TIME", oldLocale), add = TRUE)
parseUtc = function(x) {
x = gsub("[[:space:]]+", " ", trimws(as.character(x)))
x[x == "" | x == "NA"] = NA_character_
as.POSIXct(x, format = "%Y-%m-%d %I:%M%p", tz = "UTC")
}
readExport = function(fileName) {
path = file.path(dataDir, fileName)
if (!file.exists(path)) {
stop("Missing export file: ", path)
}
raw = utils::read.csv(path, stringsAsFactors = FALSE, check.names = FALSE, fileEncoding = "UTF-8-BOM")
if (ncol(raw) == 0) {
return(raw)
}
names(raw)[1] = sub("^\ufeff", "", names(raw)[1])
names(raw) = gsub(" \\(in UTC\\)", "", names(raw))
names(raw) = gsub("[^A-Za-z0-9]+", "_", names(raw))
names(raw) = gsub("^_|_$", "", names(raw))
raw
}
idChar = function(x) {
out = rep(NA_character_, length(x))
ok = !is.na(x) & as.character(x) != ""
out[ok] = as.character(x[ok])
out
}
daysBetween = function(a, b) {
as.numeric(difftime(b, a, units = "days"))
}
firstTime = function(x) {
x = x[!is.na(x)]
if (length(x) == 0) {
return(as.POSIXct(NA, tz = "UTC"))
}
min(x)
}
lastTime = function(x) {
x = x[!is.na(x)]
if (length(x) == 0) {
return(as.POSIXct(NA, tz = "UTC"))
}
max(x)
}
fmt = function(x, digits = 1) {
if (length(x) == 0 || all(is.na(x))) {
return("-")
}
format(round(x, digits), nsmall = digits, trim = TRUE)
}
htmlEscape = function(x) {
x = gsub("&", "&", x, fixed = TRUE)
x = gsub("<", "<", x, fixed = TRUE)
x = gsub(">", ">", x, fixed = TRUE)
x = gsub("\"", """, x, fixed = TRUE)
x
}
statRow = function(label, x) {
x = x[!is.na(x)]
cells = if (length(x) == 0) {
c("0", "-", "-", "-", "-")
} else {
qs = stats::quantile(x, c(0.25, 0.75))
c(as.character(length(x)), fmt(mean(x)), fmt(stats::median(x)), fmt(qs[1]), fmt(qs[2]))
}
paste0("<tr><th>", htmlEscape(label), "</th>", paste0("<td>", cells, "</td>", collapse = ""), "</tr>")
}
statTable = function(rows) {
paste0(
"<table><thead><tr><th></th><th>n</th><th>Mean (days)</th><th>Median</th><th>25th</th><th>75th</th></tr></thead><tbody>",
paste(rows, collapse = ""),
"</tbody></table>"
)
}
rawToBase64 = function(x) {
alphabet = c(LETTERS, letters, as.character(0:9), "+", "/")
n = length(x)
pad = (3 - n %% 3) %% 3
if (pad > 0) {
x = c(x, raw(pad))
}
bytes = as.integer(x)
b1 = bytes[seq(1, length(bytes), by = 3)]
b2 = bytes[seq(2, length(bytes), by = 3)]
b3 = bytes[seq(3, length(bytes), by = 3)]
enc = paste0(
alphabet[bitwShiftR(b1, 2) + 1L],
alphabet[bitwOr(bitwShiftL(bitwAnd(b1, 3L), 4L), bitwShiftR(b2, 4L)) + 1L],
alphabet[bitwOr(bitwShiftL(bitwAnd(b2, 15L), 2L), bitwShiftR(b3, 6L)) + 1L],
alphabet[bitwAnd(b3, 63L) + 1L],
collapse = ""
)
if (pad > 0) {
substr(enc, nchar(enc) - pad + 1, nchar(enc)) = strrep("=", pad)
}
enc
}
plotUri = list()
embedPlot = function(name, plot, width, height) {
tmpPng = tempfile(fileext = ".png")
ggplot2::ggsave(tmpPng, plot, width = width, height = height, dpi = 120, bg = "white")
raw = readBin(tmpPng, "raw", n = file.info(tmpPng)$size)
unlink(tmpPng)
plotUri[[name]] <<- paste0("data:image/png;base64,", rawToBase64(raw))
}
shortTitle = function(title, n = 52) {
title = gsub("[[:space:]]+", " ", title)
ifelse(nchar(title) <= n, title, paste0(substr(title, 1, n - 1), "..."))
