From 3ddd1c89db06fb820dbfe59a6141c1e7b6d2bdae Mon Sep 17 00:00:00 2001 From: maurolepore Date: Tue, 15 May 2018 17:24:14 -0400 Subject: [PATCH] Update docs. --- NEWS.md | 2 +- docs/articles/read_df_write.html | 2 +- docs/news/index.html | 3 +- docs/reference/fieldforms_output.html | 8 +-- docs/reference/xl_sheets_to_output.html | 79 ++++++++++++++++++++++--- 5 files changed, 80 insertions(+), 14 deletions(-) diff --git a/NEWS.md b/NEWS.md index 700e9550..e5be843d 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,6 @@ # fgeo.tool 0.0.0.9002 -* `xl_sheets_to_csv()` and friends gain the argument `first_census` to now accept first census data. +* `xl_sheets_to_*()` gain the argument `first_census` (Sabrina Russo, #31). * Clarify the internal structure of fgeo.tool with function's prefixes. * `add_*()` diff --git a/docs/articles/read_df_write.html b/docs/articles/read_df_write.html index 1a97e237..60efd3f5 100644 --- a/docs/articles/read_df_write.html +++ b/docs/articles/read_df_write.html @@ -91,7 +91,7 @@

Read, combine, identify, and write multiple files

Mauro Lepore

-

2018-05-14

+

2018-05-15

Source: vignettes/read_df_write.Rmd diff --git a/docs/news/index.html b/docs/news/index.html index 9d0a8865..19dfb67d 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -123,6 +123,7 @@

Changelog

fgeo.tool 0.0.0.9002

diff --git a/docs/reference/fieldforms_output.html b/docs/reference/fieldforms_output.html index 41d9e0ea..5e7048fa 100644 --- a/docs/reference/fieldforms_output.html +++ b/docs/reference/fieldforms_output.html @@ -253,8 +253,8 @@

Examp #> | |.................................................................| 100% #> ordinary text without R code #> -#>

#> output file: forms_loop.knit.md
#> "C:/Users/LeporeM/AppData/Local/Pandoc/pandoc" +RTS -K512m -RTS forms_loop.utf8.md --to docx --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash+smart --output pandoc1b586e435ca.docx --highlight-style tango --reference-doc reference.docx
#> -#> Output created: C:/Users/LeporeM/AppData/Local/Temp/1/Rtmpuu17B4/fieldforms.docx
fieldforms_output( +#>
#> output file: forms_loop.knit.md
#> "C:/Users/LeporeM/AppData/Local/Pandoc/pandoc" +RTS -K512m -RTS forms_loop.utf8.md --to docx --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash+smart --output pandoc21cc60b24f5.docx --highlight-style tango --reference-doc reference.docx
#> +#> Output created: C:/Users/LeporeM/AppData/Local/Temp/1/RtmpoFtUKz/fieldforms.docx
fieldforms_output( prep, "fieldforms2.docx", header = "Custom Header", output_dir = tmp )
#> #> @@ -270,8 +270,8 @@

Examp #> | |.................................................................| 100% #> ordinary text without R code #> -#>

#> output file: forms_loop.knit.md
#> "C:/Users/LeporeM/AppData/Local/Pandoc/pandoc" +RTS -K512m -RTS forms_loop.utf8.md --to docx --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash+smart --output pandoc1b5813897950.docx --highlight-style tango --reference-doc reference.docx
#> -#> Output created: C:/Users/LeporeM/AppData/Local/Temp/1/Rtmpuu17B4/fieldforms2.docx
+#>
#> output file: forms_loop.knit.md
#> "C:/Users/LeporeM/AppData/Local/Pandoc/pandoc" +RTS -K512m -RTS forms_loop.utf8.md --to docx --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash+smart --output pandoc21cc63c35d0.docx --highlight-style tango --reference-doc reference.docx
#> +#> Output created: C:/Users/LeporeM/AppData/Local/Temp/1/RtmpoFtUKz/fieldforms2.docx
# Confirm dir(tmp)[grepl("docx$", dir(tmp))]
#> [1] "fieldforms.docx" "fieldforms2.docx"
# Cleaning temporary directory diff --git a/docs/reference/xl_sheets_to_output.html b/docs/reference/xl_sheets_to_output.html index 11f846d6..91390ce8 100644 --- a/docs/reference/xl_sheets_to_output.html +++ b/docs/reference/xl_sheets_to_output.html @@ -137,11 +137,11 @@

Combine spreadsheets from excel workbooks and output common data structures.

- 
xl_sheets_to_csv(input_dir, output_dir = "./")
+    
xl_sheets_to_csv(input_dir, output_dir = "./", first_census = FALSE)
 
-xl_sheets_to_xl(input_dir, output_dir = "./")
+xl_sheets_to_xl(input_dir, output_dir = "./", first_census = FALSE)
 
-xl_sheets_to_df(input_dir)

+xl_sheets_to_df(input_dir, first_census = FALSE)

Arguments

@@ -155,6 +155,18 @@

Arg

+ + + +
output_dir

String giving the directory where to write .csv files to.
first_census

This argument tells these functions what sheets to expect +in the input.

