Update ObservedPredicted-Plot.Rd

Big-Life-Lab / bllflow

Big Life Lab Flow (BLLFlow) - a workflow for open, reproducible research. Includes support for PMML, DDI.

https://bllflow.projectbiglife.ca

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Update ObservedPredicted-Plot.Rd #8

Closed mehcampbell closed 5 years ago

DougManuel commented 5 years ago

Looks good.

@mehcampbell can you update the data RiskDecile.csv so that the variable names more closely match our table 1 format?

DougManuel commented 5 years ago

I've made a few commits to fix:

error when I was loading data. Note that I've moved the data to the package bllFlow/inst/extdata. This is where CSV files go in R packages.
a bug in quotes in the example.
added exports in NAMESPACE
add plotly to DESCRIPTION
add NA to the function attribute call.
suggested to add 'Plot' to OvP. Let's use 'plot' or 'table' etc for our visualization names.

DougManuel commented 5 years ago

@CBjerke and @yulric I've added you as assignees. I think OK for you to review at any point.

Note that there are a bunch of check() errors and warning. And also conflicts. Many checks will resolve when pushed to master. And conflicts should be straightforward to resolve at merge time.

DougManuel commented 5 years ago

@mehcampbell I can't access those databases on the MPoRT repo.

https://github.com/Big-Life-Lab/bllFlow/blob/data-visualization/R/calibration-plot.R#L20

Could you put this data into the /int/extdata folder and access it through there using the example I put in my last commit?

DougManuel commented 5 years ago

@mehcampbell I can't access the file that you uploaded. Is it text version of a CSV file? But even when I change the extension the file doesn't load as a CSV.

inst/extdata/MPORT-TABLE1.csv.txt

DougManuel commented 5 years ago

@mehcampbell Table 1 is getting closer! It may be easiest to talk -- maybe at tomorrow's meeting. I started to make comments but then realized there were lots of 'em. The first step is for us to be clearer what the template is for Table 1. I realize from your incorporation that I wasn't clear.

Can you start a 'Table 1 dictionary? This could be a simple CSV file with two rows. Actually, the dictionary has been startedsummaryVariables` https://docs.google.com/spreadsheets/d/1oDcl0Ed-KElO_a_DBWcontVnqyTCZlT63hSPd-gId88/edit#gid=276021298

But I think that we probably need a "longLabel" or "description".

DougManuel commented 5 years ago

@mehcampbell Could you lint and clean spaces, etc. according to Tidyverse style guide?

https://style.tidyverse.org/syntax.html#spacing

I would recommend using the styler package. http://styler.r-lib.org

DougManuel commented 5 years ago

Normally we would have error bars as two columns. see: bllFlow variables.csv: predictedriskyearCI

Feel free to update now, or we could refactor later.

DougManuel commented 5 years ago

@mehcampbell I'm getting errors on devtools::check() (and I can't examine the vignettes before rebuilding the package).

    undefined exports: CalibrationPlot, OvPPlot
   Error: loading failed

This is likely occurring because you renamed those exports to calibration_plot and op_plot.