willpearse / madtraits Goto Github PK

# work fine -------------------------------------------
# .albouy.2015
data <- read.csv(unzip(suppdata("E096-203","Functional_data.zip", "esa_archives"), "Functional_data.csv"), sep=";")

# .anderson.2015
data<-read.csv(suppdata("10.1371/journal.pone.0166714",2))

# .artacho.2015
data <- read.csv2(suppdata("10.5061/dryad.qg062", "phenotypictraits.csv"), sep=';')

# .augspurger.2016a
  data <- read.csv(suppdata("10.5061/dryad.56cn4","Data File 1. Diaspore traits.csv"), as.is=TRUE)

# .bengtsson.2016
  data <- read.csv(suppdata('10.5061/dryad.62054', 'bengtsson_etal_2016_traits.csv'), as.is=TRUE)

# .comeault.2013
  data <- read.table(suppdata("10.5061/dryad.ck2cm","Tcris_FHA_phenotypes.txt"),header=TRUE)

# .edwards.2015a
    data <- read.csv(suppdata("E096-202", "Table1.csv", "esa_archives"))
# stopped adding ones that worked    

# does not work -----------------------------------------------------------------

# .ameztegui.2016
data <- as.data.frame(read_excel(suppdata("10.5061/dryad.12b0h/2","FunctionalTraits_Dryad.xlsx")))

# .arnold.2016
data <- as.data.frame(read_excel(suppdata("10.5061/dryad.t3d52", "Arnold_etal_2016_functecol_dataset.xlsx"), as.is = TRUE, skip = 3))

# .aubret.2012a
data <- as.data.frame(read_excel(suppdata("10.5061/dryad.14cr5345", "Aubret%2053172.xlsx"),  sheet=1))


#all of the above give this error

Error in read_fun(path = path, sheet = sheet, limits = limits, shim = shim,  :
  Evaluation error: error -103 with zipfile in unzGetCurrentFileInfo
.

# .bello_bedoy.2015b
data <- as.data.frame(read_excel(
        suppdata("10.6084/m9.figshare.1190766.v2","mating occurrencePzoe_2010.xls")
    ))    

# .benesh.2017
data <- read.csv(unzip(suppdata("10.1002/ecy.1680", 1), "CLC_database_lifehistory.csv"))
Error in download.file(url, destination, quiet = TRUE) : 
  cannot open URL 'https://onlinelibrary.wiley.com/action/'
In addition: Warning message:
In download.file(url, destination, quiet = TRUE) :
  cannot open URL 'https://onlinelibrary.wiley.com/action/': HTTP status was '404 Not Found'

# .engemann.2016
 data <- read.delim(unzip(suppdata("10.1002/ecy.1569", 1), "DataS1/GrowthForm_Final.txt"))
 Error in download.file(url, destination, quiet = TRUE) : 
  cannot open URL 'https://onlinelibrary.wiley.com/action/'
In addition: Warning message:
In download.file(url, destination, quiet = TRUE) :
  cannot open URL 'https://onlinelibrary.wiley.com/action/': HTTP status was '404 Not Found'

# .cariveau.2016
data <- as.data.frame(read_excel(suppdata("10.1371/journal.pone.0151482", 3), sheet="TableS1_v2"))
Error: Missing file extension.

.friedman.2014 <- function(...){
    data <- as.data.frame(read_excel(suppdata("10.5061/dryad.489c7","NILs_rawdata.xls")))

 fread: wanted 1 got 0 loc=570826752
 seek: wanted to seek to sector...
THEN R ABORTS

mydats  <- c(".artacho.2015", ".vanier.2013", ".aubret.2012b")
dat <- natdb(datasets = mydats)

Error in findPerl(verbose = verbose) : 
  perl executable not found. Use perl= argument to specify the correct path.
Error in file.exists(tfn) : invalid 'file' argument

mydats  <- c(".artacho.2015", ".vanier.2013")
dat <- natdb(datasets = mydats)

