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commit edf078a
Author: Francisco Bischoff <[email protected]>
Date:   Sun Aug 21 19:32:25 2022 +0100

    Feature/newfeature2sm (#151)

    * 2submodelsinit

commit de21180
Author: Francisco Bischoff <[email protected]>
Date:   Sun Aug 21 02:35:43 2022 +0100

    Squashed commit of the following:

    commit 20e93ac
    Author: Francisco Bischoff <[email protected]>
    Date:   Sun Aug 21 02:11:19 2022 +0100

        Build site.

    commit 1b337ae
    Author: Francisco Bischoff <[email protected]>
    Date:   Sun Aug 21 01:55:54 2022 +0100

        optimize2

    commit c1e4b44
    Author: Francisco Bischoff <[email protected]>
    Date:   Thu Aug 11 16:53:44 2022 +0100

        update shiny

    commit 1781cad
    Author: Francisco Bischoff <[email protected]>
    Date:   Thu Aug 11 09:32:26 2022 +0100

        regime2

    commit 5541b04
    Author: Francisco Bischoff <[email protected]>
    Date:   Wed Aug 10 04:05:02 2022 +0100

        premerge

    commit 7ed8844
    Author: Francisco Bischoff <[email protected]>
    Date:   Fri Jul 29 05:07:16 2022 +0100

        changes

    commit d603ece
    Author: Francisco Bischoff <[email protected]>
    Date:   Sat Jul 23 09:45:26 2022 +0100

        lint

    commit 3820214
    Author: Francisco Bischoff <[email protected]>
    Date:   Fri Jul 22 01:32:19 2022 +0100

        shiny2

    commit 3a5549d
    Author: Francisco Bischoff <[email protected]>
    Date:   Thu Jul 21 23:56:07 2022 +0100

        shiny

    commit 7ca10d7
    Author: Francisco Bischoff <[email protected]>
    Date:   Thu Jul 21 03:56:29 2022 +0100

        lint

    commit 02f5fa2
    Author: Francisco Bischoff <[email protected]>
    Date:   Thu Jul 21 01:58:26 2022 +0100

        middle

    commit f6643f0
    Author: Francisco Bischoff <[email protected]>
    Date:   Mon Jun 20 04:43:30 2022 +0100

        manual lntr

    commit d299158
    Author: Francisco Bischoff <[email protected]>
    Date:   Thu Jun 16 03:37:23 2022 +0100

        tune with multiples

    commit 3956ffe
    Author: Francisco Bischoff <[email protected]>
    Date:   Sat May 28 14:26:45 2022 +0100

        lint

    commit 6c6dcda
    Author: Francisco Bischoff <[email protected]>
    Date:   Fri May 27 08:58:41 2022 +0100

        package

    commit 34f43c6
    Author: Francisco Bischoff <[email protected]>
    Date:   Tue May 24 13:59:13 2022 +0100

        asdf

    commit d81643e
    Author: Francisco Bischoff <[email protected]>
    Date:   Tue May 24 11:02:23 2022 +0100

        starting here

    commit c2e45fb
    Author: Francisco Bischoff <[email protected]>
    Date:   Sun May 22 22:12:24 2022 +0100

        2submodelsinit
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franzbischoff committed Aug 21, 2022
1 parent f502dd4 commit dbbd1d6
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2 changes: 0 additions & 2 deletions .Rbuildignore
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Expand Up @@ -58,8 +58,6 @@
^false.alarm.*\.tgz$
^false.alarm\.Rcheck$
^flowcharts$
^inst/extdata$
^inst/testfiles$
^output$
^packrat$
^papers$
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2 changes: 1 addition & 1 deletion .devcontainer/Dockerfile
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Expand Up @@ -84,7 +84,7 @@ RUN echo "C.UTF-8 en_US.UTF-8 UTF-8" >> /etc/locale.gen \
&& locale-gen en_US.utf8 \
&& /usr/sbin/update-locale LANG=en_US.UTF-8