}
ms = readExport("manuscripts.csv")
dec = readExport("decisions.csv")
inv = readExport("reviewer-invitations.csv")
rev = readExport("reviews.csv")
trial = startsWith(ms$title, "[EXAMPLE]") | grepl("trial entries to ignore", ms$editor_tags, fixed = TRUE)
ms = ms[!trial, , drop = FALSE]
versions = data.frame(
submissionId = idChar(ms$submission_id),
manuscriptId = idChar(ms$manuscript_id),
versionNumber = as.integer(ms$version_number),
title = ms$title,
previousVersionId = idChar(ms$previous_version_id),
workflowState = ms$workflow_state,
createdAt = parseUtc(ms$created_at),
decidedAt = parseUtc(ms$decision_created_at),
stringsAsFactors = FALSE
)
decisionType = rep(NA_character_, nrow(versions))
decMid = idChar(dec$manuscript_id)
decWhen = parseUtc(dec$created_at)
for (i in seq_len(nrow(versions))) {
hit = which(decMid == versions$manuscriptId[i])
if (length(hit) == 0) {
next
}
pick = hit[which.max(decWhen[hit])]
decisionType[i] = dec$decision_type[pick]
}
versions$decisionType = decisionType
invMid = idChar(inv$manuscript_id)
invId = idChar(inv$id)
invSent = parseUtc(inv$created_at)
invAccepted = parseUtc(inv$accepted_at)
revInvId = idChar(rev$reviewer_invitation_id)
revFiled = parseUtc(rev$created_at)
nInvite = integer(nrow(versions))
nAccept = integer(nrow(versions))
nReview = integer(nrow(versions))
firstInviteAt = rep(as.POSIXct(NA, tz = "UTC"), nrow(versions))
firstAcceptAt = rep(as.POSIXct(NA, tz = "UTC"), nrow(versions))
lastReviewAt = rep(as.POSIXct(NA, tz = "UTC"), nrow(versions))
for (i in seq_len(nrow(versions))) {
hit = which(invMid == versions$manuscriptId[i])
nInvite[i] = length(hit)
if (length(hit) == 0) {
next
}
firstInviteAt[i] = firstTime(invSent[hit])
firstAcceptAt[i] = firstTime(invAccepted[hit])
nAccept[i] = sum(!is.na(invAccepted[hit]))
filed = revFiled[revInvId %in% invId[hit]]
nReview[i] = length(filed)
lastReviewAt[i] = lastTime(filed)
}
versions$nInvite = nInvite
versions$nAccept = nAccept
versions$nReview = nReview
versions$firstInviteAt = firstInviteAt
versions$firstAcceptAt = firstAcceptAt
versions$lastReviewAt = lastReviewAt
versions$journalDays = daysBetween(versions$createdAt, versions$decidedAt)
versions$triageToInviteDays = daysBetween(versions$createdAt, versions$firstInviteAt)
versions$triageToAcceptDays = daysBetween(versions$createdAt, versions$firstAcceptAt)
versions$reviewWindowDays = daysBetween(versions$firstAcceptAt, versions$lastReviewAt)
versions$editorAfterDays = daysBetween(versions$lastReviewAt, versions$decidedAt)
reviewTurns = data.frame(
invitationId = character(0),
manuscriptId = character(0),
versionNumber = integer(0),
fromInviteDays = numeric(0),
fromAcceptDays = numeric(0),
stringsAsFactors = FALSE
)
for (i in seq_len(nrow(inv))) {
filedHit = which(revInvId == invId[i])
if (length(filedHit) == 0) {
next
}
verHit = which(versions$manuscriptId == invMid[i])
versionNumber = NA_integer_
if (length(verHit) == 1) {
versionNumber = versions$versionNumber[verHit]
}
reviewTurns = rbind(reviewTurns, data.frame(
invitationId = invId[i],
manuscriptId = invMid[i],
versionNumber = versionNumber,
