njahn82
commented
3 years ago Thanks for your report, I can confirm this API behavior. As it seems to be a server issue, I think I won't be able to fix this. Maybe the option citeproc-json-ish works for you instead as it seems not be affected from this encoding issue?
rcrossref::cr_cn("10.5194/bg-2021-40", format = "citeproc-json", verbose = T)
#> Error in nchar(hh): invalid multibyte string, element 1
# Request directly
httr::GET("https://api.crossref.org/works/10.5194/bg-2021-40/transform/application/vnd.citationstyles.csl+json")
#> Error in substring(u, so, so + ml - 1L): invalid multibyte string, element 1
# instead, try
rcrossref::cr_cn("10.5194/bg-2021-40", format = "citeproc-json-ish")
#> $indexed
#> $indexed$`date-parts`
#> [,1] [,2] [,3]
#> [1,] 2021 5 7
#>
#> $indexed$`date-time`
#> [1] "2021-05-07T14:54:01Z"
#>
#> $indexed$timestamp
#> [1] 1.620399e+12
#>
#>
#> $posted
#> $posted$`date-parts`
#> [,1] [,2] [,3]
#> [1,] 2021 3 1
#>
#>
#> $`group-title`
#> [1] "Biogeochemistry: Organic Biogeochemistry"
#>
#> $`reference-count`
#> [1] 0
#>
#> $publisher
#> [1] "Copernicus GmbH"
#>
#> $license
#> URL start.date-parts
#> 1 https://creativecommons.org/licenses/by/4.0/ 2021, 3, 1
#> start.date-time start.timestamp delay-in-days content-version
#> 1 2021-03-01T00:00:00Z 1.614557e+12 0 vor
#>
#> $`content-domain`
#> $`content-domain`$domain
#> list()
#>
#> $`content-domain`$`crossmark-restriction`
#> [1] FALSE
#>
#>
#> $abstract
#> [1] "<jats:p>Abstract. Organic matter production by cyanobacteria blooms is a major environmental concern for the Baltic Sea as it promotes thespread of anoxic zones. Partial pressure of carbon dioxide (pCO2) measurements carried out on Ships of Opportunity (SOOP) since 2003 have proven to be a powerful tool to resolve the carbon dynamics of the blooms in space and time. However, SOOP measurements lack the possibility to directly constrain the depth–integrated net community production (NCP) due to their restriction to the sea surface. This study tackles the resulting knowledge gap through (1) providing a best–guess NCP estimatefor an individual cyanobacteria bloom based on repeated profiling measurements of pCO2 and (2) establishing an algorithm to accurately reconstruct depth–integrated NCP from surface pCO2 observations in combination with modelled temperature profiles. Goal (1) was achieved by deploying state–of–the–art sensor technology from a small–scale sailing vessel. The low–cost and flexible platform enabled observations covering an entire bloom event that occurred in July and August 2018 in the Eastern Gotland Sea. For the biogeochemical interpretation, recorded pCO2 profiles were converted to CT*, which is the dissolved inorganic carbon concentration normalised to alkalinity. We found that the investigated Nodularia–dominated bloom event had many biogeochemical characteristics in common with blooms in previous years. In particular, it lasted for about three weeks, caused a CT* drawdown of 80 μmol kg−1, and was accompanied by a sea surface temperature increase of 10 °C. The novel finding of this study is the vertical extension of the CT* drawdown up to 12 m water depth. Integration of the CT* drawdown across this depth and correction for vertical fluxes permit a best–guess NCP estimate of ~1.2 mol–C m−2. Addressing goal (2), we combined modelled hydrographical profiles with surface pCO2 observations recorded by SOOP Finnmaid within the study area. Introducing the temperature penetration depth (TPD) as a new parameter to integrate SOOP observations across depth, we achieve a reconstructed NCP estimate that agrees to the best–guess within 10 %. Applying the TPD approach to almost two decades of surface pCO2 observations available for the Baltic Sea bears the potential to provide new insights into the control and long–term trends of cyanobacteria NCP. This understanding is key for an effective design and monitoring of conservation measures aiming at a Good Environmental Status of the Baltic Sea.\n </jats:p>"
