Hello.

I would like to make a forest plot that has each row in a different color. By each row, I mean the boxes and the respective confidence intervals.

Taking an example from the vignette [https://cran.r-project.org/web/packages/forestplot/vignettes/forestplot.html],

library(forestplot)
# Cochrane data from the 'rmeta'-package
cochrane_from_rmeta <- 
  structure(list(
    mean  = c(NA, NA, 0.578, 0.165, 0.246, 0.700, 0.348, 0.139, 1.017, NA, 0.531), 
    lower = c(NA, NA, 0.372, 0.018, 0.072, 0.333, 0.083, 0.016, 0.365, NA, 0.386),
    upper = c(NA, NA, 0.898, 1.517, 0.833, 1.474, 1.455, 1.209, 2.831, NA, 0.731)),
    .Names = c("mean", "lower", "upper"), 
    row.names = c(NA, -11L), 
    class = "data.frame")

tabletext<-cbind(
  c("", "Study", "Auckland", "Block", 
    "Doran", "Gamsu", "Morrison", "Papageorgiou", 
    "Tauesch", NA, "Summary"),
  c("Deaths", "(steroid)", "36", "1", 
    "4", "14", "3", "1", 
    "8", NA, NA),
  c("Deaths", "(placebo)", "60", "5", 
    "11", "20", "7", "7", 
    "10", NA, NA),
  c("", "OR", "0.58", "0.16", 
    "0.25", "0.70", "0.35", "0.14", 
    "1.02", NA, "0.53"))

forestplot(tabletext, 
           cochrane_from_rmeta,new_page = TRUE,
           is.summary=c(TRUE,TRUE,rep(FALSE,8),TRUE),
           clip=c(0.1,2.5), 
           xlog=TRUE, 
           col=fpColors(box="royalblue",line="darkblue", summary="royalblue"))

I want each study to have its own color. Auckland can be blue, Block can be red, Doran can be green, and so on.

Is there any way to do this?

Sorry, this is a quotation for stack overflow

Thanks - with a good issue report it is easy to help. If you feel that the docs could be improved then send a PR and I'll update it in the next release.

Yesterday I created a Consort diagram for a clinical trial that I am reporting. Fortunately I saved a copy of the printout (attached). CIT Consort diagram..docx This AM I updated R to 4.03 and reran the r program below:

#  CIT long-term outcomes Consort diagram
library(Gmisc, quietly = TRUE)
library(glue, quietly = TRUE)
library(htmlTable, quietly = TRUE)
library(grid, quietly = TRUE)
library(magrittr, quietly = TRUE)

CIT07 <- boxGrob(glue("Transplanted in", "CIT-07, n = 48", .sep = "\n"), 
                txt_gp = gpar(fontsize = 11), width = .2, height = .08,
                y = 0.92, x = 0.14)
EarlyX07 <- boxGrob(glue("Failed, n = 2", "Withdrew*, n = 5",.sep = "\n"), 
                txt_gp = gpar(fontsize = 11), width = .2, height = .08,
                y = 0.78, x = 0.38)
Comp07 <- boxGrob(glue("Completed CIT-07", "n = 48", .sep = "\n"), 
                txt_gp = gpar(fontsize = 11), width = .2, height = .08,
                y = 0.64, x = 0.14)
Not8_07 <- boxGrob(glue("Exited CIT*, n= 5", "n = 48", .sep = "\n"), 
                txt_gp = gpar(fontsize = 11), width = .2, height = .08,
                y = 0.50, x = 0.38)
CIT8_07 <- boxGrob(glue("Entered CIT-08", "n = 5", .sep = "\n"),
                txt_gp = gpar(fontsize = 11), width = .2, height = .08,
                y = 0.36, x = 0.14)
EarlyX8_07 <- boxGrob(glue("Failed, n = 4", "Withdrew*, n = 3", .sep = "\n"),
                txt_gp = gpar(fontsize = 11), width = .2, height = .08,
                y = 0.22, x = 0.28)
Complete07 <-boxGrob(glue("Completed CIT-08", "n = 5", .sep = "\n"),
                txt_gp = gpar(fontsize = 11), width = .2, height = .08,
                y = .08, x = 0.14)
                     
