R: Convert regression output to a HTML table

htmlreg {texreg}

R Documentation

Convert regression output to a HTML table

Description

Conversion of R regression output to a HTML table.

Usage

htmlreg(
  l,
  file = NULL,
  single.row = FALSE,
  stars = c(0.001, 0.01, 0.05),
  custom.header = NULL,
  custom.model.names = NULL,
  custom.coef.names = NULL,
  custom.coef.map = NULL,
  custom.gof.names = NULL,
  custom.gof.rows = NULL,
  custom.note = NULL,
  digits = 2,
  leading.zero = TRUE,
  star.symbol = "&#42;",
  symbol = "&middot;",
  override.coef = 0,
  override.se = 0,
  override.pvalues = 0,
  override.ci.low = 0,
  override.ci.up = 0,
  omit.coef = NULL,
  reorder.coef = NULL,
  reorder.gof = NULL,
  ci.force = FALSE,
  ci.force.level = 0.95,
  ci.test = 0,
  groups = NULL,
  custom.columns = NULL,
  custom.col.pos = NULL,
  bold = 0,
  center = TRUE,
  caption = "Statistical models",
  caption.above = FALSE,
  inline.css = TRUE,
  doctype = FALSE,
  html.tag = FALSE,
  head.tag = FALSE,
  body.tag = FALSE,
  indentation = "",
  margin = 10,
  padding = 5,
  color = "#000000",
  outer.rules = 2,
  inner.rules = 1,
  ...
)

