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Merged
efletcherPIFSC merged 4 commits into from
Apr 29, 2026
Merged

attempt to support runs test for size frequency data #139

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e7d849c
attempt to support runs test for size frequency data
iantaylor-NOAA Apr 17, 2026
fe2c775
use current r4ss version on main
iantaylor-NOAA Apr 17, 2026
7a7c7b2
Updated RoxyenNote to 7.3.3
efletcherPIFSC Apr 17, 2026
92e7b85
SSrunstest function documention parameter quants updated with value '…
efletcherPIFSC Apr 17, 2026
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4 changes: 2 additions & 2 deletions DESCRIPTION
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Expand Up @@ -33,7 +33,7 @@ Suggests:
rmarkdown,
testthat (>= 3.0.0)
Remotes:
r4ss/r4ss@*release
r4ss/r4ss
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
RoxygenNote: 7.3.3
6 changes: 5 additions & 1 deletion R/SScompsTA1.8.R
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Expand Up @@ -131,7 +131,11 @@ SScompsTA1.8 <- function(ss3rep, type = c("len", "age", "size", "con"), fleet =
}

if (gender.flag) pldat <- cbind(pldat, pick.gender = 0)
if (method.flag) pldat <- cbind(pldat, method = 0)
if (method.flag) {
pldat <- cbind(pldat, method = 0)
# vector to store units (which are strings and don't fit in pldat matrix)
plunits <- rep(NA, nrow(pldat))
}

# Find the weighting factor for this combination of factors
if (type[1] == "con") {
Expand Down
20 changes: 10 additions & 10 deletions R/SSplotRunstest.R
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Expand Up @@ -184,12 +184,12 @@ SSplotRunstest <- function(ss3rep,
}

subplots <- subplots[1]
datatypes <- c("Index", "Mean length", "Mean age", "Conditional age-at-length")
ylabel <- datatypes[which(c("cpue", "len", "age", "con") %in% subplots)]
datatypes <- c("Index", "Mean length", "Mean age", "Conditional age-at-length", "Size frequency")
ylabel <- datatypes[which(c("cpue", "len", "age", "con", "size") %in% subplots)]
if (length(ylabel) == 0) {
stop(subplots, "is not a valid type. Please choose from the options cpue, len, age, size, or con")
stop(subplots, " is not a valid type. Please choose from the options cpue, len, age, size, or con")
}
if (verbose) message("Running Runs Test Diagnostics w/ plots for", datatypes[which(c("cpue", "len", "age", "con") %in% subplots)])
if (verbose) message("Running Runs Test Diagnostics w/ plots for", datatypes[which(c("cpue", "len", "age", "con", "size") %in% subplots)])
if (subplots == "cpue") {
cpue <- ss3rep[["cpue"]]
cpue[["residuals"]] <- ifelse(is.na(cpue[["Obs"]]) | is.na(cpue[["Like"]]), NA, log(cpue[["Obs"]]) - log(cpue[["Exp"]]))
Expand Down Expand Up @@ -435,13 +435,13 @@ SSplotRunstest <- function(ss3rep,

SSrunstest <- function(ss3rep,
mixing = "less",
quants = c("cpue", "len", "age", "con")[1],
quants = c("cpue", "len", "age", "con", "size")[1],
indexselect = NULL,
verbose = TRUE) {
datatypes <- c("Index", "Mean length", "Mean age", "Conditional age-at-length")
datatypes <- c("Index", "Mean length", "Mean age", "Conditional age-at-length", "Size frequency")
subplots <- quants
ylabel <- datatypes[which(c("cpue", "len", "age", "con") %in% subplots)]
if (verbose) cat("Running Runs Test Diagnosics for", datatypes[which(c("cpue", "len", "age", "con") %in% subplots)], "\n")
ylabel <- datatypes[which(c("cpue", "len", "age", "con", "size") %in% subplots)]
if (verbose) cat("Running Runs Test Diagnosics for", datatypes[which(c("cpue", "len", "age", "con", "size") %in% subplots)], "\n")
if (subplots == "cpue") {
cpue <- ss3rep[["cpue"]]
cpue[["residuals"]] <- ifelse(is.na(cpue[["Obs"]]) | is.na(cpue[["Like"]]), NA, log(cpue[["Obs"]]) - log(cpue[["Exp"]]))
Expand All @@ -452,7 +452,7 @@ SSrunstest <- function(ss3rep,
Res <- cpue
}

if (subplots == "len" | subplots == "age") {
if (subplots == "len" | subplots == "age" | subplots == "size") {
comps <- SScompsTA1.8(ss3rep, fleet = NULL, type = subplots, plotit = FALSE)[["runs_dat"]]
comps[["residuals"]] <- ifelse(is.na(comps[["Obs"]]), NA, log(comps[["Obs"]]) - log(comps[["Exp"]]))
if (is.null(comps[["Fleet_name"]])) { # Deal with Version control
Expand Down Expand Up @@ -521,7 +521,7 @@ SSrunstest <- function(ss3rep,

runstable <- data.frame(Index = indices, runs.p = as.matrix(runs)[, 1], Test = ifelse(is.na(as.matrix(runs)[, 1]), "Excluded", ifelse(as.matrix(runs)[, 1] < 0.05, "Failed", "Passed")), sigma3.lo = as.matrix(runs)[, 2], sigma3.hi = as.matrix(runs)[, 3], type = subplots)
colnames(runstable) <- c("Index", "runs.p", "test", "sigma3.lo", "sigma3.hi", "type")
if (verbose) cat(paste0("Residual Runs Test stats by ", datatypes[which(c("cpue", "len", "age", "con") %in% subplots)], ":", "\n"))
if (verbose) cat(paste0("Residual Runs Test stats by ", datatypes[which(c("cpue", "len", "age", "con", "size") %in% subplots)], ":", "\n"))
return(runstable)
} # end of SSplotRuns()
#-----------------------------------------------------------------------------------------
2 changes: 1 addition & 1 deletion man/SSrunstest.Rd
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