ENV R_BASE_VERSION 4.1.2
ENV R_BASE_VERSION 4.2.1
ENV RENV_PATHS_ROOT "${HOME_WORK}/.cache/R/renv"
ENV RENV_PATHS_LIBRARY_ROOT "${HOME_WORK}/.cache/R/renv/library"
ENV TZ UTC
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4 changes: 2 additions & 2 deletions .gitignore
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Expand Up @@ -92,6 +92,7 @@ README.html
Rplots.pdf
dev
dev/
dev
packrat/lib*/
packrat/src/
src-*/
Expand All @@ -113,5 +114,4 @@ mpxtest.RData
.devcontainer/mathjax.tgz
docs/thesis/*.log
docs/thesis/__*.tex
analysis/shiny/rsconnect/shinyapps.io/franzbischoff/FLOSS.dcf
analysis/shiny_land/rsconnect/shinyapps.io/franzbischoff/FLOSS_land.dcf
**/rsconnect/**
6 changes: 3 additions & 3 deletions .vscode/settings.json
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Expand Up @@ -115,8 +115,7 @@
"**/log/**": true,
"**/logs/**": true,
"**/man/**": true,
"**/pdfs/**": true,
"**/renv/**": true
"**/pdfs/**": true
},
"files.insertFinalNewline": true,
"files.trimTrailingWhitespace": true,
Expand Down Expand Up @@ -288,5 +287,6 @@
"grammarly.config.suggestions.InformalPronounsAcademic": false,
"grammarly.config.suggestions.OxfordComma": false,
"grammarly.config.suggestions.PassiveVoice": false,
"grammarly.startTextCheckInPausedState": true
"grammarly.startTextCheckInPausedState": true,
"grammarly.config.suggestions.PunctuationWithQuotation": false
}
42 changes: 21 additions & 21 deletions .vscode/tasks.json
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Expand Up @@ -74,7 +74,7 @@
{
"type": "process",
"label": "R: misc: knit and view",
"command": "C:/Program Files/R/R-4.1.2/bin/x64/Rscript.exe",
"command": "C:/Program Files/R/R-4.2.0/bin/x64/Rscript.exe",
"linux": {
"command": "/bin/Rscript"
},
Expand All @@ -100,7 +100,7 @@
{
"type": "process",
"label": "R: routine: Style project",
"command": "C:/Program Files/R/R-4.1.2/bin/x64/Rscript.exe",
"command": "C:/Program Files/R/R-4.2.0/bin/x64/Rscript.exe",
"linux": {
"command": "/bin/Rscript"
},
Expand All @@ -122,7 +122,7 @@
{
"type": "process",
"label": "R: targets: gittargets",
"command": "C:/Program Files/R/R-4.1.2/bin/x64/Rscript.exe",
"command": "C:/Program Files/R/R-4.2.0/bin/x64/Rscript.exe",
"linux": {
"command": "/bin/Rscript"
},
Expand All @@ -143,7 +143,7 @@
{
"type": "process",
"label": "R: routine: Update codemeta",
"command": "C:/Program Files/R/R-4.1.2/bin/x64/Rscript.exe",
"command": "C:/Program Files/R/R-4.2.0/bin/x64/Rscript.exe",
"linux": {
"command": "/bin/Rscript"
},
Expand All @@ -166,7 +166,7 @@
{
"type": "process",
"label": "R: routine: Update docs and self install",
"command": "C:/Program Files/R/R-4.1.2/bin/x64/Rscript.exe",
"command": "C:/Program Files/R/R-4.2.0/bin/x64/Rscript.exe",
"linux": {
"command": "/bin/Rscript"
},
Expand Down Expand Up @@ -210,13 +210,13 @@
{
"type": "process",
"label": "R: routine: Lint project",
"command": "C:/Program Files/R/R-4.1.2/bin/x64/Rscript.exe",
"command": "C:/Program Files/R/R-4.2.0/bin/x64/Rscript.exe",
"linux": {
"command": "/bin/Rscript"
},
"args": [
"-e",
