bring in confirmed DOI's

COMPASS-DOE · Mar 2, 2022 · 5d44811 · 5d44811
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diff --git a/rs-synthesis.Rmd b/rs-synthesis.Rmd
@@ -254,7 +254,7 @@ Summary of the studies included in this meta-analysis:
 ```{r studies-table}
 read_csv("rs/srdb-studies.csv", 
          col_types = "iccccccciccccccicccccciic") %>% 
-  select(Study_number, Authors, Title, Source, PubYear, DOI) ->
+  select(Study_number, Authors, Title, Source) ->
   studies
 
 # Three studies are missing DOIs in the SRDB data
@@ -264,16 +264,22 @@ studies[studies$Study_number == 1421, "DOI"] <- "10.2136/sssaj1999.6361848x"
 studies[studies$Study_number == 1639, "DOI"] <- "10.1139/x99-218"
 # Note that a fourth (7593 Wang) has no DOI at all, according to Scopus 
 
+#Possible frame shift in SRDB study numbers
+#Opened an issue to correct: https://github.com/bpbond/srdb/issues/135
+#DOI's confirmed for 82 studies included
+read_csv("rs/DOIcheck.csv",
+         col_types = "iici") -> ConfirmedDOI
+
 meta_df %>% 
-  group_by(Study_number, Ecosystem_type, Manipulation) %>% 
+  group_by(Study_number, Ecosystem_type, Manipulation, Author) %>% 
   summarise(Observations = n(), .groups = "drop") %>% 
-  left_join(studies, by = "Study_number") %>% 
-  mutate(Authors = gsub(",.*$", "", Authors),
-         Authors = paste0(Authors, " et al. (", PubYear, ")")) %>% 
+  left_join(ConfirmedDOI, by = "Study_number") %>% 
+  mutate(Author = gsub(",.*$", "", Author),
+         Author = paste0(Author, " et al. (", PubYear, ")")) %>% 
   arrange(PubYear) %>% 
-  select(ID = Study_number, Authors, DOI, Observations, Ecosystem_type, Manipulation) %>% 
+  select(ID = Study_number, Author, DOI, Observations, Ecosystem_type, Manipulation) %>% 
   pivot_wider(names_from = "Manipulation", values_from = "Observations", values_fill = 0) %>% 
-  group_by(ID, Authors, DOI) %>% 
+  group_by(ID, Author, DOI) %>% 
   summarise(Ecosystem_type = paste(unique(Ecosystem_type), collapse = ", "),
             Drought = sum(Drought), Irrigation = sum(Irrigation),
             .groups = "drop") %>%  

diff --git a/rs/DOIcheck.csv b/rs/DOIcheck.csv
@@ -0,0 +1,83 @@
+Count,Study_number,DOI,PubYear
+1,1268,10.1139/x98-145,1998
+2,1421,10.2136/sssaj1999.6361848x,1999
+3,1639,10.1139/x99-218,2000
+4,2694,10.1111/j.1529-8817.2003.00809.x,2004
+5,2809,10.1029/2003GB002210,2004
+6,2952,10.1111/j.1365-2486.2005.00899.x,2005
+7,3263,10.1111/j.1365-2486.2005.001058.x,2006
+8,3710,10.1029/2005GB002526,2006
+9,3730,10.1016/j.atmosenv.2006.05.008,2007
+10,3978,10.2136/sssaj2006.0303,2007
+11,3983,10.1029/2007JG000443,2007
+12,4051,10.1007/s10533-007-9148-5,2007
+13,4085,10.1111/j.1365-2486.2007.01416.x,2007
+14,4257,10.1111/j.1365-2486.2008.01572.x,2008
+15,4270,10.1111/j.1365-2486.2008.01694.x,2008