* installing *source* package 'MADtraits' ...
** using staged installation
** R
Error in load(srcFile, e) : 
  (converted from warning) strings not representable in native encoding will be translated to UTF-8
ERROR: unable to build sysdata DB for package 'MADtraits'
* removing 'C:/Users/as80fywe/idiv/sTeTra/sTeTra/renv/library/R-4.0/x86_64-w64-mingw32/MADtraits'
Error: Failed to install 'MADtraits' from GitHub:
  (converted from warning) installation of package ‘C:/Users/as80fywe/AppData/Local/Temp/Rtmpqalzq5/file1fd479567573/MADtraits_1.0-0.tar.gz’ had non-zero exit status
In addition: Warning messages:
1: In untar2(tarfile, files, list, exdir, restore_times) :
  skipping pax global extended headers
2: In untar2(tarfile, files, list, exdir, restore_times) :
  skipping pax global extended headers

> withr::with_envvar(c(R_REMOTES_NO_ERRORS_FROM_WARNINGS="true"), 
+                    remotes::install_github('willpearse/MADtraits')
+ )

* installing *source* package 'MADtraits' ...
** using staged installation
** R
Warning in load(srcFile, e) :
  strings not representable in native encoding will be translated to UTF-8
Warning in load(srcFile, e) :
  input string 'diplopylidium_nü¾�¦˜¼lleri' cannot be translated to UTF-8, is it valid in 'UTF-8' ?
** inst
** byte-compile and prepare package for lazy loading
n*** Successfully loaded .Rprofile ***n
** help
*** installing help indices
  converting help for package 'MADtraits'
    finding HTML links ... done
    MADtraits                               html  
    MADtraits_citations                     html  
    MADtraits_datasets                      html  
    citations                               html  
    clean.MADtraits                         html  
    datasets                                html  
** building package indices
n*** Successfully loaded .Rprofile ***n
** installing vignettes
   'MADtraits-intro.Rnw' 
** testing if installed package can be loaded from temporary location
n*** Successfully loaded .Rprofile ***n
** testing if installed package can be loaded from final location
n*** Successfully loaded .Rprofile ***n
** testing if installed package keeps a record of temporary installation path
* DONE (MADtraits)

> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
[1] drake_7.12.5    MADtraits_1.0-0

loaded via a namespace (and not attached):
  [1] nlme_3.1-149      fs_1.5.0          bold_1.1.0        usethis_1.6.3    
  [5] lubridate_1.7.9   devtools_2.3.2    progress_1.2.2    filelock_1.0.2   
  [9] httr_1.4.2        rprojroot_1.3-2   tools_4.0.2       backports_1.1.10 
 [13] R6_2.4.1          DT_0.15           withr_2.3.0       tidyselect_1.1.0 
 [17] prettyunits_1.1.1 processx_3.4.4    curl_4.3          compiler_4.0.2   
 [21] cli_2.0.2         xml2_1.3.2        desc_1.2.0        triebeard_0.3.0  
 [25] mvtnorm_1.1-1     callr_3.4.4       handlr_0.2.0      convertr_0.1     
 [29] stringr_1.4.0     digest_0.6.25     txtq_0.2.3        rmarkdown_2.4    
 [33] pkgconfig_2.0.3   htmltools_0.5.0   bibtex_0.4.2.3    sessioninfo_1.1.1
 [37] fastmap_1.0.1     htmlwidgets_1.5.2 rlang_0.4.7       readxl_1.3.1     
 [41] rstudioapi_0.11   httpcode_0.3.0    shiny_1.5.0       generics_0.0.2   
 [45] zoo_1.8-8         jsonlite_1.7.1    gtools_3.8.2      dplyr_1.0.2      
 [49] magrittr_1.5      Rcpp_1.0.5        fansi_0.4.1       ape_5.4-1        
 [53] RefManageR_1.2.12 lifecycle_0.2.0   stringi_1.5.3     yaml_2.2.1       
 [57] storr_1.2.1       MASS_7.3-53       pkgbuild_1.1.0    plyr_1.8.6       
 [61] grid_4.0.2        parallel_4.0.2    gdata_2.18.0      promises_1.1.1   
 [65] crayon_1.3.4      miniUI_0.1.1.1    lattice_0.20-41   conditionz_0.1.0 
 [69] hms_0.5.3         knitr_1.30        ps_1.3.4          pillar_1.4.6     
 [73] uuid_0.1-4        taxize_0.9.98     igraph_1.2.5      caper_1.0.1      
 [77] base64url_1.4     codetools_0.2-16  reshape2_1.4.4    pkgload_1.1.0    
 [81] crul_1.0.0        glue_1.4.2        rcrossref_1.1.0   evaluate_0.14    
 [85] data.table_1.13.0 remotes_2.2.0     renv_0.12.0       foreach_1.5.0    
 [89] vctrs_0.3.4       httpuv_1.5.4      urltools_1.7.3    testthat_2.3.2   
 [93] cellranger_1.1.0  purrr_0.3.4       tidyr_1.1.2       reshape_0.8.8    
 [97] assertthat_0.2.1  xfun_0.18         mime_0.9          xtable_1.8-4     
[101] later_1.1.0.1     tibble_3.0.3      iterators_1.0.12  suppdata_1.1-4   
[105] tinytex_0.26      memoise_1.1.0     ellipsis_0.3.1   