fromInviteDays = daysBetween(invSent[i], revFiled[filedHit[1]]),
fromAcceptDays = daysBetween(invAccepted[i], revFiled[filedHit[1]]),
stringsAsFactors = FALSE
))
}
childOf = list()
for (i in seq_len(nrow(versions))) {
parent = versions$previousVersionId[i]
if (!is.na(parent)) {
childOf[[parent]] = c(childOf[[parent]], versions$manuscriptId[i])
}
}
for (parent in names(childOf)) {
if (length(childOf[[parent]]) > 1) {
stop("Version ", parent, " has more than one resubmission: ", paste(childOf[[parent]], collapse = ", "))
}
}
rootRows = which(is.na(versions$previousVersionId))
papers = data.frame(
submissionId = character(0),
rootId = character(0),
latestId = character(0),
title = character(0),
nRounds = integer(0),
outcome = character(0),
workflowState = character(0),
firstCreated = as.POSIXct(character(0), tz = "UTC"),
lastDecided = as.POSIXct(character(0), tz = "UTC"),
round1Journal = numeric(0),
laterJournal = numeric(0),
journalDays = numeric(0),
authorDays = numeric(0),
calendarDays = numeric(0),
round1Reviewed = logical(0),
stringsAsFactors = FALSE
)
authorGaps = data.frame(
rootId = character(0),
title = character(0),
fromVersion = integer(0),
days = numeric(0),
decidedAt = as.POSIXct(character(0), tz = "UTC"),
returnedAt = as.POSIXct(character(0), tz = "UTC"),
stringsAsFactors = FALSE
)
revisionRounds = data.frame(
manuscriptId = character(0),
title = character(0),
versionNumber = integer(0),
decisionType = character(0),
journalDays = numeric(0),
nReview = integer(0),
stringsAsFactors = FALSE
)
openRows = list()
for (r in rootRows) {
chain = versions$manuscriptId[r]
guard = 0
repeat {
kids = childOf[[chain[length(chain)]]]
if (is.null(kids)) {
break
}
chain = c(chain, kids)
guard = guard + 1
if (guard > 20) {
stop("Version chain did not end, starting at ", versions$manuscriptId[r])
}
}
idx = match(chain, versions$manuscriptId)
latest = versions[idx[length(idx)], ]
state = latest$workflowState
if (state == "ready_to_publish") {
outcome = "accepted"
} else if (state %in% c("rejected", "desk_rejected")) {
outcome = "rejected"
} else if (startsWith(state, "withdrawn")) {
outcome = "withdrawn"
} else if (state == "revise_and_resubmit") {
outcome = "with_author"
} else {
outcome = "in_review"
}
round1 = versions[idx[1], ]
round1Journal = round1$journalDays
laterJournal = 0
authorSum = 0
if (length(idx) > 1) {
later = versions$journalDays[idx[-1]]
later = later[!is.na(later)]
if (length(later) > 0) {
laterJournal = sum(later)
}
}
for (k in seq_len(length(idx) - 1)) {
gap = daysBetween(versions$decidedAt[idx[k]], versions$createdAt[idx[k + 1]])
authorSum = authorSum + gap
authorGaps = rbind(authorGaps, data.frame(
rootId = versions$manuscriptId[idx[1]],
title = versions$title[idx[length(idx)]],
fromVersion = versions$versionNumber[idx[k]],
days = gap,
decidedAt = versions$decidedAt[idx[k]],
returnedAt = versions$createdAt[idx[k + 1]],
stringsAsFactors = FALSE
))
}
for (k in idx[-1]) {
if (is.na(versions$journalDays[k])) {
next
}
revisionRounds = rbind(revisionRounds, data.frame(
manuscriptId = versions$manuscriptId[k],