+16,4412,10.1556/comec.9.2008.1.4,2008
+17,4549,10.1111/j.1365-2664.2008.01460.x,2008
+18,4564,10.1111/j.1365-2486.2008.01643.x,2008
+19,4849,10.1007/s11104-008-9851-6,2009
+20,4895,10.1111/j.1365-2486.2008.01793.x,2009
+21,5308,10.1007/s11104-009-0041-y,2010
+22,5448,10.5194/bg-7-1223-2010,2010
+23,5536,10.1111/j.1365-2486.2009.02091.x,2010
+24,5587,10.1111/j.1365-2486.2009.02121.x,2010
+25,6048,10.1111/j.1365-2486.2010.02365.xCitations: 71,2011
+26,6112,10.1111/j.1365-2486.2010.02285.x,2011
+27,6166,"10.5194/bg-8-2729-2011, 2011",2011
+28,6168,10.5194/bg-8-3053-2011,2011
+29,6185,10.1007/s11104-010-0548-2,2011
+30,6248,10.5194/bg-9-3739-2012,2012
+31,6272,10.1371/journal.pone.0041493,2012
+32,6299,10.1016/j.agrformet.2011.12.008,2012
+33,6489,10.1016/j.agrformet.2012.05.015,2012
+34,6502,10.1111/j.1365-2486.2012.02696.x,2012
+35,6505,10.1111/j.1365-2486.2011.02634.x,2012
+36,6540,10.1111/j.1365-2486.2011.02516.x,2012
+37,7046,10.1007/s11104-013-1771-4,2013
+38,7048,10.5194/bg-10-3963-2013,2013
+39,7115,10.1371/journal.pone.0077659,2013
+40,7436,/10.1590/S0102-77862013000100009,2013
+41,7593,,2013
+42,8163,10.1007/s00374-014-0901-3,2014
+43,8350,10.1007/s00442-013-2845-y,2014
+44,8401,10.1007/s10533-013-9881-x,2014
+45,8509,10.1007/s11104-013-1944-1,2014
+46,8694,10.1080/17550874.2013.798366,2014
+47,9324,10.1007/s11104-015-2523-4,2015
+48,9557,10.1016/j.soilbio.2015.03.012,2015
+49,9649,10.1016/j.apsoil.2015.01.015,2015
+50,10066,10.1007/s10533-014-0059-y,2015
+51,10104,10.1016/j.agrformet.2014.09.013,2015
+52,10404,10.1111/gcb.12732,2015
+53,11859,10.1016/j.soilbio.2014.09.019,2015
+54,11031,10.3390/f7110263,2016
+55,11064,10.1038/srep34801,2016
+56,11078,10.1088/1748-9326/11/10/105005,2016
+57,11261,10.1002/2015JG003256,2016
+58,10483,10.1002/ece3.3536,2017
+59,10526,10.1038/s41598-017-15157-3,2017
+60,10816,10.3390/f8030075,2017
+61,10878,10.1016/j.scitotenv.2016.11.199,2017
+62,13000,10.1071/RJ16083,2018
+63,13001,10.1071/RJ16080,2018
+64,13004,10.5194/bg-15-2007-2018,2018
+65,13007,10.1016/j.apsoil.2018.02.005,2018
+66,13008,10.1016/j.soilbio.2018.02.023,2018
+67,13009,10.1111/1365-2435.13118,2018
+68,13015,10.1016/j.agrformet.2018.06.020,2018
+69,13018,10.1016/j.scitotenv.2018.08.111,2019
+70,13022,10.1016/j.scitotenv.2018.08.111,2019
+71,13024,10.1016/j.soilbio.2018.12.010,2019
+72,13030,10.3390/su11092597,2019
+73,13033,10.1016/j.agrformet.2019.03.019,2019
+74,13044,10.5194/bg-15-2007-2018,2019
+75,13072,10.1016/j.agrformet.2020.108039,2020
+76,13079,10.1016/j.agrformet.2020.108126,2020
+77,13094,10.1007/s11284-017-1529-1,2018
+78,13096,10.1007/s11104-017-3485-5,2018
+79,13112,10.1016/j.apsoil.2018.02.005,2018
+80,13189,10.1007/s11104-019-04025-w,2019
+81,13193,10.1016/j.agrformet.2019.03.021,2019
+82,13242,10.1111/aje.12670,2020