CIT06 <- boxGrob(glue("Transplanted", "in CIT-06, n = 24", .sep = "\n"), 
                txt_gp = gpar(fontsize = 11), width = .2, height = .08,
                y = 0.92, x = 0.86)
EarlyX06 <- boxGrob(glue("Failed, n = 5", "Withdrew*, n = 5",.sep = "\n"),
                txt_gp = gpar(fontsize = 11), width = .2, height = .08,
                y = 0.78, x = 0.64)
Comp06 <- boxGrob(glue("Completed CIT-06", "n = 3", .sep = "\n"),
                txt_gp = gpar(fontsize = 11), width = .2, height = .08,
                y = 0.64, x = 0.86)
Not8_06 <- boxGrob(glue("Exited CIT*, n= 5", "n = 48", .sep = "\n"),
                txt_gp = gpar(fontsize = 11), width = .2, height = .08,
                y = 0.50, x = 0.64)
CIT8_06 <- boxGrob(glue("Entered CIT-08", "n = 48", .sep = "\n"),
                txt_gp = gpar(fontsize = 11), width = .2, height = .08,
                y = 0.36, x = 0.70)
EarlyX8_6 <- boxGrob(glue("Failed, n = 4", "Withdrew*, n = ",.sep = "\n"),
                txt_gp = gpar(fontsize = 11), width = .2, height = .08,
                y = 0.22, x = 0.55)
CompIn06 <- boxGrob(glue("Completed CIT", "in CIT-06, n = 5", .sep = "\n"),
                txt_gp = gpar(fontsize = 11), width = .2, height = .08,
                y = 0.08, x = 0.86)
CompIn08 <- boxGrob(glue("Completed CIT", "in CIT-08, n = 5", .sep = "\n"),
                txt_gp = gpar(fontsize = 11), width = .2, height = .08,
                y = 0.08, x = 0.54)
                    
windows(height = 9, width = 6.5)
CIT07; EarlyX07; Comp07; Not8_07; CIT8_07; EarlyX8_07; Complete07
CIT06; EarlyX06; Comp06; Not8_06; CIT8_06; EarlyX8_6; CompIn06; CompIn08 

connectGrob(CIT07, Comp07, type = 'N')
connectGrob(CIT07, EarlyX07, type = 'L')
connectGrob(Comp07, CIT8_07, type = 'N')
connectGrob(Comp07, Not8_07, type = 'L')
connectGrob(CIT8_07, Complete07, type = 'N')
connectGrob(CIT8_07, EarlyX8_07, type = 'L')
connectGrob(CIT06, Comp06, type = 'N')
connectGrob(Comp06, CompIn06, type = 'N')
connectGrob(CIT06, EarlyX06, type = 'L')
connectGrob(Comp06, Not8_06, type = 'L')
connectGrob(Comp06, CIT8_06, type = 'L')
connectGrob(CIT8_06, EarlyX8_6, type = 'N')
connectGrob(CIT8_06, CompIn08, type = 'L')

The boxGrobs are plotting correctly, but the connectGrobs are messed up. Repeatable on two Windows 10 desktops.

messed up Consort.docx

Something in the new version of R is messing up the mapping or something. I suspect that this is not your bug, but you folks will probably be stuck with fixing it. Meanwhile I may have to drop back to R 4.02. Many thanks for any help you can give me. Larry Hunsicker

Oh, you set the size of the boxes after they've been created: windows(height = 9, width = 6.5) must be before the firs section

No worries. My guess is that you resized the image at some stage - the connections are fixed to a certain point and thus if you resize the image later they will not automatically be updated.

Not sure about that, my feeling is that the async is within the authenticate action where the login just moves the user into the express-session - the login function is defined in Passport.

Excellent idea although I don't think I can manage to add this anytime soon. You're welcome to do PR on a fix and I can have a look at it.

• [x] Use a meaningful title for the pull request. Include the name of the package modified.
• [x] Test the change in your own code. (Compile and run.)
• [x] Add or edit tests to reflect the change. (Run with npm test mongoose-delete.)
• [x] Follow the advice from the readme.
• [x] Avoid common mistakes.
• [x] Run npm run lint package-name (or tsc if no tslint.json is present).
• [x] Provide a URL to documentation or source code which provides context for the suggested changes: https://github.com/dsanel/mongoose-delete/blob/79d7f611bd47238ecd02feb3b87b96c84c060673/index.js#L64-L68
• [x] Include tests for your changes

This fixes a simple error with the indexFields that is parsed using:

function parseIndexFields (options) {
    var indexFields = {
        deleted: false,
        deletedAt: false,
        deletedBy: false
    };

    if (!options.indexFields) {
        return indexFields;
    }

    if ((typeof options.indexFields === 'string' || options.indexFields instanceof String) && options.indexFields === 'all') {
        indexFields.deleted = indexFields.deletedAt = indexFields.deletedBy = true;
    }

    if (typeof(options.indexFields) === "boolean" && options.indexFields === true) {
        indexFields.deleted = indexFields.deletedAt = indexFields.deletedBy = true;
    }

    if (Array.isArray(options.indexFields)) {
        indexFields.deleted = options.indexFields.indexOf('deleted') > -1;
        indexFields.deletedAt = options.indexFields.indexOf('deletedAt') > -1;
        indexFields.deletedBy = options.indexFields.indexOf('deletedBy') > -1;
    }

    return indexFields;
}

Hmm... that seems like an error from my part. The login function is controlled by the main passport library as I understand it: https://github.com/jaredhanson/passport/blob/master/lib/http/request.js#L10-L57

It suggests that the login should accept a full user object. Although - every time I look into the passport code I seem to end up in an evil loop searching for where the different functions are defined and I can't claim that I fully grasp passport. My grasp of this is just too weak.

