.buildignore/issue_21/issue_21.md

In forestgeo/fgeo.misc: Miscellaneous Functions

Issue 21

Jess,

I downloaded the data (and removed the link).

From the two issues you mention, I think only one is actionable.

• (not actionable) xl_to_df() does not exist in the package. Did it ever existed? I suspect that what you are trying to accomplish it already done by some of the xlff_to_*() variants. I have now made the help file visible on the package website. The examples section should clarify what these functions do.

• (actionable) I changed the code to not-fail when the column tag doesn’t exist. I’m not sure why isn’t there (although you may have explained)–I leave it to you to decide. Now the code produces output but there are a bunch of warnings that I encourage you to read and try to make sense of. See below:

library(purrr)
library(dplyr)
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union
library(readr)
library(fs)
library(here)
#> here() starts at C:/Users/LeporeM/Documents/Dropbox/git/fgeo.misc

# install.packages("fgeo.tool")
library(fgeo.tool)
#> 
#> Attaching package: 'fgeo.tool'
#> The following object is masked from 'package:stats':
#> 
#>     filter
# devtools::install_github("forestgeo/fgeo.misc")
library(fgeo.misc)

packageVersion("fgeo.tool")
#> [1] '1.2.4'
packageVersion("fgeo.misc")
#> [1] '0.0.0.9002'

input <- here(".buildignore/issue_21/input")

# The input/ folder contains .xlsx file
dir_ls(input)
#> C:/Users/LeporeM/Documents/Dropbox/git/fgeo.misc/.buildignore/issue_21/input/15106_13112019-05-02_AS_t.xlsx
#> C:/Users/LeporeM/Documents/Dropbox/git/fgeo.misc/.buildignore/issue_21/input/15712019-05-10MS_t.xlsx

list_of_dataframes <- xlff_to_list(input, first_census = FALSE)
#> Warning: Unknown or uninitialised column: 'new_stem'.
#> Warning: Length of logical index must be 1 or 64, not 0
#> Warning: `new_secondary_stems` has cero rows.
#> Warning: Filling every cero-row dataframe with NAs (new_secondary_stems).
#> Warning: Unknown or uninitialised column: 'new_stem'.
#> Warning: Length of logical index must be 1 or 33, not 0
#> Warning: `new_secondary_stems` has cero rows.
#> Warning: Filling every cero-row dataframe with NAs (new_secondary_stems).
single_dataframe <- reduce(list_of_dataframes, bind_rows)

as_tibble(single_dataframe)
#> # A tibble: 113 x 24
#>    submission_id start_form_time~ end_form_time_s~ sheet section_id quadrat
#>    <chr>         <chr>            <chr>            <chr> <chr>      <chr>  
#>  1 1f11a77f-dea~ 2019-05-01 09:5~ 2019-05-10 09:1~ form~ <NA>       <NA>   
#>  2 1f11a77f-dea~ <NA>             <NA>             orig~ <NA>       1311   
#>  3 1f11a77f-dea~ <NA>             <NA>             orig~ <NA>       1311   
#>  4 1f11a77f-dea~ <NA>             <NA>             orig~ <NA>       1311   
#>  5 1f11a77f-dea~ <NA>             <NA>             orig~ <NA>       1311   
#>  6 1f11a77f-dea~ <NA>             <NA>             orig~ <NA>       1311   
#>  7 1f11a77f-dea~ <NA>             <NA>             orig~ <NA>       1311   
#>  8 1f11a77f-dea~ <NA>             <NA>             orig~ <NA>       1311   
#>  9 1f11a77f-dea~ <NA>             <NA>             orig~ <NA>       1311   
#> 10 1f11a77f-dea~ <NA>             <NA>             orig~ <NA>       1311   
#> # ... with 103 more rows, and 18 more variables: mainstem_tag <chr>,
#> #   stem_tag <chr>, spcode <chr>, px <chr>, py <chr>, dbh <chr>,
#> #   status <chr>, codes <chr>, hom <chr>, notes <chr>, dbh_2019 <chr>,
#> #   status_2019 <chr>, codes_2019 <chr>, notes_2019 <chr>,
#> #   new_secondary <chr>, scientific_name <chr>, unique_stem <chr>,
#> #   date <chr>

glimpse(single_dataframe)
#> Observations: 113
#> Variables: 24
#> $ submission_id         <chr> "1f11a77f-deae-477b-97ac-68d61399336a", ...
#> $ start_form_time_stamp <chr> "2019-05-01 09:58:07 AM", NA, NA, NA, NA...
#> $ end_form_time_stamp   <chr> "2019-05-10 09:18:52 AM", NA, NA, NA, NA...
#> $ sheet                 <chr> "form_meta_data", "original_stems", "ori...
#> $ section_id            <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, ...
#> $ quadrat               <chr> NA, "1311", "1311", "1311", "1311", "131...
#> $ mainstem_tag          <chr> NA, "130903", "132986", "130902", "13090...
#> $ stem_tag              <chr> NA, "130903", "132986", "130902", "13090...
#> $ spcode                <chr> NA, "LIST2", "TORA2", "LIST2", "ACRU", "...
#> $ px                    <chr> NA, "1.6", "1.6", "1.1", "0", "0.6", "1....
#> $ py                    <chr> NA, "0.6", "0.6", "1.3", "0.3", "2", "6....
#> $ dbh                   <chr> NA, "32.5", "2.7", "28.5", "20", "3.1", ...
#> $ status                <chr> NA, "LI", "LI", "LI", "LI", "LI", "LI", ...
#> $ codes                 <chr> NA, "A", "NA", "NA", "L", "NA", "NA", "M...
#> $ hom                   <chr> NA, "1.32", "1.3", "1.3", "1.3", "1.3", ...
#> $ notes                 <chr> NA, "NA", "on 130903", "NA", "changed fr...
#> $ dbh_2019              <chr> NA, "32.9", "3.5", "29.2", "20", "3.4", ...
#> $ status_2019           <chr> NA, "LI", "LI", "LI", "LI", "LI", "LI", ...
#> $ codes_2019            <chr> NA, NA, NA, NA, "L", NA, NA, NA, "XY", N...
#> $ notes_2019            <chr> NA, "TORAR 132986", NA, NA, NA, NA, "Epi...
#> $ new_secondary         <chr> NA, "False", "False", "False", "False", ...
#> $ scientific_name       <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, ...
#> $ unique_stem           <chr> "notag_NA", "notag_130903", "notag_13298...
#> $ date                  <chr> "2019-05-02", "2019-05-02", "2019-05-02"...

# You can now save it as you please, for example, as a .csv
output <- here(".buildignore/issue_21/output/single_dataframe.csv")
write_csv(single_dataframe, path = output)

# The output/ folder now contains the file we just saved
dir_ls(path_dir(output))
#> C:/Users/LeporeM/Documents/Dropbox/git/fgeo.misc/.buildignore/issue_21/output/single_dataframe.csv

forestgeo/fgeo.misc documentation built on June 23, 2019, 6:26 p.m.