pubs fixes

Author: jarochi

R/create_ppl_page.R

@@ -2,7 +2,7 @@
 # whois <- whois
 # whois <- "Asia"
 
-load("bg_df_data.RData")
+load("data/bg_df_data.RData")
 source('R/resume_fun.R')
 
 create_ppl_page <- function(whois_full_name, whois, file_name){

R/resume_fun.R

@@ -65,13 +65,8 @@ pubs <- function(whois, openalex_id){
     unlist(.) %>%
     tibble(position = .) %>% 
     cbind(pub_mod, .)
-  
-  # for (i in pub_overwrite %>% filter(who == whois) %>% select(doi) %>% as.vector()) {
-  #   pub_mod <- pub_mod %>% 
-  #       mutate(position = if_else(str_detect(doi, i), "first", position))
-  #   }
-    
 
+  
   pub_mod <- pub_mod$author %>% 
     lapply(., function(x){
       number <- x$au_id %>% str_detect(openalex_id) %>% which(.)
@@ -81,10 +76,18 @@ pubs <- function(whois, openalex_id){
     tibble(corresponding = .) %>% 
     cbind(pub_mod, .)
 
-  # for (i in pub_overwrite %>% filter(who == whois) %>% select(doi) %>% as.vector()) {
-  #   pub_mod <- pub_mod %>% 
-  #     mutate(corresponding = if_else(str_detect(doi, i), TRUE, corresponding))
-  # }
+
+  if((pub_overwrite %>% filter(who == whois & position == "first") %>% nrow()) > 0){
+  for (i in pub_overwrite %>% filter(who == whois & position == "first") %>% select(doi) %>% as.vector()) {
+    pub_mod <- pub_mod %>%
+      mutate(position = if_else(str_detect(doi, i), "first", position))
+  }}
+  
+  if((pub_overwrite %>% filter(who == whois & corresponding == TRUE) %>% nrow()) > 0){
+  for (i in pub_overwrite %>% filter(who == whois & corresponding == TRUE) %>% select(doi) %>% as.vector()) {
+    pub_mod <- pub_mod %>%
+      mutate(corresponding = if_else(str_detect(doi, i), TRUE, corresponding))
+  }}
 