• Added spacer cell option for vertical borders
• Fixed ignored align.header
• Fix for wrapped styles (issue #80)
• Updated old http:/ urls to https
• Minor theme updates

• Added spacer cell option for vertical borders
• Fixed ignored align.header
• Fix for wrapped styles (issue #80)
• Updated old http:/ urls to https
• Minor theme updates

Closing the issue as it seems resolved

Describe the bug Hi, Thank you for this wonderful package.

I have noticed that - the tidyHtmlTable wrapper does not allow rnames or rgroup to accept anything other than a character string. Thus, nested row groups are not able to be passed to the function.

To Reproduce

tidy.DF_FULL  %>%
  tidyHtmlTable(x = .,
                header = "ColumnLevel02",
                cgroup1 = "ColumnLevel01",
                value = "formattedValue",
                rnames = "RowLevel03",
                rgroup = c("RowLevel01", "RowLevel02"))

creates the following error:

Error in argument_checker(x, value = value, header = header, rnames = rnames, : The following parameters must be of type character: rgroup

Expected behavior Row Level 2 would be nested within Row Level 1 - just like Row Level 3 is nested within Row Level 2 i.e. Rows would be nested Level 1 > Level 2 > Level 3

Versions (please complete the following information):

• OS: Windows 10
• R IDE: RStudio
• Package version: 1.13.1

Additional context The Tidy Html Table wrapper is fantastic and works perfectly in all over situations. It is simply not responding to multiple nested groups. Is it possible to get an interim data structure out that could be manipulated before rendering in html?

I looked through the documentation but did not find an option that suits my needs. When adding grouped headers using cgroup and n.cgroup I want to have borders to the left and right of those grouped columns. I ended up extracting the raw HTML table code, parsing it using xml2, use the n.cgroup indices to identify the td elements to which I need to add the CSS border styles and return the modified HTML code into the htmlTable object.

did I miss anything or is this the only way to go?

Take the MWE:

library(htmlTable)

customTable <- function(x, css = c("custom-table", "custom-table-small")) {
  css.table <- match.arg(css)

  x <- addHtmlTableStyle(x, css.table = css.table)
  htmlTable(x)
}

customTable(x = mtcars)

I basically want to add different values for css.table . My real customTable is a little more complex. I get the error thet css.table cannot be found. I guess that this is a scoping issue. Is it intentional and what is the work-around besides adding the styles outside of my customTable function?

I am using the current developer branch feature/flexible_spacer_cells.

Thanks! That was certainly an evil bug :imp: as the argument had to be manually traversed through the environments. Should work now. It has been merged into develop. Please check that it works. I'll try to submit 2.1 to CRAN within a few days.

• Added options for how the empty spacer cell appears (see addHtmlTableStyle() spacer.* options)
• Fixed ignored align.header

• Added options for how the empty spacer cell appears (see addHtmlTableStyle() spacer.* options)
• Fixed ignored align.header

The current version of forestplot is 1.10, have you tried upgrading?

Greg seems to have dependency on the etm package, which was removed from CRAN. Using R version 4,.0.2, loading Greg gives the following error: Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called ‘etm’

Would be great if you could look into it!

I'm not getting any errors... The deps are:

Imports:
    Hmisc,
    stringr,
    rms,
    sandwich,
    stats,
    nlme,
    methods,
    htmlTable (>= 2.0.0),
    magrittr,
    knitr,
    Epi,
    utils,
    graphics,
    grDevices
Depends:
    forestplot,
    Gmisc (>= 1.0.3)
Suggests:
    boot,
    testthat,
    cmprsk,
    survival,
    dplyr,
    ggplot2,
    parallel,
    rmarkdown,
    rmeta

Can't find an etm package

I don't think this bug is MacOS specific, similar issue appears in Ubuntu. When running NodeJS 12 and above the below Dockerfile will fail, here is the simplest possible container that I could think of that triggers the error:

FROM ubuntu:20.04

RUN apt-get update && \
  apt-get install curl -y

RUN curl -sL https://deb.nodesource.com/setup_12.x | bash -
RUN apt-get install -y nodejs build-essential

RUN mkdir -p /root/test

WORKDIR /root/test
RUN npm init -y
RUN npm install node-gyp
RUN npm install x509

CMD ["/bin/bash"]

The error does not occur at the RUN npm install node-gyp step but at the RUN npm install x509 that rebuilds the node-gyp package.