Arguments

`l`	A statistical model or a list of statistical models. Lists of models can be specified as `l = list(model.1, model.2, ...)`. Different object types can also be mixed.
`file`	Using this argument, the resulting table is written to a file rather than to the R prompt. The file name can be specified as a character string. Writing a table to a file can be useful for working with MS Office or LibreOffice. For example, using the `htmlreg` function, an HTML table can be written to a file with the extension `.doc` and opened with MS Word. The table can then be simply copied into any Word document, retaining the formatting of the table. Note that LibreOffice can import only plain HTML; CSS decorations are not supported; the resulting tables do not retain the full formatting in LibreOffice.
`single.row`	By default, a model parameter takes up two lines of the table: the standard error is listed in parentheses under the coefficient. This saves a lot of horizontal space on the page and is the default table format in most academic journals. If `single.row = TRUE` is activated, however, both coefficient and standard error are placed in a single table cell in the same line.
`stars`	The significance levels to be used to draw stars. Between 0 and 4 threshold values can be provided as a numeric vector. For example, `stars = numeric(0)` will not print any stars and will not print any note about significance levels below the table. `stars = 0.05` will attach one single star to all coefficients where the p value is below 0.05. `stars = c(0.001, 0.01, 0.05, 0.1)` will print one, two, or three stars, or a symbol as specified by the `symbol` argument depending on the p-values.
`custom.header`	An optional named list of multi-column headers that are placed above the model names. For example, `custom.header = list("abc" = 1:3, "ef" = 4:5)` will add the label `"abc"` to the first three models and `"ef"` to the fourth and fifth model. The column with coefficient names and any custom columns added by the `"custom.columns"` argument are not counted towards these positions. If `booktabs = TRUE`, `\cmidrule` rules are added below the respective labels; otherwise `\cline` lines are used.
`custom.model.names`	A character vector of labels for the models. By default, the models are named "Model 1", "Model 2", etc. Specifying `model.names = c("My name 1", "My name 2")` etc. overrides the default behavior.
`custom.coef.names`	By default, texreg uses the coefficient names which are stored in the models. The `custom.coef.names` argument can be used to replace them by other character strings in the order of appearance. For example, if a table shows a total of three different coefficients (including the intercept), the argument `custom.coef.names = c("Intercept", "variable 1", "variable 2")` will replace their names in this order. Sometimes it happens that the same variable has a different name in different models. In this case, the user can use this function to assign identical names. If possible, the rows will then be merged into a single row unless both rows contain values in the same column. Where the argument contains an `NA` value, the original name of the coefficient is kept. For example, `custom.coef.names = c(NA, "age", NA)` will only replace the second coefficient name and leave the first and third name as they are in the original model. See also `custom.coef.map` for an easier and more comprehensive way to rename, omit, and reorder coefficients.
`custom.coef.map`	The `custom.coef.map` argument can be used to select, omit, rename, and reorder coefficients. Users must supply a named list of this form: `list("x" = "First variable", "y" = NA, "z" = "Third variable")`. With that particular example of `custom.coef.map`, coefficients will be presented in order: `"x"`, `"y"`, `"z"`. variable `"x"` will appear as `"First variable"`, variable `"y"` will appear as `"y"`, and variable `"z"` will appear as "Third variable". all variables not named `"x"`, `"y"`, or `"z"` will be omitted from the table.
`custom.gof.names`	A character vector which is used to replace the names of the goodness-of-fit statistics at the bottom of the table. The vector must have the same length as the number of GOF statistics in the final table. The argument works like the `custom.coef.names` argument, but for the GOF values. `NA` values can be included where the original GOF name should be kept.
`custom.gof.rows`	A named list of vectors for new lines at the beginning of the GOF block of the table. For example, `list("Random effects" = c("YES", "YES", "NO"), Observations = c(25, 25, 26))` would insert two new rows into the table, at the beginning of the GOF block (i.e., after the coefficients). The rows can contain integer, numeric, or `character` objects. Note that this argument is processed after the `custom.gof.names` argument (meaning `custom.gof.names` should not include any of the new GOF rows) and before the `reorder.gof` argument (meaning that the new GOF order specified there should contain values for the new custom GOF rows). Arguments for custom columns are not affected because they only insert columns into the coefficient block.
`custom.note`	With this argument, a replacement text for the significance note below the table can be provided. If an empty `character` object is provided (`custom.note = ""`), the note will be omitted completely. If some character string is provided (e.g., `custom.note = "My note"`), the significance legend is replaced by `My note`. The original significance legend can be included by inserting the `%stars` wildcard. For example, a custom note can be added right after the significance legend by providing `custom.note = "%stars. My note."`. If the `threeparttable` argument is used, any note should be preceded by `"\\item"`, for example `"\\item %stars. \\item Second note. \\item Third note."`, and it is possible to create line breaks in the formatted table by including `"\\\\"` and line breaks in the LaTeX code by including `"\n"`, for example `"\n\\item %stars.\\\\\n\\item Second line.\n"`.
`digits`	Set the number of decimal places for coefficients, standard errors and goodness-of-fit statistics. Do not use negative values! The argument works like the `digits` argument in the `round` function of the base package.
`leading.zero`	Most journals require leading zeros of coefficients and standard errors (for example, `0.35`). This is also the default texreg behavior. Some journals, however, require omission of leading zeros (for example, `.35`). This can be achieved by setting `leading.zero = FALSE`.
`star.symbol`	Alternative characters for the significance stars can be specified. This is useful if knitr and Markdown are used for HTML report generation. In Markdown, asterisks or stars are interpreted as special characters, so they have to be escaped. To make a HTML table compatible with Markdown, specify `star.symbol = "*"`. Note that some other modifications are recommended for usage with knitr in combination with Markdown or HTML (see the `inline.css`, `doctype`, `html.tag`, `head.tag`, and `body.tag` arguments in the `htmlreg` function).