title = versions$title[k],
versionNumber = versions$versionNumber[k],
decisionType = versions$decisionType[k],
journalDays = versions$journalDays[k],
nReview = versions$nReview[k],
stringsAsFactors = FALSE
))
}
journalDays = NA_real_
calendarDays = NA_real_
decidedIdx = idx[!is.na(versions$decidedAt[idx])]
if (outcome %in% c("accepted", "rejected") && length(decidedIdx) == length(idx)) {
journalDays = sum(versions$journalDays[idx])
calendarDays = daysBetween(versions$createdAt[idx[1]], versions$decidedAt[idx[length(idx)]])
}
papers = rbind(papers, data.frame(
submissionId = versions$submissionId[idx[1]],
rootId = versions$manuscriptId[idx[1]],
latestId = latest$manuscriptId,
title = latest$title,
nRounds = length(idx),
outcome = outcome,
workflowState = state,
firstCreated = versions$createdAt[idx[1]],
lastDecided = if (is.na(latest$decidedAt)) as.POSIXct(NA, tz = "UTC") else latest$decidedAt,
round1Journal = round1Journal,
laterJournal = laterJournal,
journalDays = journalDays,
authorDays = if (outcome %in% c("accepted", "rejected")) authorSum else NA_real_,
calendarDays = calendarDays,
round1Reviewed = round1$nReview > 0,
stringsAsFactors = FALSE
))
if (outcome == "in_review") {
openRows[[length(openRows) + 1]] = data.frame(
title = latest$title,
workflowState = state,
versionNumber = latest$versionNumber,
elapsedDays = daysBetween(latest$createdAt, asOfClock),
stringsAsFactors = FALSE
)
}
if (outcome == "with_author") {
openRows[[length(openRows) + 1]] = data.frame(
title = latest$title,
workflowState = "with author since revise and resubmit",
versionNumber = latest$versionNumber,
elapsedDays = daysBetween(latest$decidedAt, asOfClock),
stringsAsFactors = FALSE
)
}
}
accepted = papers[papers$outcome == "accepted", , drop = FALSE]
round1 = versions[is.na(versions$previousVersionId), , drop = FALSE]
round1Decided = round1[!is.na(round1$journalDays), , drop = FALSE]
round1Reviewed = round1[round1$nReview > 0, , drop = FALSE]
deskOnly = round1Decided[round1Decided$nInvite == 0, , drop = FALSE]
acceptRounds = revisionRounds[!is.na(revisionRounds$decisionType) & revisionRounds$decisionType == "accept", , drop = FALSE]
# Figures. ggplot objects are built and saved. They are not printed.
journalBlue = "#1B4F72"
journalLight = "#5DADE2"
authorGold = "#B9770E"
if (nrow(accepted) > 0) {
stack = accepted
stack$label = shortTitle(stack$title)
if (any(duplicated(stack$label))) {
stack$label = paste0(stack$label, " [", stack$latestId, "]")
}
stack = stack[order(stack$calendarDays, stack$label), , drop = FALSE]
long = data.frame(
label = rep(stack$label, 3),
piece = rep(c("Round 1 with the journal", "Later rounds with the journal", "With the author"), each = nrow(stack)),
days = c(stack$round1Journal, stack$laterJournal, stack$authorDays),
stringsAsFactors = FALSE
)
long$label = factor(long$label, levels = stack$label)
long$piece = factor(long$piece, levels = c("Round 1 with the journal", "Later rounds with the journal", "With the author"))
pAccepted = ggplot2::ggplot(long, ggplot2::aes(x = .data$days, y = .data$label, fill = .data$piece))