   pub_mod %>% 
     filter(type != "dataset") %>% 

_freeze/subsite/colab/ks/execute-results/html.json

@@ -466,7 +466,7 @@
     "href": "subsite/colab/ks.html",
     "title": "Katarzyna (Kasia) Sidorczuk",
     "section": "",
-    "text": "📝 Bio\n\nHi! My name is Katarzyna Sidorczuk and I’m a bioinformatician interested in gut microbiome and use of machine learning for analysis of biological data.\nDuring my PhD I worked with BioGenies and created multiple tools for prediction of peptide activity and protein localization. This led us to the work on negative data sampling for AMP prediction in which we showed that commonly used strategies introduce significance bias and leads to unreliable benchmarks.\nCurrently, I’m a postdoc in the Hildebrand group at the Quadram Institute, where I work with strain-resolved metagenomics. I’m interested in evolution of gut microbiota, how microbes are transferred between family members, and what are the factors that contribute to successful colonization and persistence.\n\n\n📱 Contact\n\n  \n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n👏🏻 Conferences, workshops, training schools 🤝🏻"
+    "text": "📝 Bio\n\nHi! My name is Katarzyna Sidorczuk and I’m a bioinformatician interested in gut microbiome and use of machine learning for analysis of biological data.\nDuring my PhD I worked with BioGenies and created multiple tools for prediction of peptide activity and protein localization. This led us to the work on negative data sampling for AMP prediction in which we showed that commonly used strategies introduce significance bias and leads to unreliable benchmarks.\nCurrently, I’m a postdoc in the Hildebrand group at the Quadram Institute, where I work with strain-resolved metagenomics. I’m interested in evolution of gut microbiota, how microbes are transferred between family members, and what are the factors that contribute to successful colonization and persistence.\n\n\n📱 Contact\n\n  \n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n👏🏻 Conferences, workshops, training schools 🤝🏻\n\n\n\n\n\n\n\n\n\n📖 Publications\n\n\n\nError in mutate(., position = if_else(str_detect(doi, i), \"first\", position)) : \n  ℹ In argument: `position = if_else(str_detect(doi, i), \"first\",\n  position)`.\nCaused by error in `str_detect()`:\n! Can't recycle `string` (size 22) to match `pattern` (size 0).\nError in mutate(., corresponding = if_else(str_detect(doi, i), TRUE, corresponding)) : \n  ℹ In argument: `corresponding = if_else(str_detect(doi, i), TRUE,\n  corresponding)`.\nCaused by error in `str_detect()`:\n! Can't recycle `string` (size 22) to match `pattern` (size 0)."
   },
   {
     "objectID": "subsite/colab/ea.html",
@@ -760,7 +760,7 @@
     "href": "subsite/posts/2025_02_24.html",
     "title": "Farewell to Ronja – our first Erasmus+ student! 🇩🇪💙",
     "section": "",
-    "text": "Ronja’s Praxissemester with us has officially come to an end 😢. It feels like just yesterday she arrived, and now we’re saying goodbye to an amazing colleague and friend. We made sure her last days were filled with great memories!\n\n\n\nAs per BioGenies tradition, we ate a lot during these last days! 🥟🍰\n\n\n\n\nWe took a trip to Suprasł, where we learned how to read icons and soaked in the local history! 🎨\nRonja’s friend, Robin, also joined us to help her on her return trip, and he got to experience Supraśl with us as well! 🚗🌲\n \n \n\n\n\nBetween science and sightseeing, we even managed to learn some German and Polish together! 🇩🇪🇵🇱\n\n\n\n\n\n\n\n\nAnd of course, what would a BioGenies goodbye be without rushing to the train station at the last minute? As always, we were very late 😆 🏃‍♂️💨\n \nThe train station was bustling with people, and in a surprise twist, the Jagiellonia Białystok football team was also there, taking the train! ⚽😲\nRonja, thank you for everything – your dedication, hard work, and all the fun moments we shared. We’ll miss you, but we know you’ll do amazing things in the future! 💙"
+    "text": "Ronja’s Praxissemester with us has officially come to an end 😢. It feels like just yesterday she arrived, and now we’re saying goodbye to an amazing colleague and friend. We made sure her last days were filled with great memories!\n\n\nAs per BioGenies tradition, we ate a lot during these last days! 🥟🍰\n\n\n\n\nWe took a trip to Suprasł, where we learned how to read icons and soaked in the local history! 🎨\nRonja’s friend, Robin, also joined us to help her on her return trip, and he got to experience Supraśl with us as well! 🚗🌲\n \n \n\n\n\nBetween science and sightseeing, we even managed to learn some German and Polish together! 🇩🇪🇵🇱\n\n\n\n\n\n\n\n\nAnd of course, what would a BioGenies goodbye be without rushing to the train station at the last minute? As always, we were very late 😆 🏃‍♂️💨\n \nThe train station was bustling with people, and in a surprise twist, the Jagiellonia Białystok football team was also there, taking the train! ⚽😲\nRonja, thank you for everything – your dedication, hard work, and all the fun moments we shared. We’ll miss you, but we know you’ll do amazing things in the future! 💙"
   },
   {
     "objectID": "subsite/posts/2025_02_24.html#eating-our-way-through-farewell-week",
@@ -858,7 +858,7 @@
     "href": "subsite/team/vi.html",
     "title": "Valentín Iglesias",
     "section": "",
-    "text": "📱 Contact\n\n    \n\n\n🚀 Research stays\n\n\n\n\n\n\n\n\n\n💻🧫 Experience\n\n\n\n\n\n\n\n\n\n🎓 Education\n\n\n Universitat Autònoma de Barcelona\n\n\nBiochemistry, Molecular Biology and Biomedicine (PhD Programme in Biochemistry, Molecular Biology and Biomedicine\n\n2025-02-25 - 2025-02-25 PhD thesis: Bioinformatic analysis on the determinants of protein aggregation and conformational conversion 📍 Bellaterra, Spain\n\n Universitat Autònoma de Barcelona\n\n\nBiochemistry\n\n2025-02-25 - 2025-02-25 📍 Bellaterra, Spain\n\n Universitat Autònoma de Barcelona\n\n\nAdvanced Biotechnology\n\n2025-02-25 - 2025-02-25 📍 Bellaterra, Spain\n\n Universitat de Girona\n\n\nMolecular Biology and Biomedicine\n\n2025-02-25 - 2025-02-25 📍 Girona, Spain\n\n\n👏🏻 Conferences, workshops, training schools 🤝🏻\n\n\n\n\n\n\n\n\n\n📖 Publications"
+    "text": "📱 Contact\n\n    \n\n\n🚀 Research stays\n\n\n\n\n\n\n\n\n\n💻🧫 Experience\n\n\n\n\n\n\n\n\n\n🎓 Education\n\n\n Universitat Autònoma de Barcelona\n\n\nBiochemistry, Molecular Biology and Biomedicine (PhD Programme in Biochemistry, Molecular Biology and Biomedicine\n\n2025-02-25 - 2025-02-25 PhD thesis: Bioinformatic analysis on the determinants of protein aggregation and conformational conversion 📍 Bellaterra, Spain\n\n Universitat Autònoma de Barcelona\n\n\nBiochemistry\n\n2025-02-25 - 2025-02-25 📍 Bellaterra, Spain\n\n Universitat Autònoma de Barcelona\n\n\nAdvanced Biotechnology\n\n2025-02-25 - 2025-02-25 📍 Bellaterra, Spain\n\n Universitat de Girona\n\n\nMolecular Biology and Biomedicine\n\n2025-02-25 - 2025-02-25 📍 Girona, Spain\n\n\n👏🏻 Conferences, workshops, training schools 🤝🏻\n\n\n\n\n\n\n\n\n\n📖 Publications\n\n\n\nError in mutate(., position = if_else(str_detect(doi, i), \"first\", position)) : \n  ℹ In argument: `position = if_else(str_detect(doi, i), \"first\",\n  position)`.\nCaused by error in `str_detect()`:\n! Can't recycle `string` (size 51) to match `pattern` (size 0).\nError in mutate(., corresponding = if_else(str_detect(doi, i), TRUE, corresponding)) : \n  ℹ In argument: `corresponding = if_else(str_detect(doi, i), TRUE,\n  corresponding)`.\nCaused by error in `str_detect()`:\n! Can't recycle `string` (size 51) to match `pattern` (size 0)."
   },
   {
     "objectID": "subsite/team.html",