352 updates to vignette for loec changes #354
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sedavid01
requested changes
Apr 15, 2025
| @@ -1861,6 +1861,29 @@ htmlTable(output, | |||
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| In addition, there may be situations where traditional modeling under tcplfit2 is not totally appropriate. Data which have limited efficacy or limited number of concentrations tested may be candidates for "loec", or the lowest observed effective concentration, potency and hitcalling determinations. A "loec" is defined as the lowest experimental dose where all responses surpass the cutoff. | |||
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- Make sure to add the emphasis quotes around
tcplfit2 - Suggest adding "For example," at the beginning of the second sentence.
- Second sentence also suggest updating to include data that are not continuous endpoints: "limited efficacy, do not have continuous response values, or have a limited number of experimental concentrations ..." (Or something like this.)
- Suggest updating the final sentence in this paragraph to: 'A "loec" in
tcplis defined as the lowest ...", basically just specify that this is how tcpl is defining a LOEC but recognizing this is not necessarily a universal definition for loec.
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Updated text and added wrappers like
| @@ -1861,6 +1861,29 @@ htmlTable(output, | |||
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| ``` | |||
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| In addition, there may be situations where traditional modeling under tcplfit2 is not totally appropriate. Data which have limited efficacy or limited number of concentrations tested may be candidates for "loec", or the lowest observed effective concentration, potency and hitcalling determinations. A "loec" is defined as the lowest experimental dose where all responses surpass the cutoff. | |||
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| There are two methods for including a "loec" within the output of level 5 processing and stored within the mc5_param table. The "include" method stores the "loec" alongside regular tcplfit2 winning model fitting, whereas the "ow" (overwrite) method does the same while also overwriting key values, i.e. model_type, hitc, fitc (fit category), and modl (winning model), based on whether a "loec" occurs. See [Plotting](#additional-examples) for how "loec"-fit data are plot. | |||
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- Make sure to add the emphasis quotes around mc5_param,
tcplfit2, model_type, hitc, fitc, and model as done elsewhere in the vignette. - Do you describe elsewhere in the vignette what model_type, hitc, fitc, and modl are assigned to when using the overwrite method both when a loec occurs and when it does not occur? If not, suggest adding that here or somewhere else where it is appropriate.
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Made overwrite values more clear and added wrappers like
| Method <- c(15,34) | ||
| Method_Name <- c("ow_loec.coff", "include_loec.coff") | ||
| Description <- c( | ||
| "Identify the lowest observed effective concentration (loec) where the values of all responses are outside the cutoff band (i.e. abs(resp) > cutoff). loec is stored alongside winning model and potency estimates. If loec exists, assume hit call = 1, fitc = 100, model_type = 1, and if not, assume hit call = 0.", |
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I think this kind of gets at my second bullet above. However, a bullet list that one can scan to find these assignments would be useful. Not sure all users will want to read a full description to find this information.
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updated text to be more clear about what is overwritten and when, also made into bulleted list
| @@ -3251,7 +3274,9 @@ tcplPlot(dat = plot_data, by = "aeid", multi = TRUE, output = "pdf", fileprefix | |||
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| ### - Plot LOEC (Lowest Observed Effective Concentration) | |||
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| <font face="CMTT10">tcplPlot</font> now supports the plotting of vertical "LOEC" lines, automatically detecting when multi-concentration data is hit-called using the new level 5 processing method "loec.coff". Comparison LOEC plotting with other LOEC samples or crossed with traditional hit-called data with winning models is also supported. | |||
| <font face="CMTT10">tcplPlot</font> now supports the plotting of vertical "LOEC" lines, automatically detecting when multi-concentration data is hit-called using the new level 5 processing method "ow_loec.coff". Comparison LOEC plotting with other LOEC samples or crossed with traditional hit-called data with winning models is also supported. | |||
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Suggest updating this description to:
"tcplPlot now supports automatically adding the "loec" to the plot, i.e., a vertical line, when detecting multi-concentration data with hit-calling using the new level 5 processing method "ow_loec.coff". Comparison plotting with "loec" across samples or with traditional hit-calling results using the winning models is also supported."
| <font face="CMTT10">tcplPlot</font> now supports the plotting of vertical "LOEC" lines, automatically detecting when multi-concentration data is hit-called using the new level 5 processing method "loec.coff". Comparison LOEC plotting with other LOEC samples or crossed with traditional hit-called data with winning models is also supported. | ||
| <font face="CMTT10">tcplPlot</font> now supports the plotting of vertical "LOEC" lines, automatically detecting when multi-concentration data is hit-called using the new level 5 processing method "ow_loec.coff". Comparison LOEC plotting with other LOEC samples or crossed with traditional hit-called data with winning models is also supported. | ||
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| Note - for data processed with the level 5 method "include_loec.coff", <font face="CMTT10">tcplPlot</font> will not automatically generate this kind of plot. A current workaround is to pre-load the plot data using `tcplPlotLoadData` and update the $\mathit{model\_type}$ column to `1` for any or all sample(s). Future <font face="CMTT10">tcpl</font> versions may include additive "LOEC" lines as an option. |
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- Update "pre-load the plot data" to "pre-load the plotting data"
- "loec" rather than "LOEC"
sedavid01
reviewed
Apr 15, 2025
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These updates look good to me. Thanks, @cthunes, for making the minor tweaks to the text.
Waiting final approval from @madison-feshuk.
sedavid01
approved these changes
Apr 15, 2025
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Closes #352