Error in type.convert(data[[i]], as.is = as.is[i], dec = dec, numerals = numerals,  : 
  invalid multibyte string at '<ba> 26<27> 23''S'
In addition: Warning message:
In scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  :
  EOF within quoted string

.perez.2014 <- function(...){
  data <- read.xls(ft_get_si('10.5061/dryad.d61jk/1', 'leaf%20traits%2c%20foliar%20freezing%20resistance%2c%20climatic%20niche.xlsx'), as.is=TRUE, sheet=1)
  data$Species <- tolower(gsub(" ", "_", data$Species, ignore.case = TRUE))
  metadata <- data[,c(2:4)]
  data <- data[,-c(2:4)]
  units <- c("cm^2", "gr/m^2", rep("N/mm^2",2), "NA", "latitude", "longitude")
  data <- .df.melt(data, "Species", units, metadata)
  return(data)
}

#similar issue for this as above.  I think it is the quotes in lat and long
.delaRiva.2015 <- function(...){
  data <- read.xls(ft_get_si('10.5061/dryad.dr275.2', 'Dryad_database.xls'), as.is=TRUE, sheet='Traits')
  data$Species <- tolower(gsub(" ", "_", data$Species, ignore.case = TRUE))
  metadata <- data[,c(2:7)]
  data <- data[,-c(2:7)]
  units <- c("m", "m^2", "cm^2", "g^-1", "m^2 Kg^-1", "μg g^-1", "%", "%", "g^-1", "g cm^-3", "g g^-1", "m g^-1", rep("NA", 4), "Latitude", "Longitude")
  data <- .df.melt(data, "Species", units, metadata)
  return(data)
}

> library(MADtraits)
> data <- MADtraits(cache = "./data/downloaded data/traits/MADtraits/cache")
Downloading/loading data
'.' --> 1%; '|' --> 10% complete
|.........|.........|.........|.........|.........|.........|..No encoding supplied: defaulting to UTF-8.
.......|....Error in output[[i]] : subscript out of bounds
In addition: There were 45 warnings (use warnings() to see them)

> data <- as.data.frame(readxl::read_xls(unzip(unzip(suppdata::suppdata("10.1002/ece3.1456", 
+                                                     1)))[2], sheet = 2, na = c("", "NA")))
Error in unzip(unzip(suppdata::suppdata("10.1002/ece3.1456", 1))) : 
  invalid zip name argument
In addition: Warning message:
In unzip(suppdata::suppdata("10.1002/ece3.1456", 1)) : zip file is corrupt

> .paquette.2015 <- function(...) {
+ data <- as.data.frame(readxl::read_xls(unzip(suppdata::suppdata("10.1002/ece3.1456", 
+                                                     1))[2], sheet = 2, na = c("", "NA")))
+ data <- data[8:nrow(data), 2:8]
+ colnames(data) <- c("species", "occurrence", 
+                     "average_maximum_height", "wood_density", 
+                     "seed_mass", "shade_tolerance", "nitrogen_per_leaf_mass_unit")
+ data <- data[, names(data) != "occurrence"]
+ units <- c("m", "g/cm^3", "mg", NA, "%")
+ data$species <- tolower(gsub(" ", "_", data$species))
+ for (i in 2:6) data[, i] <- as.numeric(data[, i])
+ allNAs <- apply(data[2:6], 2, is.na)
+ data <- data[rowSums(allNAs) < 5, ]
+ return(MADtraits:::.df.melt(data, "species", units = units))
+ }
> .paquette.2015()
New names:
* `` -> ...3
* `` -> ...4
* `` -> ...5
* `` -> ...6
* `` -> ...7
* ...
A Trait DataBase containing:
            Species Traits Data-points:
Numeric          61      5          297
Categorical       0      0            0
Total            61      5          297
Units present. 
Warning message:
In .paquette.2015() : NAs introduced by coercion