"library(lintr); for (i in c('analysis', 'R', 'scripts', 'review', 'thesis', 'output')) {print(lint_dir(path = i, linters = with_defaults(open_curly_linter = NULL, T_and_F_symbol_linter, assignment_linter, closed_curly_linter = NULL, commas_linter, commented_code_linter = NULL, cyclocomp_linter(50), object_name_linter(styles = 'snake_case'), object_length_linter(30), equals_na_linter, function_left_parentheses_linter, infix_spaces_linter, line_length_linter(500), no_tab_linter, object_usage_linter = NULL, paren_brace_linter, absolute_path_linter(lax = TRUE), nonportable_path_linter = NULL, pipe_continuation_linter, semicolon_terminator_linter(semicolon = 'trailing'), seq_linter, single_quotes_linter, spaces_inside_linter, spaces_left_parentheses_linter, trailing_blank_lines_linter, trailing_whitespace_linter, undesirable_function_linter, undesirable_operator_linter, unneeded_concatenation_linter), exclusions = list('R/RcppExports.R')))}"
"library(lintr); for (i in c('analysis', 'R', 'scripts', 'review', 'thesis', 'output')) {print(lint_dir(path = i, linters = linters_with_defaults(brace_linter, T_and_F_symbol_linter, assignment_linter, commas_linter, commented_code_linter = NULL, cyclocomp_linter(50), object_name_linter(styles = 'snake_case'), object_length_linter(30), equals_na_linter, function_left_parentheses_linter, infix_spaces_linter, line_length_linter(500), no_tab_linter, object_usage_linter = NULL, absolute_path_linter(lax = TRUE), nonportable_path_linter = NULL, pipe_continuation_linter, semicolon_linter(allow_compound = TRUE), seq_linter, single_quotes_linter, spaces_inside_linter, spaces_left_parentheses_linter, trailing_blank_lines_linter, trailing_whitespace_linter, undesirable_function_linter, undesirable_operator_linter, unneeded_concatenation_linter), exclusions = list('R/RcppExports.R')))}"
],
"options": {
"cwd": "${workspaceFolder}"
Expand All @@ -235,7 +235,7 @@
{
"type": "process",
"label": "R: routine: Test units",
"command": "C:/Program Files/R/R-4.1.2/bin/x64/Rscript.exe",
"command": "C:/Program Files/R/R-4.2.0/bin/x64/Rscript.exe",
"linux": {
"command": "/bin/Rscript"
},
Expand All @@ -260,7 +260,7 @@
{
"type": "process",
"label": "R: routine: Update renv and isolate",
"command": "C:/Program Files/R/R-4.1.2/bin/x64/Rscript.exe",
"command": "C:/Program Files/R/R-4.2.0/bin/x64/Rscript.exe",
"linux": {
"command": "/bin/Rscript"
},
Expand All @@ -286,7 +286,7 @@
"type": "process",
"label": "R: misc: test coverage",
"dependsOn": "R: routine: test units",
"command": "C:/Program Files/R/R-4.1.2/bin/x64/Rscript.exe",
"command": "C:/Program Files/R/R-4.2.0/bin/x64/Rscript.exe",
"linux": {
"command": "/bin/Rscript"
},
Expand All @@ -308,7 +308,7 @@
{
"type": "process",
"label": "R: targets: Start watch page",
"command": "C:/Program Files/R/R-4.1.2/bin/x64/Rscript.exe",
"command": "C:/Program Files/R/R-4.2.0/bin/x64/Rscript.exe",
"linux": {
"command": "/bin/Rscript"
},
Expand All @@ -330,7 +330,7 @@
{
"type": "process",
"label": "R: targets: zDESTROY targets",
"command": "C:/Program Files/R/R-4.1.2/bin/x64/Rscript.exe",
"command": "C:/Program Files/R/R-4.2.0/bin/x64/Rscript.exe",
"linux": {
"command": "/bin/Rscript"
},
Expand All @@ -355,7 +355,7 @@
{
"type": "process",
"label": "R: targets: zPRUNE targets",
"command": "C:/Program Files/R/R-4.1.2/bin/x64/Rscript.exe",
"command": "C:/Program Files/R/R-4.2.0/bin/x64/Rscript.exe",
"linux": {
"command": "/bin/Rscript"
},
Expand All @@ -380,7 +380,7 @@
{
"type": "process",
"label": "R: targets: zPROFILE targets",
"command": "C:/Program Files/R/R-4.1.2/bin/x64/Rscript.exe",
"command": "C:/Program Files/R/R-4.2.0/bin/x64/Rscript.exe",
"linux": {
"command": "/bin/Rscript"
},
Expand Down Expand Up @@ -453,7 +453,7 @@
// config file is stored on ./index/_bookdown.yml
"type": "process",
"label": "R: workflowr: Render thesisdown",
"command": "C:/Program Files/R/R-4.1.2/bin/x64/Rscript.exe",
"command": "C:/Program Files/R/R-4.2.0/bin/x64/Rscript.exe",
"linux": {
"command": "/bin/Rscript"
},
Expand All @@ -478,7 +478,7 @@
{
"type": "process",
"label": "R: workflowr: Live-preview thesisdown",
"command": "C:/Program Files/R/R-4.1.2/bin/x64/Rscript.exe",
"command": "C:/Program Files/R/R-4.2.0/bin/x64/Rscript.exe",
"linux": {
"command": "/bin/Rscript"
},
Expand All @@ -503,7 +503,7 @@
{
"type": "process",
"label": "R: workflowr: Live-preview workflowr",
"command": "C:/Program Files/R/R-4.1.2/bin/x64/Rscript.exe",
"command": "C:/Program Files/R/R-4.2.0/bin/x64/Rscript.exe",
"linux": {
"command": "/bin/Rscript"
},
Expand All @@ -529,7 +529,7 @@
// config file is stored on ./analysis/_site.yml
"type": "process",
"label": "R: workflowr: Pre-build workflowr", // Used while editing. Only project .Rprofile is used.
"command": "C:/Program Files/R/R-4.1.2/bin/x64/Rscript.exe",
"command": "C:/Program Files/R/R-4.2.0/bin/x64/Rscript.exe",
"linux": {
"command": "/bin/Rscript"
},
Expand All @@ -550,7 +550,7 @@
{
"type": "process",
"label": "R: targets: Run main pipeline",
"command": "C:/Program Files/R/R-4.1.2/bin/x64/Rscript.exe",
"command": "C:/Program Files/R/R-4.2.0/bin/x64/Rscript.exe",
"linux": {
"command": "/bin/Rscript"
},
Expand All @@ -575,7 +575,7 @@
{
"type": "process",
"label": "R: targets: Run classifier pipeline",
"command": "C:/Program Files/R/R-4.1.2/bin/x64/Rscript.exe",
"command": "C:/Program Files/R/R-4.2.0/bin/x64/Rscript.exe",
"linux": {
"command": "/bin/Rscript"
},
Expand All @@ -600,7 +600,7 @@
{
"type": "process",
"label": "R: targets: Run regime pipeline",
"command": "C:/Program Files/R/R-4.1.2/bin/x64/Rscript.exe",
"command": "C:/Program Files/R/R-4.2.0/bin/x64/Rscript.exe",
"linux": {
"command": "/bin/Rscript"
},
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13 changes: 9 additions & 4 deletions DESCRIPTION
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Expand Up @@ -16,7 +16,8 @@ License: CC BY-NC-SA 4.0
URL: https://github.com/franzbischoff/false.alarm
BugReports: https://github.com/franzbischoff/false.alarm/issues
Depends:
R (>= 4.2)
R (>= 4.2),
parsnip (>= 1.0.0)
Imports:
bookdown (>= 0.22),
checkmate (>= 2.0.0),
Expand All @@ -26,6 +27,8 @@ Imports:
gridExtra (>= 2.3),
here (>= 0.1.0),
kableExtra (>= 1.3.4),
magrittr (>= 2.0.3),
parsnip (>= 1.0.0),
plotly (>= 4.9.3),
purrr (>= 0.3.4),
Rcpp (>= 1.0.6),
Expand All @@ -35,10 +38,11 @@ Imports:
targets (>= 0.2.0),
thesisdown (>= 0.1.9),
tibble (>= 3.1.6),
tidymodels (>= 0.1.4),
tune (>= 1.0.0.9000),
visNetwork (>= 2.1.0),
workflowr (>= 1.6.2),
yardstick (>= 0.0.9)
workflows (>= 1.0.0),
yardstick (>= 1.0.0)
Suggests:
clustermq (>= 0.8.95),
codemetar (>= 0.3.3),
Expand Down Expand Up @@ -75,7 +79,8 @@ Remotes:
r-lib/testthat,
rstudio/bookdown,
rstudio/rmarkdown,
wlandau/gittargets
wlandau/gittargets,
franzbischoff/tune@539e1eea1426e9ace11b4e71ac4dafadddda7f0a
Config/testthat/edition: 3
Config/testthat/parallel: false
Encoding: UTF-8
Expand Down
33 changes: 33 additions & 0 deletions NAMESPACE
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@@ -1,12 +1,27 @@
# Generated by roxygen2: do not edit by hand