For the purpose of this error being easier to Google the main error seems to be these lines:

../../nan/nan_implementation_12_inl.h:356:37: error: no matching function for call to 'v8::StringObject::New(v8::Local<v8::String>&)'
  356 |   return v8::StringObject::New(value).As<v8::StringObject>();
      |                                     ^
In file included from /root/.cache/node-gyp/12.18.3/include/node/node.h:67,
                 from ../include/addon.h:4,
                 from ../src/addon.cc:4:
/root/.cache/node-gyp/12.18.3/include/node/v8.h:5531:23: note: candidate: 'static v8::Local<v8::Value> v8::StringObject::New(v8::Isolate*, v8::Local<v8::String>)'
 5531 |   static Local<Value> New(Isolate* isolate, Local<String> value);
      |                       ^~~
/root/.cache/node-gyp/12.18.3/include/node/v8.h:5531:23: note:   candidate expects 2 arguments, 1 provided
In file included from ../../nan/nan_new.h:189,
                 from ../../nan/nan.h:223,
                 from ../include/x509.h:7,
                 from ../src/addon.cc:5:
../../nan/nan_implementation_12_inl.h:356:58: error: expected primary-expression before '>' token
  356 |   return v8::StringObject::New(value).As<v8::StringObject>();
      |                                                          ^
../../nan/nan_implementation_12_inl.h:356:60: error: expected primary-expression before ')' token
  356 |   return v8::StringObject::New(value).As<v8::StringObject>();

With the end section having looking like this:

make: *** [x509.target.mk:116: Release/obj.target/x509/src/addon.o] Error 1
make: Leaving directory '/root/test/node_modules/x509/build'
gyp ERR! build error 
gyp ERR! stack Error: `make` failed with exit code: 2
gyp ERR! stack     at ChildProcess.onExit (/usr/lib/node_modules/npm/node_modules/node-gyp/lib/build.js:194:23)
gyp ERR! stack     at ChildProcess.emit (events.js:315:20)
gyp ERR! stack     at Process.ChildProcess._handle.onexit (internal/child_process.js:275:12)
gyp ERR! System Linux 5.4.0-45-generic
gyp ERR! command "/usr/bin/node" "/usr/lib/node_modules/npm/node_modules/node-gyp/bin/node-gyp.js" "rebuild"
gyp ERR! cwd /root/test/node_modules/x509
gyp ERR! node -v v12.18.3
gyp ERR! node-gyp -v v5.1.0

Actually "double" should work as I use match.arg(). One thought I had was that maybe "center" or "split" would be more intuitive where you don't specify how the cells work

Great! I've been wanting to do this for a while but haven't really gotten around to it.

Do you have any input on the documentation and naming of the arguments? Will people understand "double_cell" - it's probably a bit technical...

I think I've fixed it in the feature/flexible_spacer_cells branch (checkout https://github.com/gforge/htmlTable/tree/). Do you mind testing it a bit before I push it to CRAN?

Yeah, the empty column is there so that the header bottom border doesn't blend into one unit. I guess an option could be added for removing it but the question is if the result will be what you truly want. Another would be to use css.cell or add an argument similar to col.columns that takes not only color but also CSS-rules.

And the option of align = "rr|rr|rr|r" doesn't give you the desired outcome?

This should be doable but I've never worked with the more advanced strategies. The GraphQLLocalStrategy is implemented but it would be awesome if all of the strategies passport provides could be available.

Could you show the HTML-code, what you get together with a small PNG and then what you want and the CSS. Shouldn't bee too difficult to fix.

Sorry for the delayed response. The project where I had been using this package was put on hold and I got some new test-errors after updating the packages. First, if anyone stumbles upon issues with your Request not being valid, make sure that you have the correct definitions (see this issue) by deleting your lock-files and re-installing everything.

I'm not sure that I actually understand the original code example. The definition for the PassportContext requires 4 arguments:

export declare type PassportContext<
  UserObjectType extends {}, 
  Credentials extends {}, 
  AuthInfoTemplate extends {} = {}, 
  Request extends object = ExpressRequest
> = SharedPassportContext<UserObjectType, Credentials, AuthInfoTemplate, Request>;

In the example provided there are only two arguments provided, Context and ExpressRequest. My definitions look something like this:

export interface Credentials {
  username: string;
  password: string;
}

declare interface MyContext extends PassportContext<UserModelInterface, Credentials, {}, express.Request> {
  dataSources: MyDataSourcesInterface;
}

As of TS 2.2 there you can add the prisma and smtpTransport just as I did with dataSources even though the original context is a type and not an interface. If you want it stricter then perhaps an intersection is a better choice.