Last updated: 2019-08-19

Checks: 2 0

Knit directory: polymeRID/

This reproducible R Markdown analysis was created with workflowr (version 1.4.0.9001). 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! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated.

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:    .Rprofile
    Ignored:    .Rproj.user/
    Ignored:    analysis/library.bib
    Ignored:    fun/
    Ignored:    output/20190810_1538/
    Ignored:    output/20190810_1546/
    Ignored:    output/20190810_1609/
    Ignored:    output/20190813_1044/
    Ignored:    output/logs/
    Ignored:    output/natural/
    Ignored:    output/nnet/
    Ignored:    output/svm/
    Ignored:    output/testRunII/
    Ignored:    output/testRunIII/
    Ignored:    packrat/lib-R/
    Ignored:    packrat/lib-ext/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/00LOCK-curl/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/BH/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/FactoMineR/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/IDPmisc/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/KernSmooth/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/MASS/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/Matrix/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/MatrixModels/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/ModelMetrics/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/R6/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/RColorBrewer/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/RCurl/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/Rcpp/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/RcppArmadillo/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/RcppEigen/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/RcppGSL/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/RcppZiggurat/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/Rfast/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/Rgtsvm/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/Rmisc/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/SQUAREM/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/SparseM/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/abind/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/askpass/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/assertthat/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/backports/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/base64enc/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/baseline/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/bit/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/bit64/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/bitops/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/boot/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/callr/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/car/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/carData/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/caret/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/cellranger/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/class/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/cli/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/clipr/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/cluster/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/codetools/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/colorspace/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/config/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/cowplot/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/crayon/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/crosstalk/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/curl/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/data.table/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/dendextend/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/digest/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/doParallel/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/dplyr/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/e1071/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/ellipse/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/ellipsis/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/evaluate/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/factoextra/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/fansi/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/flashClust/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/forcats/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/foreach/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/foreign/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/fs/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/generics/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/getPass/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/ggplot2/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/ggpubr/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/ggrepel/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/ggsci/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/ggsignif/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/git2r/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/glue/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/gower/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/gridExtra/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/gtable/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/haven/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/hexbin/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/highr/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/hms/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/htmltools/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/htmlwidgets/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/httpuv/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/httr/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/ipred/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/iterators/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/jsonlite/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/keras/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/kerasR/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/knitr/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/labeling/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/later/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/lattice/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/lava/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/lazyeval/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/leaps/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/lme4/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/lubridate/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/magrittr/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/maptools/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/markdown/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/mgcv/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/mime/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/minqa/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/munsell/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/nlme/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/nloptr/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/nnet/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/numDeriv/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/openssl/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/openxlsx/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/packrat/tests/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/pbkrtest/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/pillar/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/pkgconfig/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/plogr/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/plotly/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/plyr/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/polynom/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/prettyunits/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/processx/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/prodlim/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/progress/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/promises/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/prospectr/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/ps/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/purrr/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/quantreg/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/randomForest/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/readr/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/readxl/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/recipes/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/rematch/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/reshape2/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/reticulate/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/rio/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/rlang/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/rmarkdown/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/rpart/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/rprojroot/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/rsconnect/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/rstudioapi/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/scales/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/scatterplot3d/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/shiny/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/sourcetools/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/sp/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/stringi/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/stringr/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/survival/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/sys/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/tensorflow/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/tfruns/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/tibble/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/tidyr/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/tidyselect/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/timeDate/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/tinytex/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/utf8/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/vctrs/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/viridis/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/viridisLite/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/whisker/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/withr/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/workflowr/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/xfun/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/xtable/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/yaml/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/zeallot/
    Ignored:    packrat/lib/x86_64-pc-linux-gnu/3.6.1/zip/
    Ignored:    packrat/src/
    Ignored:    polymeRID.Rproj
    Ignored:    smp/20190812_1723_NNET/files/
    Ignored:    smp/20190812_1723_NNET/plots/
    Ignored:    smp/20190812_1729_NNET/files/
    Ignored:    smp/20190812_1729_NNET/plots/
    Ignored:    smp/20190812_1731_NNET/files/
    Ignored:    smp/20190812_1731_NNET/plots/
    Ignored:    smp/20190812_1733_NNET/files/
    Ignored:    smp/20190812_1733_NNET/plots/
    Ignored:    smp/20190815_1847_FUSION/
    Ignored:    website/

Untracked files:
    Untracked:  smp/120619_W2_1000_1.txt
    Untracked:  smp/120619_W2_1000_2.txt
    Untracked:  smp/120619_W2_300_1.txt
    Untracked:  smp/120619_W2_300_2.txt
    Untracked:  smp/120619_W2_300_3.txt
    Untracked:  smp/120619_W2_300_4.txt
    Untracked:  smp/120619_W2_300_5.txt
    Untracked:  smp/120619_W2_500_1.txt
    Untracked:  smp/120619_W2_500_2.txt
    Untracked:  smp/120619_W2_500_3.txt
    Untracked:  smp/120619_W2_500_4.txt
    Untracked:  smp/120619_W2_500_5.txt
    Untracked:  smp/120619_W2_500_6.txt
    Untracked:  smp/120619_W2_500_7.txt

Unstaged changes:
    Deleted:    Rplots.pdf
    Deleted:    analysis/cnn_calibration.Rmd
    Modified:   classification.R
    Modified:   code/FUSION.R
    Modified:   code/cnn_cv_K70.R
    Modified:   code/functions.R
    Modified:   code/nnet.R
    Modified:   code/plot_functions.R
    Modified:   code/shiny_apps/app.R
    Deleted:    code/shiny_apps/rsconnect/documents/spectra.Rmd/shinyapps.io/goergen95/spectra.dcf
    Modified:   code/shiny_apps/rsconnect/shinyapps.io/goergen95/spectra.dcf
    Deleted:    code/shiny_apps/spectra_app.tar.gz

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 R Markdown and HTML files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view them.

File Version Author Date Message
html 2385fbc goergen95 2019-08-14 republish for layout change
html c52182b goergen95 2019-08-13 rebuid website
html 6e92d01 goergen95 2019-08-13 Build site.
html 5e196cc goergen95 2019-08-08 initiated packrat package tracking system
Rmd 6c813f4 goergen95 2019-07-29 implemented workflowr
Rmd d525cc2 goergen95 2019-07-29 Start workflowr project.

Describe your project.