From a72894455518bf9420bcb5ec067266433e44cc01 Mon Sep 17 00:00:00 2001 From: Felix T Petersma Date: Sat, 23 Nov 2024 13:17:45 +0100 Subject: [PATCH 1/3] Updated documentation of flnl.grad.R - title was added - a type in the description was resolved --- R/flnl.grad.R | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/R/flnl.grad.R b/R/flnl.grad.R index e162762e..d0b08557 100644 --- a/R/flnl.grad.R +++ b/R/flnl.grad.R @@ -1,9 +1,11 @@ +#' Gradient of the negative log likelihood function +#' #' This function derives the gradients of the negative log likelihood function, #' with respect to all parameters. It is based on the theory presented in #' Introduction to Distance Sampling (2001) and Distance Sampling: Methods and #' Applications (2015). It is not meant to be called by users of the \code{mrds} #' and \code{Distance} packages directly but rather by the gradient-based -#' solver. This solver is use when our distance sampling model is for +#' solver. This solver is used when our distance sampling model is for #' single-observer data coming from either line or point transect and only when #' the detection function contains an adjustment series but no covariates. It is #' implement for the following key + adjustment series combinations for the From f336a5a6b39a58e91a5d62fc782dba81dce692e8 Mon Sep 17 00:00:00 2001 From: Laura Marshall Date: Mon, 20 Jan 2025 12:40:49 +0000 Subject: [PATCH 2/3] bump package version and add NEWS --- DESCRIPTION | 2 +- NEWS.md | 6 ++++++ 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index d3b39d6f..9709ad72 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -18,7 +18,7 @@ Description: Animal abundance estimation via conventional, multiple covariate fitting is performed via maximum likelihood. Also included are diagnostics and plotting for fitted detection functions. Abundance estimation is via a Horvitz-Thompson-like estimator. -Version: 3.0.0.9000 +Version: 3.0.0.9001 URL: https://github.com/DistanceDevelopment/mrds/ BugReports: https://github.com/DistanceDevelopment/mrds/issues Depends: diff --git a/NEWS.md b/NEWS.md index c392ef72..231f16b3 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,9 @@ +# mrds 3.0.1 + +Bug Fixes + +* Fixed formatting issue in flnl.grad help + # mrds 3.0.0 New features From 744d5c4c1c6cc9b1070e26467167af86e060b294 Mon Sep 17 00:00:00 2001 From: Laura Marshall Date: Mon, 20 Jan 2025 12:50:01 +0000 Subject: [PATCH 3/3] Fixed the title ... I introduced an error --- R/flnl.grad.R | 2 +- man/flnl.grad.Rd | 16 ++-------------- 2 files changed, 3 insertions(+), 15 deletions(-) diff --git a/R/flnl.grad.R b/R/flnl.grad.R index 0c220aee..d0b08557 100644 --- a/R/flnl.grad.R +++ b/R/flnl.grad.R @@ -1,4 +1,4 @@ -#' @title Gradient of the negative log likelihood function +#' Gradient of the negative log likelihood function #' #' This function derives the gradients of the negative log likelihood function, #' with respect to all parameters. It is based on the theory presented in diff --git a/man/flnl.grad.Rd b/man/flnl.grad.Rd index e9566204..00bb4987 100644 --- a/man/flnl.grad.Rd +++ b/man/flnl.grad.Rd @@ -2,19 +2,7 @@ % Please edit documentation in R/flnl.grad.R \name{flnl.grad} \alias{flnl.grad} -\title{This function derives the gradients of the negative log likelihood function, -with respect to all parameters. It is based on the theory presented in -Introduction to Distance Sampling (2001) and Distance Sampling: Methods and -Applications (2015). It is not meant to be called by users of the \code{mrds} -and \code{Distance} packages directly but rather by the gradient-based -solver. This solver is use when our distance sampling model is for -single-observer data coming from either line or point transect and only when -the detection function contains an adjustment series but no covariates. It is -implement for the following key + adjustment series combinations for the -detections function: the key function can be half-normal, hazard-rate or -uniform, and the adjustment series can be cosine, simple polynomial or -Hermite polynomial. Data can be either binned or exact, but a combination -of the two has not been implemented yet.} +\title{Gradient of the negative log likelihood function} \usage{ flnl.grad(pars, ddfobj, misc.options, fitting = "all") } @@ -41,7 +29,7 @@ with respect to all parameters. It is based on the theory presented in Introduction to Distance Sampling (2001) and Distance Sampling: Methods and Applications (2015). It is not meant to be called by users of the \code{mrds} and \code{Distance} packages directly but rather by the gradient-based -solver. This solver is use when our distance sampling model is for +solver. This solver is used when our distance sampling model is for single-observer data coming from either line or point transect and only when the detection function contains an adjustment series but no covariates. It is implement for the following key + adjustment series combinations for the