Merge pull request #11 from AlissonRP/templates

version 0.5

.Rbuildignore

@@ -1,3 +1,4 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^\.github$
+^codecov\.yml$

DESCRIPTION

@@ -9,7 +9,7 @@ Description: Rmarkdown template for writing pdf reports using Latex syntax (PT-B
 License: GPL
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
 Imports: 
     dplyr,
     ggplot2,
@@ -18,8 +18,10 @@ Imports:
     magrittr,
     stats,
     janitor,
-    lifecycle
+    lifecycle,
+    tidyr
 Suggests: 
+    covr,
     testthat (>= 3.0.0)
 Config/testthat/edition: 3
 Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -2,7 +2,6 @@
 
 export("%>%")
 export(as_tabyl)
-export(pdf1_freq.tbl)
 export(pdf1_na)
 export(pdf1_summary)
 export(pdf1_tbl)

R/freq-table.R

@@ -6,7 +6,6 @@
 #' @param obj     Object used to create the table. Data frame, list or environment
 #' (or object coercible by as.data.frame to a data frame)
 #' @param var       Variable that you want the table (not written in string format)
-#' @param ...     Other arguments
 #' @examples
 #' iris %>%
 #'   mypdf1::pdf1_tbl_freq(Species) %>%

R/freq-table2.R

@@ -8,21 +8,22 @@
 #'
 #' @param obj     Object used to create the table. Data frame, list or environment
 #' (or object coercible by as.data.frame to a data frame)
-#' @param title     titlele for the table, write in string format
+#' @param title     title for the table, write in string format
 #' @param var1       Variable that you want the table (not written in string format)
 #' @param var2       Variable that you want on the top of the table (not written in string format)
-#' @param ...     Other arguments
 #' @param marg   Marginal row table, default is FALSE
 
 #' @examples
 #' mtcars |>
 #'   mypdf1::pdf1_tbl_freq2(cyl, am, "title", marg = TRUE)
 #' @export
 pdf1_tbl_freq2 <- function(obj, var1, var2, title = '', marg = F) {
-  tab <- obj %>%
-    dplyr::group_by({{ var1 }}, {{ var2 }}) %>%
-    dplyr::summarise(n = dplyr::n()) %>%
-    tidyr::spread({{ var2 }}, n)
+  if(any(is.na(obj |> dplyr::select({{var1}},{{var2}}))) == TRUE){
+    warning('Your dataframe has NA, they will be removed from calculations')
+  }
+  tab <- obj |>
+    tab({{ var1}}, {{var2}})
+  tab[is.na(tab)] = 0
   if (marg != TRUE) {
     title2 <- obj |>
       dplyr::select({{ var2 }}) |>
@@ -49,3 +50,7 @@ pdf1_tbl_freq2 <- function(obj, var1, var2, title = '', marg = F) {
   }
   tab
 }
+
+
+
+

R/imports.R

@@ -10,7 +10,7 @@ janitor::as_tabyl
 
 
 
-
+utils::globalVariables(c("where", "median", "sd", "n", "setNames"))
 
 
 

R/pdf1_na.R

@@ -3,9 +3,9 @@
 #' @description
 #' `r lifecycle::badge("experimental")`
 #'
-#' this is a very simple table of the quantity of `NA` by variable
+#' this is a very simple table generator of the quantity of `NA` by variable
 #'
-#' @param obj     Object used to create the table.
+#' @param obj Object used to create the table.
 #'
 #' `data.frame`, `list` or environment
 #' (or object coercible by `as.data.frame` to a `data.frame`)

R/pdf1_summary.R

@@ -1,6 +1,6 @@
 #' pdf1_summary()
 #'
-#' this is a very summary  generator
+#' this is a very simple summary  generator
 #'
 #'
 #' @param obj     Object used to create the table.

R/pdf1_tbl.R

@@ -27,13 +27,13 @@
 #'   dplyr::summarise(sd = sd(wt)) |>
 #'   mypdf1::pdf1_tbl()
 #' @export
-pdf1_tbl <- function(obj, title = "", format = NULL, code = F, format.p.val = F,...) {
+pdf1_tbl <- function(obj, title = "", format = NULL, code = F,...) {
   if (code == T) {
     obj %>%
-      knitr::kable(caption = title, align = "c", format = format)
+      kableExtra::kable(caption = title, align = "c", format = format)
   } else {
     obj %>%
-      knitr::kable(caption = title, align = "c", format = format) |>
+      kableExtra::kable(caption = title, align = "c", format = format) |>
       kableExtra::kable_classic(latex_options = "HOLD_position")
   }
 }

R/tab.R

@@ -0,0 +1,9 @@
+tab = function(obj, var1, var2) {
+  obj %>%
+    dplyr::group_by({{ var1 }}, {{ var2 }}) %>%
+    dplyr::summarise(n = dplyr::n()) %>%
+    tidyr::spread({{ var2 }}, n)
+
+}
+
+

README.md

@@ -1,7 +1,9 @@
-# mypdf1 <img src='figures\mypdf1.png' align="right" height="130" /></a>
+# mypdf1 <img src='man/figures/fig/mypdf1.png' align="right" height="130" /></a>
 
 [![R build
-status](https://github.com/tidyverse/dplyr/workflows/R-CMD-check/badge.svg)](https://github.com/AlissonRP/mypdf1/actions/workflows/check-release.yaml)
+status](https://github.com/tidyverse/ggplot2/workflows/R-CMD-check/badge.svg)](https://github.com/AlissonRP/mypdf1/actions)
+[![Codecov 
+test coverage](https://codecov.io/gh/AlissonRP/mypdf1/branch/main/graph/badge.svg)](https://app.codecov.io/gh/AlissonRP/mypdf1?branch=main)
 
 
 
@@ -16,9 +18,14 @@ So this package provides a template for pdf reports in Rmarkdown and quite usual
 ```r
 devtools::install_github("https://github.com/AlissonRP/mypdf1")
 ```
-## Use of template
+## Use of default template
 ```r
-rmarkdown::draft("namefile.Rmd", template = "pdf1", package = "mypdf1", create_dir = FALSE)
+rmarkdown::draft("namefile.Rmd", template = "pdf1", package = "mypdf1")
+```
+## Use of paper template
+
+```r
+rmarkdown::draft("namefile.Rmd", template = "pdf1 - paper", package = "mypdf1", create_dir = FALSE)
 ```
 
 ## Some functions already available

codecov.yml

@@ -0,0 +1,14 @@
+comment: false
+
+coverage:
+  status:
+    project:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true
+    patch:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true

inst/rmarkdown/templates/pdf1/skeleton/skeleton.Rmd

@@ -5,16 +5,13 @@ abstract: "abstract"
 header-includes:
    - \usepackage[brazil]{babel}
    - \usepackage{bm}
+   - \usepackage{float}
 geometry: left=1.7cm, right=1.7cm, top=3cm, bottom=3cm
 output:
   bookdown::pdf_document2:
 editor_options:
   chunk_output_type: console
 indent: true
-bibliography: bib.bib 
-csl: statistics.csl
-nocite: '@*'
-link-citations: true
 ---
 
 
@@ -24,7 +21,7 @@ link-citations: true
 options(digits=3)  #Arrendodamento
 options(scipen=999)
 ggplot2::theme_set(ggplot2::theme_minimal()) #Tema dos gráficos produzidos no ggplot2
-knitr::opts_chunk$set(echo=F,message=F,warning=F,fig.pos = 'H',fig.align = 'center',fig.width=7.8, fig.height=4.85)
+knitr::opts_chunk$set(echo=F,message=F,warning=F,fig.pos = 'H',fig.align = 'center',fig.width=6, fig.height=4.0)
 scale_fill_discrete = \(...) ggplot2::scale_fill_brewer(... , palette="Set2") #Fixa a scale do fill dos gráficos do ggplot2
 
 ```
@@ -40,7 +37,7 @@ iris |>
 ```{r crftable}
 
 iris |>  
-mypdf1::pdf1_freq.tbl(Species,"seila") |> 
+mypdf1::pdf1_tbl_freq(Species,"seila") |> 
   mypdf1::pdf1_tbl("You can combine this function too!")
     
 ```

inst/rmarkdown/templates/pdf1_paper/skeleton/beforebody.tex

@@ -0,0 +1 @@
+\newpage

inst/rmarkdown/templates/pdf1_paper/skeleton/skeleton.Rmd

@@ -0,0 +1,66 @@
+---
+title: "title"
+author: "author"
+abstract: "abstract"
+header-includes:
+   - \usepackage[brazil]{babel}
+   - \usepackage{bm}
+   - \usepackage{float}
+geometry: left=1.7cm, right=1.7cm, top=3cm, bottom=3cm
+output:
+  bookdown::pdf_document2:
+    includes:
+      before_body: beforebody.tex
+editor_options:
+  chunk_output_type: console
+indent: true
+toc: True
+bibliography: bib.bib 
+csl: style.csl
+nocite: '@*'
+link-citations: true
+---
+
+\clearpage
+\tableofcontents
+
+```{r setup,include=F}
+
+options(digits=3)  #Arrendodamento
+options(scipen=999)
+ggplot2::theme_set(ggplot2::theme_minimal()) #Tema dos gráficos produzidos no ggplot2
+knitr::opts_chunk$set(echo=F,message=F,warning=F,fig.pos = 'H',fig.align = 'center',fig.width=7.8, fig.height=4)
+scale_fill_discrete = \(...) ggplot2::scale_fill_brewer(... , palette="Set2") #Fixa a scale do fill dos gráficos do ggplot2
+
+```
+
+
+\section{Section name}
+```{r }
+#R code
+iris |> 
+  mypdf1::pdf1_summary()
+  
+```
+```{r crftable}
+
+iris |>  
+mypdf1::pdf1_tbl_freq(Species) |> 
+  mypdf1::pdf1_tbl("You can combine this function too!")
+    
+```
+You cross-reference tables like this: Table \@ref(tab:crftable)
+
+```{r crfgraph, fig.cap = "fig name"}
+plot(rnorm(500))
+```
+
+You cross-reference figures like this: Figure \@ref(fig:crfgraph)
+
+
+# Bibliography
+
+```{r}
+
+```
+

inst/rmarkdown/templates/pdf1_paper/template.yaml

@@ -0,0 +1,4 @@
+name: pdf1-paper
+description: >
+  Rmarkdown template for writing pdf reports using Latex syntax.
+create_dir: false

tests/testthat/test-frequency.R

@@ -5,4 +5,9 @@ test_that("sum total", {
     mypdf1::pdf1_tbl_freq(Species) |> (\(x) x[4, 2])() |> as.numeric(), 150)
   expect_equal(iris %>%
     mypdf1::pdf1_tbl_freq(Species) |> (\(x) x[4, 3])() |> round(2) |> as.numeric(), 1)
+  expect_warning(
+    airquality |>
+      mypdf1::pdf1_tbl_freq2(Ozone, Month),'Your dataframe has NA, they will be removed from calculations'
+  )
 })
+