`symbol`	If four threshold values are handed over to the `stars` argument, p-values smaller than the largest threshold value but larger than the second-largest threshold value are denoted by this symbol. The default symbol is `"\\cdot"` for the LaTeX dot, `"·"` for the HTML dot, or simply `"."` for the ASCII dot. If the `texreg` function is used, any other mathematical LaTeX symbol or plain text symbol can be used, for example `symbol = "\\circ"` for a small circle (note that backslashes must be escaped). If the `htmlreg` function is used, any other HTML character or symbol can be used. For the `screenreg` function, only plain text characters can be used.
`override.coef`	Set custom values for the coefficients. New coefficients are provided as a list of numeric vectors. The list contains vectors of coefficients for each model. There must be as many vectors of coefficients as there are models. For example, if there are two models with three model terms each, the argument could be specified as `override.coef = list(c(0.1, 0.2, 0.3), c(0.05, 0.06, 0.07))`. If there is only one model, custom values can be provided as a plain vector (not embedded in a list). For example: `override.coef = c(0.05, 0.06, 0.07)`.
`override.se`	Set custom values for the standard errors. New standard errors are provided as a list of numeric vectors. The list contains vectors of standard errors for each model. There must be as many vectors of standard errors as there are models. For example, if there are two models with three coefficients each, the argument could be specified as `override.se = list(c(0.1, 0.2, 0.3), c(0.05, 0.06, 0.07))`. If there is only one model, custom values can be provided as a plain vector (not embedded in a list).For example: `override.se = c(0.05, 0.06, 0.07)`. Overriding standard errors can be useful for the implementation of robust SEs, for example.
`override.pvalues`	Set custom values for the p-values. New p-values are provided as a list of numeric vectors. The list contains vectors of p-values for each model. There must be as many vectors of p-values as there are models. For example, if there are two models with three coefficients each, the argument could be specified as `override.pvalues = list(c(0.1, 0.2, 0.3), c(0.05, 0.06, 0.07))`. If there is only one model, custom values can be provided as a plain vector (not embedded in a list). For example: `override.pvalues = c(0.05, 0.06, 0.07)`. Overriding p-values can be useful for the implementation of robust SEs and p-values, for example.
`override.ci.low`	Set custom lower confidence interval bounds. This works like the other override arguments, with one exception: if confidence intervals are provided here and in the `override.ci.up` argument, the standard errors and p-values as well as the `ci.force` argument are ignored.
`override.ci.up`	Set custom upper confidence interval bounds. This works like the other override arguments, with one exception: if confidence intervals are provided here and in the `override.ci.low` argument, the standard errors and p values as well as the `ci.force` argument are ignored.
`omit.coef`	A character string which is used as a regular expression to remove coefficient rows from the table. For example, `omit.coef = "group"` deletes all coefficient rows from the table where the name of the coefficient contains the character sequence `"group"`. More complex regular expressions can be used to filter out several kinds of model terms, for example `omit.coef = "(thresh)\|(ranef)"` to remove all model terms matching either `"thresh"` or `"ranef"`. The `omit.coef` argument is processed after the `custom.coef.names` argument, so the regular expression should refer to the custom coefficient names. To omit GOF entries instead of coefficient entries, use the custom arguments of the extract functions instead (see the help entry of the `extract` function.
`reorder.coef`	Reorder the rows of the coefficient block of the resulting table in a custom way. The argument takes a vector of the same length as the number of coefficients. For example, if there are three coefficients, `reorder.coef = c(3, 2, 1)` will put the third coefficient in the first row and the first coefficient in the third row. Reordering can be sensible because interaction effects are often added to the end of the model output although they were specified earlier in the model formula. Note: Reordering takes place after processing custom coefficient names and after omitting coefficients, so the `custom.coef.names` and `omit.coef` arguments should follow the original order.
`reorder.gof`	Reorder the rows of the goodness-of-fit block of the resulting table in a custom way. The argument takes a vector of the same length as the number of GOF statistics. For example, if there are three goodness-of-fit rows, `reorder.gof = c(3, 2, 1)` will exchange the first and the third row. Note: Reordering takes place after processing custom GOF names and after adding new custom GOF rows, so the `custom.gof.names` and `custom.gof.rows` arguments should follow the original order, and the `reorder.gof` argument should contain values for any rows that are added through the `custom.gof.rows` argument.
`ci.force`	Should confidence intervals be used instead of the default standard errors and p-values? Most models implemented in the texreg package report standard errors and p-values by default while few models report confidence intervals. However, the functions in the texreg package can convert standard errors and into confidence intervals using z-scores if desired. To enforce confidence intervals instead of standard errors, the `ci.force` argument accepts either a logical value indicating whether all models or none of the models should be forced to report confidence intervals (`ci.force = TRUE` for all and `ci.force = FALSE` for none) or a vector of logical values indicating for each model separately whether the model should be forced to report confidence intervals (e.g., `ci.force = c(FALSE, TRUE, FALSE)`). Confidence intervals are computed using the standard normal distribution (z-values based on the `qnorm` function). The t-distribution is currently not supported because this would require each `extract` method to have an additional argument for the degrees of freedom.
`ci.force.level`	If the `ci.force` argument is used to convert standard errors to confidence intervals, what confidence level should be used? By default, `0.95` is used (i.e., an alpha value of 0.05).
`ci.test`	If confidence intervals are reported, the `ci.test` argument specifies the reference value to establish whether a coefficient/CI is significant. The default value `ci.test = 0`, for example, will attach a significance star to coefficients if the confidence interval does not contain `0`. A value of `ci.test = 1` could be useful if coefficients are provided on the odds-ratio scale, for example. If no star should be printed at all, `ci.test = NA` can be used. It is possible to provide a single value for all models or a vector with a separate value for each model. The `ci.test` argument works both for models with native support for confidence intervals and in cases where the `ci.force` argument is used.
`groups`	This argument can be used to group the rows of the table into blocks. For example, there could be one block for hypotheses and another block for control variables. Each group has a heading, and the row labels within a group are indented. The partitions must be handed over as a list of named numeric vectors, where each number is a row index and each name is the heading of the group. Example: `groups = list("first group" = 1:4, "second group" = 7:8)`.
`custom.columns`	An optional list of additional text columns to be inserted into the coefficient block of the table, for example coefficient types. The list should contain one or more character vectors with as many character or numeric elements as there are coefficients/model terms. If the vectors in the list are named, the names are used as labels in the table header. For example, `custom.columns = list(type = c("a", "b", "c"), 1:3)` will add two columns; the first one is labeled while the second one is not. Note that the numeric elements of the second column will be converted to `character` objects in this example. The consequence is that decimal alignment with the dcolumn package is switched off in these columns. Note that this argument is processed after any arguments that affect the number of rows.
`custom.col.pos`	An optional integer vector of positions for the columns given in the `custom.columns` argument. For example, if there are three custom columns, `custom.col.pos = c(1, 3, 3)` will insert the first custom column before the first column of the original table and the remaining two custom columns after the second column of the original table. By default, all custom columns are placed after the first column, which usually contains the coefficient names.
`bold`	The p-value threshold below which the coefficient shall be formatted in a bold font. For example, `bold = 0.05` will cause all coefficients that are significant at the 95% level to be formatted in bold. Note that this is not compatible with the `dcolumn` or `siunitx` arguments in the `texreg` function. If both `bold` and `dcolumn` or `siunitx` are `TRUE`, `dcolumn` and `siunitx` are switched off, and a warning message appears. Note also that it is advisable to use `stars = FALSE` together with the `bold` argument because having both bolded coefficients and significance stars usually does not make any sense.
`center`	Should the table be horizontally aligned at the center of the page?
`caption`	Set the caption of the table.
`caption.above`	Should the caption of the table be placed above the table? By default, it is placed below the table.
`inline.css`	Should the CSS stylesheets be embedded directly in the code of the table (`inline.css = TRUE`), or should the CSS stylesheets be enclosed in the <head> tag, that is, separated from the table code (`inline.css = FALSE`)? Having inline CSS code makes the code of the table more complex, but sometimes it may be helpful when only the table shall be printed, without the head of the HTML file (for example when the table is embedded in a knitr report). As a rule of thumb: use inline CSS if the table is not saved to a file.
`doctype`	Should the first line of the HTML code contain the DOCTYPE definition? If `TRUE`, the HTML 4 TRANSITIONAL version is used. If `FALSE`, no DOCTYPE will be included. Omitting the DOCTYPE can be helpful when the knitr package is used to generate HTML code because knitr requires only the plain table, not the whole HTML document including the document type declaration. Including the DOCTYPE can be helpful when the code is saved to a file, for example as an MS Word document.
`html.tag`	Should the table code (and possibly the <body> and <head> tags) be enclosed in an <html> tag? Suppressing this tag is recommended when knitr is used for dynamic HTML or Markdown report generation. Including this tag is recommended when the code is saved to a file, for example as an MS Word document.
`head.tag`	Should the <head> tag (including CSS definitions and title/caption) be included in the HTML code? Suppressing this tag is recommended when knitr is used for dynamic HTML or Markdown report generation. Including this tag is recommended when the code is saved to a file, for example as an MS Word document.
`body.tag`	Should the table code be enclosed in a <body> HTML tag? Suppressing this tag is recommended when knitr is used for dynamic HTML or Markdown report generation. Including this tag is recommended when the code is saved to a file, for example as an MS Word document.
`indentation`	Characters used for indentation of the HTML code. By default, `indentation = ""` uses no indentation. Any number of spaces or characters can be used instead. For example, `indentation = " "` uses two spaces of (additional) indentation for each subelement.
`margin`	The margin around the table in pixels. This determines how much space there is around the table. To remove all space around the table, set `table.margin = 0`.
`padding`	The space on the left and right of each table cell in pixels.
`color`	The color of the table, including text and rules or lines. This can be provided as a hex RGB value or as a color string that is valid in HTML (e.g., `"black"`).
`outer.rules`	The line width at the top and bottom of the table in pixels. Can be `outer.rules = 0` to omit outer lines.
`inner.rules`	The horizontal line width before and after the coefficient block of the table in pixels. Can be `outer.rules = 0` to omit inner lines.
`...`	Custom options to be passed on to the `extract` function. For example, most extract methods provide custom options for the inclusion or exclusion of specific goodness-of-fit statistics. See the help entries of `extract` for more information.

Details

The htmlreg function creates HTML code. Tables in HTML format can be saved with a ".html" extension and displayed in a web browser. Alternatively, they can be saved with a ".doc" extension and opened in MS Word for inclusion in office documents. htmlreg also works with knitr and HTML or Markdown. Note that the inline.css, doctype, html.tag, head.tag, body.tag, and star.symbol arguments must be adjusted for the different purposes (see the description of the arguments).

Author(s)

Philip Leifeld

References

Leifeld, Philip (2013). texreg: Conversion of Statistical Model Output in R to LaTeX and HTML Tables. Journal of Statistical Software 55(8): 1-24. doi:10.18637/jss.v055.i08.

Examples

library("nlme")
model.1 <- lme(distance ~ age, data = Orthodont, random = ~ 1)
model.2 <- lme(distance ~ age + Sex, data = Orthodont, random = ~ 1)
htmlreg(list(model.1, model.2),
        file = "texreg.doc",
        inline.css = FALSE,
        doctype = TRUE,
        html.tag = TRUE,
        head.tag = TRUE,
        body.tag = TRUE)
unlink("texreg.doc")

[Package texreg version 1.39.4 Index]