#>
#> $DOI
#> [1] "10.5194/bg-2021-40"
#>
#> $type
#> [1] "posted-content"
#>
#> $created
#> $created$`date-parts`
#> [,1] [,2] [,3]
#> [1,] 2021 3 1
#>
#> $created$`date-time`
#> [1] "2021-03-01T14:12:12Z"
#>
#> $created$timestamp
#> [1] 1.614608e+12
#>
#>
#> $source
#> [1] "Crossref"
#>
#> $`is-referenced-by-count`
#> [1] 0
#>
#> $title
#> [1] "Cyanobacteria net community production in the Baltic Sea as\ninferred from profiling <i>p</i>CO<sub>2</sub> measurements"
#>
#> $prefix
#> [1] "10.5194"
#>
#> $author
#> ORCID authenticated-orcid given
#> 1 http://orcid.org/0000-0003-3137-0883 FALSE Jens Daniel
#> 2 <NA> NA Bernd
#> 3 http://orcid.org/0000-0003-4007-9764 FALSE Ulf
#> 4 http://orcid.org/0000-0002-3555-1115 FALSE Peer
#> 5 http://orcid.org/0000-0002-3082-8728 FALSE Marcus Bo
#> 6 http://orcid.org/0000-0001-7656-1881 FALSE Anna
#> 7 http://orcid.org/0000-0002-7979-7176 FALSE Norbert
#> 8 <NA> NA Siegfried
#> 9 http://orcid.org/0000-0002-0597-9989 FALSE Gregor
#> family sequence affiliation
#> 1 Müller first NULL
#> 2 Schneider additional NULL
#> 3 Gräwe additional NULL
#> 4 Fietzek additional NULL
#> 5 Wallin additional NULL
#> 6 Rutgersson additional NULL
#> 7 Wasmund additional NULL
#> 8 Krüger additional NULL
#> 9 Rehder additional NULL
#>
#> $member
#> [1] "3145"
#>
#> $`container-title`
#> list()
#>
#> $`original-title`
#> list()
#>
#> $deposited
#> $deposited$`date-parts`
#> [,1] [,2] [,3]
#> [1,] 2021 5 7
#>
#> $deposited$`date-time`
#> [1] "2021-05-07T13:58:32Z"
#>
#> $deposited$timestamp
#> [1] 1.620396e+12
#>
#>
#> $score
#> [1] 1
#>
#> $subtitle
#> list()
#>
#> $`short-title`
#> list()
#>
#> $issued
#> $issued$`date-parts`
#> [,1] [,2] [,3]
#> [1,] 2021 3 1
#>
#>
#> $`references-count`
#> [1] 0
#>
#> $URL
#> [1] "http://dx.doi.org/10.5194/bg-2021-40"
#>
#> $relation
#> $relation$`has-review`
#> id-type id asserted-by
#> 1 doi 10.5194/bg-2021-40-RC1 subject
#> 2 doi 10.5194/bg-2021-40-RC2 subject
#>
#> $relation$`has-comment`
#> id-type id asserted-by
#> 1 doi 10.5194/bg-2021-40-AC1 subject
#> 2 doi 10.5194/bg-2021-40-AC2 subject
#>
#>
#> $subtype
#> [1] "preprint"Created on 2021-08-30 by the reprex package (v2.0.0)
larsvilhuber
FlukeAndFeather
schiavone1
wcerfgba
Bisaloo
jdblischak
I just installed the latest GitHub version to solve the issue with the polite pool described in #218. However, now I am getting a new error, which I suspect is due to the UTF-8 encoding changes in the new crossref API discussed in #216.
The problematic DOI is 10.5194/bg-2021-40. Both the first author's surname (Muëller) and the title (pCO2) have special characters. This worked without issue prior to the recent API changes.
Here is what I see when I run the code above:
Searching for the error message, I found this SO post that solves the problem by converting the text to UTF-8.
Session Info
```r R version 4.0.5 (2021-03-31) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Ubuntu 18.04.5 LTS Matrix products: default BLAS/LAPACK: