Last updated: 2021-05-27
Checks: 7 0
Knit directory:
fa_sim_cal/
This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.
Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.
Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.
The command set.seed(20201104) was run prior to running the code in the R Markdown file.
Setting a seed ensures that any results that rely on randomness, e.g.
subsampling or permutations, are reproducible.
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Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
The results in this page were generated with repository version f27e705. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.
Note that you need to be careful to ensure that all relevant files for the
analysis have been committed to Git prior to generating the results (you can
use wflow_publish or wflow_git_commit). workflowr only
checks the R Markdown file, but you know if there are other scripts or data
files that it depends on. Below is the status of the Git repository when the
results were generated:
Ignored files:
Ignored: .Rhistory
Ignored: .Rproj.user/
Ignored: .tresorit/
Ignored: _targets/
Ignored: data/VR_20051125.txt.xz
Ignored: data/VR_Snapshot_20081104.txt.xz
Ignored: renv/library/
Ignored: renv/local/
Ignored: renv/staging/
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
These are the previous versions of the repository in which changes were made
to the R Markdown (analysis/m_00_status.Rmd) and HTML (docs/m_00_status.html)
files. If you’ve configured a remote Git repository (see
?wflow_git_remote), click on the hyperlinks in the table below to
view the files as they were in that past version.
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | f27e705 | Ross Gayler | 2021-05-27 | wflow_publish("analysis/m_00*.Rmd") |
| Rmd | d28b1b1 | Ross Gayler | 2021-05-27 | Remove editor wrap option from main README.md |
| Rmd | 43ce139 | Ross Gayler | 2021-05-27 | Remove editor wrap option from main README.md |
| Rmd | b0c71df | Ross Gayler | 2021-05-27 | Use targets package to manage workflow |
| html | b0c71df | Ross Gayler | 2021-05-27 | Use targets package to manage workflow |
| Rmd | 0e893b2 | Ross Gayler | 2021-05-27 | Use targets package to manage workflow |
| html | 0e893b2 | Ross Gayler | 2021-05-27 | Use targets package to manage workflow |
This notebook displays the status of the project workflow, that is, whether everything is computationally up to date. It displays the status as at the time the notebook is executed, so if the status has changed since this notebook was last executed that fact won’t be reflected in this rendered notebook.
This notebook is currently intended to be run manually when you feel the need, for example, when returning to the project.
{renv} status{renv} tracks the used R packages and their versions.
# Get {targets} to tell {renv} which packages it uses
targets::tar_renv() here() starts at /home/ross/RG/projects/academic/entity_resolution/fa_sim_cal_TOP/fa_sim_calrenv::status()* The project is already synchronized with the lockfile.{targets} status{targets} is used to track the computational dependencies between the
project components and orchestrate recalculation when any components are
changed.
c_* components are in the core pipelinep_* components are in the publications pipelinesm_* components are in the meta pipelinesFunctions may be used across multiple pipeline categories, so function names are not prefixed.
Meta pipelines generally originate from a target on the core pipeline. Each meta pipeline generally explores some aspect of that source target which informs the design of the next stage of processing on the core pipeline.
Each of the meta pipelines has leaves that are reports rendered from
Rmd files that are managed jointly by {targets} and {workflowr}.
{targets} is aware of the upstream dependencies (data and functions)
and the Rmd file itself. If any of these is invalidated tar_make()
will rebuild the report using wflow_build().
{targets} is not aware of the rendered meta report files. The
rendered report files are managed exclusively by {workflowr}. This
means that you can use {workflowr} to build and publish the report
without making {targets} think that the report is out of date because
{workflowr} has re-rendered it.
# outline
targets::tar_glimpse()here() starts at /home/ross/RG/projects/academic/entity_resolution/fa_sim_cal_TOP/fa_sim_cal# core detail
targets::tar_visnetwork(allow = starts_with("c_"))here() starts at /home/ross/RG/projects/academic/entity_resolution/fa_sim_cal_TOP/fa_sim_cal# meta detail
targets::tar_visnetwork(allow = starts_with("m_"))here() starts at /home/ross/RG/projects/academic/entity_resolution/fa_sim_cal_TOP/fa_sim_cal# excruciating detail
targets::tar_visnetwork()here() starts at /home/ross/RG/projects/academic/entity_resolution/fa_sim_cal_TOP/fa_sim_cal{workflowr} status{workflowr} is used to render the meta documents
(analysis/m_*.Rmd) and build the project website.
{workflowr} is only concerned with the modification and git commit
dates of the Rmd and HTML files, whereas {targets} is concerned
with the computational dependencies. Thus, you should rely on the
{targets} status to ensure the meta reports are computationally up to
date, then rely on the {workflowr} status to manage the building and
publication of the entire website.
workflowr::wflow_status()Status of 18 Rmd files
Totals:
18 Published (13 Modified)
The following Rmd files require attention:
Mod analysis/index.Rmd
Mod analysis/m_00_status.Rmd
Mod analysis/m_01_1_read_raw_entity_data.Rmd
Mod analysis/m_01_2_exclusions.Rmd
Mod analysis/m_01_3_drop_novar.Rmd
Mod analysis/m_01_4_parse_dates.Rmd
Mod analysis/m_01_5_check_admin.Rmd
Mod analysis/m_01_6_check_resid.Rmd
Mod analysis/m_01_7_check_demog.Rmd
Mod analysis/m_01_8_check_name.Rmd
Mod analysis/m_01_9_clean_vars.Rmd
Mod analysis/notes.Rmd
Mod analysis/workflow.Rmd
Key: Mod = Modified
The current Git status is: working directory clean
To publish your changes as part of your website, use `wflow_publish()`.
To commit your changes without publishing them yet, use
`wflow_git_commit()`.
sessionInfo()R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.10
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
[5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8
[7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] targets_0.4.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 pillar_1.6.1 compiler_4.1.0 bslib_0.2.5
[5] later_1.2.0 jquerylib_0.1.4 git2r_0.28.0 workflowr_1.6.2
[9] tools_4.1.0 digest_0.6.27 jsonlite_1.7.2 evaluate_0.14
[13] lifecycle_1.0.0 tibble_3.1.2 pkgconfig_2.0.3 rlang_0.4.11
[17] igraph_1.2.6 rstudioapi_0.13 cli_2.5.0 yaml_2.2.1
[21] xfun_0.23 withr_2.4.2 stringr_1.4.0 knitr_1.33
[25] htmlwidgets_1.5.3 fs_1.5.0 vctrs_0.3.8 sass_0.4.0
[29] tidyselect_1.1.1 rprojroot_2.0.2 data.table_1.14.0 glue_1.4.2
[33] R6_2.5.0 processx_3.5.2 fansi_0.4.2 rmarkdown_2.8
[37] bookdown_0.22 purrr_0.3.4 callr_3.7.0 magrittr_2.0.1
[41] whisker_0.4 codetools_0.2-18 ps_1.6.0 promises_1.2.0.1
[45] ellipsis_0.3.2 htmltools_0.5.1.1 renv_0.13.2 httpuv_1.6.1
[49] utf8_1.2.1 stringi_1.6.2 visNetwork_2.0.9 crayon_1.4.1