# reverse = TRUE puts the first factor level at the axis, so the bar reads left to right: round 1, later rounds, author.
pAccepted = pAccepted + ggplot2::geom_col(width = 0.72, position = ggplot2::position_stack(reverse = TRUE))
pAccepted = pAccepted + ggplot2::scale_fill_manual(values = c("Round 1 with the journal" = journalBlue, "Later rounds with the journal" = journalLight, "With the author" = authorGold))
pAccepted = pAccepted + ggplot2::labs(x = "Days from first submission to acceptance", y = NULL, fill = NULL, title = "Accepted papers: journal time and author time")
pAccepted = pAccepted + ggplot2::theme_bw(base_size = 11)
pAccepted = pAccepted + ggplot2::theme(legend.position = "bottom", panel.grid.major.y = ggplot2::element_blank())
embedPlot("accepted", pAccepted, width = 10, height = max(6, 0.32 * nrow(stack) + 1.6))
}
stage = data.frame(
stage = c(
rep("To first acceptance", sum(!is.na(round1$triageToAcceptDays))),
rep("Review window", sum(!is.na(round1Reviewed$reviewWindowDays))),
rep("Editor after reviews", sum(!is.na(round1Reviewed$editorAfterDays)))
),
days = c(
round1$triageToAcceptDays[!is.na(round1$triageToAcceptDays)],
round1Reviewed$reviewWindowDays[!is.na(round1Reviewed$reviewWindowDays)],
round1Reviewed$editorAfterDays[!is.na(round1Reviewed$editorAfterDays)]
),
stringsAsFactors = FALSE
)
stage$stage = factor(stage$stage, levels = c("To first acceptance", "Review window", "Editor after reviews"))
pStages = ggplot2::ggplot(stage, ggplot2::aes(x = .data$stage, y = .data$days))
pStages = pStages + ggplot2::geom_boxplot(fill = journalBlue, alpha = 0.25, width = 0.55, outlier.shape = NA)
pStages = pStages + ggplot2::geom_jitter(width = 0.12, height = 0, size = 1.6, alpha = 0.55, colour = journalBlue)
pStages = pStages + ggplot2::labs(x = NULL, y = "Days", title = "First version, once a reviewer is involved", subtitle = "Triage, then the review window, then the editor.")
pStages = pStages + ggplot2::theme_bw(base_size = 12)
pStages = pStages + ggplot2::theme(panel.grid.major.x = ggplot2::element_blank())
embedPlot("stages", pStages, width = 8, height = 5.2)
if (nrow(reviewTurns) > 0) {
turnMed = stats::median(reviewTurns$fromAcceptDays, na.rm = TRUE)
pReviews = ggplot2::ggplot(reviewTurns, ggplot2::aes(x = .data$fromAcceptDays))
pReviews = pReviews + ggplot2::geom_histogram(binwidth = 5, fill = journalBlue, colour = "white", boundary = 0)
pReviews = pReviews + ggplot2::geom_vline(xintercept = turnMed, linetype = 2, colour = authorGold, linewidth = 0.6)
pReviews = pReviews + ggplot2::labs(x = "Days from accepting the invitation to filing the review", y = "Reviews", title = "Reviewer turnaround", subtitle = paste0("n = ", sum(!is.na(reviewTurns$fromAcceptDays)), ". Dashed line is the median, ", fmt(turnMed), " days."))
pReviews = pReviews + ggplot2::theme_bw(base_size = 12)
embedPlot("reviews", pReviews, width = 8, height = 4.6)
}
if (nrow(authorGaps) > 0) {
authorMed = stats::median(authorGaps$days)
pAuthor = ggplot2::ggplot(authorGaps, ggplot2::aes(x = .data$days))
pAuthor = pAuthor + ggplot2::geom_histogram(binwidth = 14, fill = authorGold, colour = "white", boundary = 0)
pAuthor = pAuthor + ggplot2::geom_vline(xintercept = authorMed, linetype = 2, colour = journalBlue, linewidth = 0.6)
pAuthor = pAuthor + ggplot2::labs(x = "Days from the decision to the next version arriving", y = "Revision returns", title = "Time with the author", subtitle = paste0("n = ", nrow(authorGaps), " completed returns. Dashed line is the median, ", fmt(authorMed), " days."))
pAuthor = pAuthor + ggplot2::theme_bw(base_size = 12)
embedPlot("author", pAuthor, width = 8, height = 4.6)
}
if (nrow(revisionRounds) > 0) {
revisionRounds$decisionLabel = revisionRounds$decisionType
revisionRounds$decisionLabel[revisionRounds$decisionLabel == "accept"] = "Accept"
revisionRounds$decisionLabel[revisionRounds$decisionLabel == "reject"] = "Reject"
revisionRounds$decisionLabel[revisionRounds$decisionLabel == "revise_and_resubmit"] = "Revise and resubmit"
revisionRounds$decisionLabel[is.na(revisionRounds$decisionLabel)] = "Undecided label"
pRevision = ggplot2::ggplot(revisionRounds, ggplot2::aes(x = .data$decisionLabel, y = .data$journalDays))
pRevision = pRevision + ggplot2::geom_boxplot(fill = journalLight, alpha = 0.35, width = 0.5, outlier.shape = NA)
pRevision = pRevision + ggplot2::geom_jitter(width = 0.12, height = 0, size = 1.8, alpha = 0.65, colour = journalBlue)
pRevision = pRevision + ggplot2::labs(x = NULL, y = "Days from resubmission to the decision", title = "Journal time on a revision", subtitle = "Version 2 and later. An accept with no new reviews sits near zero.")
pRevision = pRevision + ggplot2::theme_bw(base_size = 12)
pRevision = pRevision + ggplot2::theme(panel.grid.major.x = ggplot2::element_blank())
embedPlot("revision", pRevision, width = 8, height = 5)
}
createdSpan = range(versions$createdAt, na.rm = TRUE)
nAccepted = sum(papers$outcome == "accepted")
nRejected = sum(papers$outcome == "rejected")
nWithdrawn = sum(papers$outcome == "withdrawn")
nWithAuthor = sum(papers$outcome == "with_author")
nInReview = sum(papers$outcome == "in_review")
direct = accepted[accepted$nRounds == 1, , drop = FALSE]
via = accepted[accepted$nRounds > 1, , drop = FALSE]
fig = function(name, alt) {
src = plotUri[[name]]
if (is.null(src)) {
return("")
}
paste0("<figure><img alt=\"", htmlEscape(alt), "\" src=\"", src, "\"></figure>")
}
page = c(
"<!DOCTYPE html>",
"<html lang=\"en\"><head><meta charset=\"utf-8\">",
"<title>ICA editorial efficiency</title>",
"<style>",
"body { font: 16px/1.45 -apple-system, BlinkMacSystemFont, sans-serif; color: #1c2833; max-width: 920px; margin: 2rem auto; padding: 0 1.2rem 3rem; }",
"h1 { font-size: 1.6rem; margin-bottom: 0.3rem; } h2 { font-size: 1.2rem; margin: 1.8rem 0 0.4rem; }",
"p { margin: 0.45rem 0 0.7rem; } p.lead { margin: 0.15rem 0; } p.note { margin: 0.6rem 0 0.8rem; } figure { margin: 0.4rem 0 1rem; }",
"img { width: 100%; height: auto; }",
"table { border-collapse: collapse; width: 100%; margin: 0.4rem 0 0.8rem; }",
"th, td { text-align: right; padding: 0.28rem 0.5rem; border-bottom: 1px solid #d5d8dc; vertical-align: top; }",
"th:first-child, td:first-child { text-align: left; }",
"thead th { border-bottom: 2px solid #1b4f72; }",
"</style></head><body>",
"<h1>ICA editorial efficiency</h1>",
paste0("<p class=\"lead\">Report written ", htmlEscape(format(Sys.time(), "%Y-%m-%d %H:%M %Z")), "</p>"),
paste0("<p class=\"lead\">We have handled ", nrow(papers), " papers, ", nrow(versions), " versions (trial submissions dropped).</p>"),
paste0("<p class=\"lead\">Latest state: ", nAccepted, " accepted, ", nRejected, " rejected, ", nInReview, " in review, ", nWithAuthor, " with the author, ", nWithdrawn, " withdrawn.</p>"),
"<h2>Accepted papers</h2>",
statTable(c(
statRow("Calendar, first submission to acceptance", accepted$calendarDays),
statRow("With the journal", accepted$journalDays),
statRow("With the author", accepted$authorDays),
statRow("Accepted with no revision, journal time", direct$journalDays),
statRow("Revised then accepted, journal time", via$journalDays),
statRow("Revised then accepted, author time", via$authorDays),
statRow("Revised then accepted, round 1 with the journal", via$round1Journal),
statRow("Revised then accepted, later rounds with the journal", via$laterJournal)
)),
paste0("<p class=\"note\">Note: Calendar days run from the first submission to the final decision; Journal days sum, over each version, the time from that version arriving to its decision; Author days are the gaps between a decision and the next version. First submission ", format(createdSpan[1], "%Y-%m-%d"), ", most recent ", format(createdSpan[2], "%Y-%m-%d"), ".</p>"),
fig("accepted", "Accepted papers, journal time and author time"),
paste0("<p>", nrow(direct), " papers were accepted on the first version. ", nrow(via), " went out and came back at least once. On those, later rounds with the journal are much shorter than round 1, because most accepting rounds did not go out for a new review.</p>"),
"<h2>First submission</h2>",
statTable(c(
statRow("Submit to first reviewer invited", round1$triageToInviteDays),
statRow("Submit to first reviewer accepts", round1$triageToAcceptDays),
statRow("First acceptance to last review", round1Reviewed$reviewWindowDays),
statRow("Last review to the decision", round1Reviewed$editorAfterDays),
statRow("Submit to first decision, all decided first versions", round1Decided$journalDays),
statRow("No reviewer invited, submit to decision", deskOnly$journalDays)
)),
fig("stages", "First-version stage times"),
"<p>The boxplots are first versions that reached a reviewer. Desk rejects and editorial accepts with no invitation are in the row with no reviewer invited, and inside the all-decided first-decision row.</p>",
"<h2>Reviewers</h2>",
statTable(c(
statRow("Invitation sent to review filed", reviewTurns$fromInviteDays),
statRow("Invitation accepted to review filed", reviewTurns$fromAcceptDays)
)),
fig("reviews", "Reviewer turnaround"),
"<p>Each filed review is one count. The manuscript-level review window above runs from the first acceptance to the last review on that version, so it is longer than a typical single review when two reviewers are out together or the second is found late.</p>",
"<h2>Author revision</h2>",
statTable(statRow("Decision to the next version", authorGaps$days)),
fig("author", "Time with the author")
)
if (nrow(authorGaps) > 0) {
slow = authorGaps[which.max(authorGaps$days), ]
page = c(page, paste0("<p>The longest completed return is ", fmt(slow$days), " days, on “", htmlEscape(slow$title), "”, decision ", format(slow$decidedAt, "%Y-%m-%d"), ", revision in on ", format(slow$returnedAt, "%Y-%m-%d"), ".</p>"))
}
page = c(page,
"<h2>Accepting a revision</h2>",
statTable(c(
statRow("Any decided revision round", revisionRounds$journalDays),
statRow("The round that accepted", acceptRounds$journalDays),
statRow("Accepting round with a new review", acceptRounds$journalDays[acceptRounds$nReview > 0]),
statRow("Accepting round with no new review", acceptRounds$journalDays[acceptRounds$nReview == 0])
)),
fig("revision", "Journal time on a revision"),
"<h2>Still open</h2>"
)
if (length(openRows) == 0) {
page = c(page, "<p>No manuscript is in review or waiting on an author.</p>")
} else {
openHtml = paste0("<p>Elapsed days use ", format(asOf), " as the clock. These papers are not in the means above.</p>")
openHtml = paste0(openHtml, "<table><thead><tr><th>Manuscript</th><th>State</th><th>Version</th><th>Days elapsed</th></tr></thead><tbody>")
for (i in seq_along(openRows)) {
row = openRows[[i]]
openHtml = paste0(openHtml, "<tr><td>", htmlEscape(row$title), "</td><td>", htmlEscape(row$workflowState), "</td><td>", row$versionNumber, "</td><td>", fmt(row$elapsedDays), "</td></tr>")
}
page = c(page, paste0(openHtml, "</tbody></table>"))
}
acceptedHtml = "<h2>Accepted papers, one row each</h2><table><thead><tr><th>Manuscript</th><th>Rounds</th><th>Journal</th><th>Author</th><th>Calendar</th></tr></thead><tbody>"
if (nrow(accepted) > 0) {
show = accepted[order(-accepted$calendarDays), , drop = FALSE]
for (i in seq_len(nrow(show))) {
acceptedHtml = paste0(acceptedHtml, "<tr><td>", htmlEscape(show$title[i]), "</td><td>", show$nRounds[i], "</td><td>", fmt(show$journalDays[i]), "</td><td>", fmt(show$authorDays[i]), "</td><td>", fmt(show$calendarDays[i]), "</td></tr>")
}
}
page = c(page, paste0(acceptedHtml, "</tbody></table></body></html>"))
htmlFile = tempfile(pattern = "ica_report_", fileext = ".html")
writeLines(page, htmlFile)
umx_open(htmlFile)
invisible(list(
htmlFile = htmlFile,
papers = papers,
versions = versions,
authorGaps = authorGaps,
reviewTurns = reviewTurns,
revisionRounds = revisionRounds
))
}
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