From 659882303d491d7b6a1a12c4e70cded68893338e Mon Sep 17 00:00:00 2001 From: Joe Thorley Date: Mon, 15 Sep 2025 09:06:09 -0700 Subject: [PATCH 1/2] fledge: Bump version to 2.4.0.9000 --- DESCRIPTION | 2 +- NEWS.md | 4 ++++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index d8ad4a27..d5a711ec 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: ssdtools Title: Species Sensitivity Distributions -Version: 2.4.0 +Version: 2.4.0.9000 Authors@R: c( person("Joe", "Thorley", , "joe@poissonconsulting.ca", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7683-4592")), diff --git a/NEWS.md b/NEWS.md index 5cf0fd3d..1eceab4a 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,9 @@ +# ssdtools 2.4.0.9000 + +- Added following `ci_methods` to `ssd_hc()`, `ssd_hp()` and `predict()`: `"GMACL"`, `"MAW1"`, `"MAW2"`, `"GMAW1"`, `"GMAW2"`, `"arithmetic_samples"` and `"geometric_samples"`. + # ssdtools 2.4.0 ## Features From e701130726b275f5b561730d6b83dd4836d18615 Mon Sep 17 00:00:00 2001 From: Joe Thorley Date: Mon, 15 Sep 2025 09:06:30 -0700 Subject: [PATCH 2/2] params --- R/params.R | 10 ++++++++++ man/params.Rd | 10 ++++++++++ man/predict.fitdists.Rd | 10 ++++++++++ man/ssd_hc.Rd | 10 ++++++++++ man/ssd_hp.Rd | 10 ++++++++++ 5 files changed, 50 insertions(+) diff --git a/R/params.R b/R/params.R index fe7f2331..6e7d0c6b 100644 --- a/R/params.R +++ b/R/params.R @@ -43,6 +43,16 @@ #' The value `ci_method = "MACL"` (was `ci_method = "weighted_arithmetic"` but #' has been soft-deprecated) which is only included for #' historical reasons takes the weighted arithmetic mean of the confidence +#' limits and `ci_method = MGCL` which was included for a research paper +#' takes the weighted geometric mean of the confidence limits. +#' The values `ci_method = "MAW1"` and `ci_method = "MAW2"` +#' use the two alternative equations of Burnham and Anderson to +#' model average the weighted standard errors and then calculate the confidence +#' limits using the Wald approach. +#' Finally `ci_method = "arithmetic"` and `ci_method = "geometric"` +#' take the weighted arithmetic or geometric mean of the values for +#' each bootstrap iteration across all the distributions and then +#' calculate the confidence limits (and SE) from the single set of samples. #' limits. #' @param censoring A numeric vector of the left and right censoring values. #' @param color A string of the column in data for the color aesthetic. diff --git a/man/params.Rd b/man/params.Rd index b92d8870..8bb24a47 100644 --- a/man/params.Rd +++ b/man/params.Rd @@ -48,6 +48,16 @@ calculates the confidence limits (and SE) from this single set. The value \code{ci_method = "MACL"} (was \code{ci_method = "weighted_arithmetic"} but has been soft-deprecated) which is only included for historical reasons takes the weighted arithmetic mean of the confidence +limits and \code{ci_method = MGCL} which was included for a research paper +takes the weighted geometric mean of the confidence limits. +The values \code{ci_method = "MAW1"} and \code{ci_method = "MAW2"} +use the two alternative equations of Burnham and Anderson to +model average the weighted standard errors and then calculate the confidence +limits using the Wald approach. +Finally \code{ci_method = "arithmetic"} and \code{ci_method = "geometric"} +take the weighted arithmetic or geometric mean of the values for +each bootstrap iteration across all the distributions and then +calculate the confidence limits (and SE) from the single set of samples. limits.} \item{censoring}{A numeric vector of the left and right censoring values.} diff --git a/man/predict.fitdists.Rd b/man/predict.fitdists.Rd index 30978999..c24d7db5 100644 --- a/man/predict.fitdists.Rd +++ b/man/predict.fitdists.Rd @@ -61,6 +61,16 @@ calculates the confidence limits (and SE) from this single set. The value \code{ci_method = "MACL"} (was \code{ci_method = "weighted_arithmetic"} but has been soft-deprecated) which is only included for historical reasons takes the weighted arithmetic mean of the confidence +limits and \code{ci_method = MGCL} which was included for a research paper +takes the weighted geometric mean of the confidence limits. +The values \code{ci_method = "MAW1"} and \code{ci_method = "MAW2"} +use the two alternative equations of Burnham and Anderson to +model average the weighted standard errors and then calculate the confidence +limits using the Wald approach. +Finally \code{ci_method = "arithmetic"} and \code{ci_method = "geometric"} +take the weighted arithmetic or geometric mean of the values for +each bootstrap iteration across all the distributions and then +calculate the confidence limits (and SE) from the single set of samples. limits.} \item{parametric}{A flag specifying whether to perform parametric bootstrapping as opposed to non-parametrically resampling the original data with replacement.} diff --git a/man/ssd_hc.Rd b/man/ssd_hc.Rd index 02317127..d2dafb48 100644 --- a/man/ssd_hc.Rd +++ b/man/ssd_hc.Rd @@ -91,6 +91,16 @@ calculates the confidence limits (and SE) from this single set. The value \code{ci_method = "MACL"} (was \code{ci_method = "weighted_arithmetic"} but has been soft-deprecated) which is only included for historical reasons takes the weighted arithmetic mean of the confidence +limits and \code{ci_method = MGCL} which was included for a research paper +takes the weighted geometric mean of the confidence limits. +The values \code{ci_method = "MAW1"} and \code{ci_method = "MAW2"} +use the two alternative equations of Burnham and Anderson to +model average the weighted standard errors and then calculate the confidence +limits using the Wald approach. +Finally \code{ci_method = "arithmetic"} and \code{ci_method = "geometric"} +take the weighted arithmetic or geometric mean of the values for +each bootstrap iteration across all the distributions and then +calculate the confidence limits (and SE) from the single set of samples. limits.} \item{parametric}{A flag specifying whether to perform parametric bootstrapping as opposed to non-parametrically resampling the original data with replacement.} diff --git a/man/ssd_hp.Rd b/man/ssd_hp.Rd index a87388ac..1d5e6181 100644 --- a/man/ssd_hp.Rd +++ b/man/ssd_hp.Rd @@ -86,6 +86,16 @@ calculates the confidence limits (and SE) from this single set. The value \code{ci_method = "MACL"} (was \code{ci_method = "weighted_arithmetic"} but has been soft-deprecated) which is only included for historical reasons takes the weighted arithmetic mean of the confidence +limits and \code{ci_method = MGCL} which was included for a research paper +takes the weighted geometric mean of the confidence limits. +The values \code{ci_method = "MAW1"} and \code{ci_method = "MAW2"} +use the two alternative equations of Burnham and Anderson to +model average the weighted standard errors and then calculate the confidence +limits using the Wald approach. +Finally \code{ci_method = "arithmetic"} and \code{ci_method = "geometric"} +take the weighted arithmetic or geometric mean of the values for +each bootstrap iteration across all the distributions and then +calculate the confidence limits (and SE) from the single set of samples. limits.} \item{parametric}{A flag specifying whether to perform parametric bootstrapping as opposed to non-parametrically resampling the original data with replacement.}