    +

  • Use TRUE if this is your first census. The expected input must have +sheets (1) "root", (2) "multi_stems", (3) "secondary_stems", and +(4) "single_stems".

    • +

  • Use FALSE (default) if this is not your first census. The expected +input must have sheets (1) "root", (2) "original_stems", (3) +"new_secondary_stems", and (4) "recruits".

    • +

Value

@@ -168,8 +180,8 @@

Details function does:

+

Acknowledgment

+ + +

Sabrina Russo helped to make these functions useful with first censuses.

+

Examples

library(fs)
+library(readr)
+library(readxl)
 
+# NOT A FIRST CENSUS
 # Path to the folder I want to read excel files from
 input_dir <- dirname(example_path("two_files/new_stem_1.xlsx"))
 input_dir
#> [1] "C:/Users/LeporeM/Dropbox/git_repos/fgeo.tool/inst/extdata/two_files"

@@ -189,11 +209,54 @@ 
Examp
 # Path to the folder I want to write .csv files to
 output_dir <- tempdir()
 
-# Do the work
+# Output a csv file
 xl_sheets_to_csv(input_dir, output_dir)
 
 # Confirm
-path_file(dir_ls(output_dir, regexp = "new_stem.*csv$"))
#> new_stem_1.csv new_stem_2.csv
+path_file(dir_ls(output_dir, regexp = "new_stem.*csv$"))
#> new_stem_1.csv new_stem_2.csv
+# Also possible to output excel and a list of dataframe. See next section. + +# FIRST CENSUS +input_dir <- dirname(example_path("first_census/census.xlsx")) +# As a reminder you'll get a warning of missing sheets +# Output list of dataframes (one per input workbook -- here only one) +xl_sheets_to_df(input_dir, first_census = TRUE)
#> Warning: `.x` has no dataframe new_secondary_stems
#> Warning: `.x` has no dataframe recruits
#> $census.xlsx +#> # A tibble: 49 x 15 +#> submission_id quadrat tag stem_tag species species_code dbh status codes +#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> +#> 1 c01b37d5-2c3~ 0816 007 1 Americ~ TILIAM 51.2 LI M +#> 2 efd8e991-2e3~ 0916 004 1 Americ~ TILIAM 31.6 LI M +#> 3 efd8e991-2e3~ 0916 007 1 Ironwo~ OSTRVI 10.2 LI M +#> 4 efd8e991-2e3~ 0916 008 1 Ironwo~ OSTRVI 2.7 LI M;L +#> 5 efd8e991-2e3~ 0916 010 1 Hackbe~ CELTOC 25.9 LI M +#> 6 efd8e991-2e3~ 0916 012 1 Bur Oak QUERMA 35.2 LI M;FS~ +#> 7 7997596a-c94~ 1017 001 1 Americ~ TILIAM 65.3 LI M;FS~ +#> 8 572ddae1-d02~ 0816 002 1 Hackbe~ CELTOC 45.1 LI M +#> 9 c01b37d5-2c3~ 0816 007 2 TILIAM <NA> 42.4 LI S;L +#> 10 c01b37d5-2c3~ 0816 007 3 TILIAM <NA> 39.8 LI S +#> # ... with 39 more rows, and 6 more variables: notes <chr>, pom <chr>, +#> # sheet <chr>, section_id <chr>, unique_stem <chr>, date <chr> +#>
+# Output excel +xl_sheets_to_xl(input_dir, output_dir, first_census = TRUE)
#> Warning: `.x` has no dataframe new_secondary_stems
#> Warning: `.x` has no dataframe recruits
# Read back +filename <- path(output_dir, "census.xlsx") +out <- read_excel(filename) +str(out, give.attr = FALSE)
#> Classes ‘tbl_df’, ‘tbl’ and 'data.frame': 49 obs. of 15 variables: +#> $ submission_id: chr "c01b37d5-2c30-4086-b4a1-78327dfa0a9a" "efd8e991-2e34-40c8-b503-44def6e542d9" "efd8e991-2e34-40c8-b503-44def6e542d9" "efd8e991-2e34-40c8-b503-44def6e542d9" ... +#> $ quadrat : chr "0816" "0916" "0916" "0916" ... +#> $ tag : chr "007" "004" "007" "008" ... +#> $ stem_tag : chr "1" "1" "1" "1" ... +#> $ species : chr "American Basswood/Linden" "American Basswood/Linden" "Ironwood" "Ironwood" ... +#> $ species_code : chr "TILIAM" "TILIAM" "OSTRVI" "OSTRVI" ... +#> $ dbh : chr "51.2" "31.6" "10.2" "2.7" ... +#> $ status : chr "LI" "LI" "LI" "LI" ... +#> $ codes : chr "M" "M" "M" "M;L" ... +#> $ notes : chr NA NA NA "In brush pile" ... +#> $ pom : chr "1.3" "1.3" "1.3" "1.3" ... +#> $ sheet : chr "multi_stems" "multi_stems" "multi_stems" "multi_stems" ... +#> $ section_id : chr NA NA NA NA ... +#> $ unique_stem : chr "007_1" "004_1" "007_1" "008_1" ... +#> $ date : chr "2018.05.14" "2018.05.14" "2018.05.14" "2018.05.14" ...