S3method(floss_error,data.frame)
S3method(multi_predict,"_floss_regime_model")
S3method(predict,floss_regime_model)
S3method(print,floss_regime_model)
S3method(translate,floss_regime_model)
S3method(update,floss_regime_model)
export("%>%")
export(.check_floss_regime_threshold_fit)
export(binary_split)
export(complexity)
export(contrast)
export(corr_ed)
export(ed_corr)
export(floss_error)
export(floss_error_macro)
export(floss_error_micro)
export(floss_regime_model)
export(floss_train_model)
export(floss_train_regimes)
export(mass)
export(mass_pre)
export(min_grid.floss_regime_model)
export(mode)
export(motif_quality)
export(mov_max)
Expand All @@ -16,18 +31,36 @@ export(mov_std)
export(mov_sum)
export(mov_var)
export(movmean_std)
export(mp_threshold_par)
export(mpx)
export(mpx_stream_right)
export(mpx_stream_s_right)
export(mpx_stream_start)
export(muinvn)
export(normalize)
export(regime_landmark_par)
export(regime_threshold_par)
export(scrimp)
export(stamp)
export(std)
export(stomp)
export(time_constraint_par)
export(trans_round)
export(window_size_par)
export(zero_crossing)
export(znorm)
importFrom(Rcpp,sourceCpp)
importFrom(RcppParallel,RcppParallelLibs)
importFrom(dials,new_quant_param)
importFrom(magrittr,"%>%")
importFrom(parsnip,multi_predict)
importFrom(parsnip,set_new_model)
importFrom(parsnip,translate)
importFrom(purrr,map_lgl)
importFrom(rlang,enquo)
importFrom(stats,predict)
importFrom(stats,update)
importFrom(tibble,as_tibble)
importFrom(tibble,is_tibble)
importFrom(withr,with_options)
useDynLib(false.alarm, .registration = TRUE)
6 changes: 6 additions & 0 deletions R/false.alarm-package.R
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Expand Up @@ -28,6 +28,10 @@
#'
#' @name false.alarm
#' @rdname false.alarm
#' @keywords internal
"_PACKAGE"

# nocov start

## usethis namespace: start
#' @useDynLib false.alarm, .registration = TRUE
Expand All @@ -39,3 +43,5 @@ NULL
## usethis namespace: end
#' @importFrom RcppParallel RcppParallelLibs
NULL

# nocov end
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