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Merged
merged 42 commits into from
Nov 18, 2022
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a94f753
add more flexibility with delays
sbfnk Jul 21, 2022
404d04c
update man pages
sbfnk Jul 21, 2022
7bcf7a6
check if truncation mean is uncertain
sbfnk Jul 25, 2022
3553b49
start on static delays
sbfnk Sep 11, 2022
f075f1d
add generation time and truncation opts
sbfnk Sep 11, 2022
2c51993
update trunc_opts docs
sbfnk Sep 11, 2022
0479e32
add NEWS
sbfnk Sep 11, 2022
381ed5a
run documentation update
sbfnk Sep 11, 2022
c8f9c71
mention doc update in NEWS
sbfnk Sep 11, 2022
8e9c79d
optimise discrete pmfs
sbfnk Sep 10, 2022
cc31fc9
explicit zero for first element of gt
sbfnk Sep 11, 2022
564ac99
remove deprecated discretised gamma pmf
sbfnk Sep 11, 2022
e01a7a4
fix link
sbfnk Sep 11, 2022
84dd939
only revert after delta pmf
sbfnk Sep 11, 2022
33277f4
simplify discrete delta pmf
sbfnk Sep 11, 2022
ec536c5
implement fixed delays in stan model
sbfnk Sep 13, 2022
d2c00b7
clarify NEWS
sbfnk Sep 15, 2022
56c33ec
fix check for gt uncertainty
sbfnk Sep 16, 2022
8ae1cbf
create `gt_fixed` with the correct type
sbfnk Sep 19, 2022
63ba0ed
update simulation model for flexible delays
sbfnk Sep 19, 2022
93aa345
only calculate max fixed delay if we can
sbfnk Sep 19, 2022
f922fcf
use correct sd in gt
sbfnk Sep 30, 2022
c9b52d2
work out pmf parameters
sbfnk Sep 30, 2022
35a5838
don't reverse delay pmf
sbfnk Sep 30, 2022
f49443d
update docs
sbfnk Sep 30, 2022
8a0b944
use log parameters in lognormal
sbfnk Sep 30, 2022
32ba0b0
fix truncation parameters
sbfnk Sep 30, 2022
243cd99
fix no delay case
sbfnk Oct 5, 2022
0f79151
document missing options
sbfnk Oct 5, 2022
0361d02
adapt test to new function syntax
sbfnk Oct 5, 2022
ed003a8
change expected tests results (rounding differences)
sbfnk Oct 5, 2022
3f01a21
simplify treatment of delay distributions
sbfnk Oct 31, 2022
7c6bfa3
fixes following more thorough testing
sbfnk Nov 1, 2022
20593d0
more sensible default for max of distribution
sbfnk Nov 15, 2022
c3fc270
fix tests
sbfnk Nov 15, 2022
6b25de6
flexible generation time weights
sbfnk Nov 15, 2022
91a006c
size -> linewidth
sbfnk Nov 15, 2022
c353f3a
doc update
sbfnk Nov 15, 2022
6d031ed
bring size back for geom_point
sbfnk Nov 15, 2022
3d07292
update snaps
sbfnk Nov 15, 2022
aaf2d1e
update documentation
sbfnk Nov 15, 2022
0ede0b4
fix examples
sbfnk Nov 16, 2022
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update trunc_opts docs
  • Loading branch information
sbfnk committed Oct 31, 2022
commit 2c51993839c26f69accfa6724e49fc9f6a1cd910
9 changes: 7 additions & 2 deletions R/opts.R
Original file line number Diff line number Diff line change
Expand Up @@ -163,13 +163,18 @@ delay_opts <- function(..., fixed = FALSE) {
#' downstream functions. See `estimate_truncation()` for an approach to
#' estimate this distribution.
#' @param mean Numeric, defaults to 0. Mean on the log scale of the truncation
#' distribution
#' distribution.
#'
#' @param sd Numeric, defaults to 0. Sets the standard deviation for the log
#' normal truncation distribution
#' normal truncation distribution.
#'
#' @param mean_sd Numeric, defaults to 0. The prior uncertainty for the log
#' normal truncation distribution.
#'
#' @param sd_sd Numeric, defaults to 0. The prior uncertainty for the standard
#' deviation of the log normal truncation distribution.
#'
#' @param max Numeric, maximum value to allow. Defaults to 0.
#' @seealso convert_to_logmean convert_to_logsd bootstrapped_dist_fit
#' @return A list summarising the input truncation distribution.
#' @export
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