diff --git a/DESCRIPTION b/DESCRIPTION
index ad9106d..b002ddb 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -9,7 +9,7 @@ License: `use_mit_license()`, `use_gpl3_license()` or friends to pick a
     license
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 Imports: 
     mvbutils,
     tools
diff --git a/TextAnalysis/top10_analysis.R b/TextAnalysis/top10_analysis.R
index 99c1b5f..26aa218 100644
--- a/TextAnalysis/top10_analysis.R
+++ b/TextAnalysis/top10_analysis.R
@@ -3,20 +3,20 @@ library(here)
 library(pdftools)
 library(tm)
 library(stringr)
-library(xlsx)
-library(ggplot2)
-library(patchwork) #devtools::install_github("thomasp85/patchwork")
 library(wordcloud)
 library(RColorBrewer)
+library(ggplot2)
+library(scales)
+library(viridis)
 
 # Define keyword ---------------------------------------------------------------
 
-z <- data.frame(
-  keyword = c(
-    "instantaneous mortality rate|z"
-  ),
-  group = "instantaneous mortality rate"
-)
+# z <- data.frame(
+#   keyword = c(
+#     "instantaneous total mortality rate|z"
+#   ),
+#   group = "instantaneous mortality rate"
+# )
 
 spawning_biomass <- data.frame(
   keyword = c(
@@ -33,10 +33,8 @@ cpue <- data.frame(
     "catch per unit effort|cpue",
     "catch rate", 
     "index of abundance",
-    "standardized fishery catch time series",
     "catch per effort",
-    "fishing success",
-    "availability"
+    "fishing success"
   ),
   group = "catch per unit effort"
 )
@@ -44,7 +42,8 @@ cpue <- data.frame(
 catch <- data.frame(
   keyword = c(
     "catch",
-    "total mortality"
+    "total mortality", 
+    "harvest"
   ),
   group = "catch"
 )
@@ -52,8 +51,7 @@ catch <- data.frame(
 landings <- data.frame(
   keyword = c(
     "landings",
-    "retained catch",
-    "wanted catch"
+    "retained catch"
   ),
   group = "landings"
 )
@@ -75,13 +73,13 @@ sex <- data.frame(
   group = "sex"
 )
 
-spr <- data.frame(
-  keyword = c(
-    "spawner per recruit|spr",
-    "30%spr|spr30%|30spr|spr30"
-  ),
-  group = "spawner per recruit"
-)
+# spr <- data.frame(
+#   keyword = c(
+#     "spawner per recruit|spr",
+#     "spawning potential ratio"
+#   ),
+#   group = "spawner per recruit"
+# )
 
 weight <- data.frame(
   keyword = c(
@@ -102,8 +100,8 @@ lnr0 <- data.frame(
   group = "natural log of unfished recruitment"
 )
 
-keyword_map <- rbind(z, spawning_biomass, cpue, catch, landings,
-                 projection, sex, spr, weight, lnr0)
+keyword_map <- rbind(catch, cpue, landings,
+                     lnr0, projection, sex, spawning_biomass, weight)
 keyword_map$keyword_id <- as.factor(1:nrow(keyword_map))
 keyword <- keyword_map$keyword
 
@@ -114,7 +112,7 @@ subfolder_path <- list.dirs(path = working_path, full.names = TRUE, recursive =
 subfolder_name <- list.dirs(path = working_path, full.names = FALSE, recursive = FALSE)
 
 # Create keyword database
-col_name <- c("ID", "Science_Center", "File_Path", keyword)
+col_name <- c("ID", "Source", "File_Path", keyword)
 frequency_database <- presence_database <- proportion_database <- 
   data.frame(matrix(NA, ncol = length(col_name))) 
 colnames(frequency_database) <- colnames(presence_database) <- colnames(proportion_database) <- 
@@ -216,47 +214,60 @@ proportion_database <- rbind(
 )
 proportion_database[nrow(proportion_database), "ID"] <- "Sum"
 
-xlsx_path <- here::here("TextAnalysis", "top10_analysis.xlsx")
-xlsx::write.xlsx(frequency_database, file=xlsx_path, sheetName="frequency", row.names=FALSE)
-xlsx::write.xlsx(presence_database, file=xlsx_path, sheetName="presence", append=TRUE, row.names=FALSE)
-xlsx::write.xlsx(proportion_database, file=xlsx_path, sheetName="proportion", append=TRUE, row.names=FALSE)
+write.csv(frequency_database, file=here::here("TextAnalysis", "top10_frequency.csv"), row.names=FALSE)
+write.csv(presence_database, file=here::here("TextAnalysis", "top10_presence.csv"), row.names=FALSE)
+write.csv(proportion_database, file=here::here("TextAnalysis", "top10_proportion.csv"), row.names=FALSE)
 
 # Upload xlsx to Google Drive
-# Google Drive folder id
-id_googledrive <- "1BUsYYd11lE2TECqHru5tX6LwkMniVnKv"
-googledrive::drive_upload(media = xlsx_path, path = as_id(id_googledrive), overwrite = TRUE, type="spreadsheet")
+authorize_GoogleDrive <- FALSE
+if (authorize_GoogleDrive) {
+  # Google Drive folder id
+  id_googledrive <- "1BUsYYd11lE2TECqHru5tX6LwkMniVnKv"
+  googledrive::drive_upload(media = xlsx_path, path = as_id(id_googledrive), overwrite = TRUE, type="spreadsheet")
+}
 
 # Plot results ------------------------------------------------------------
-xlsx_path <- here::here("TextAnalysis", "top10_analysis.xlsx")
-frequency_database <- xlsx::read.xlsx(file=xlsx_path, sheetName="frequency")
-presence_database<-xlsx::read.xlsx(file=xlsx_path, sheetName="presence")
-proportion_database<-xlsx::read.xlsx(file=xlsx_path, sheetName="proportion")
+frequency_database <- read.csv(file=here::here("TextAnalysis", "top10_frequency.csv"))
+presence_database<-read.csv(file=here::here("TextAnalysis", "top10_presence.csv"))
+proportion_database<-read.csv(file=here::here("TextAnalysis", "top10_proportion.csv"))
 
 colnames(presence_database) <- col_name
 data_reshape <- reshape2::melt(
   presence_database[, c(2, 4:ncol(presence_database))],
-  id = c("Science_Center")
+  id = c("Source")
 )
-colnames(data_reshape) <- c("Science_Center", "keyword", "value")
+colnames(data_reshape) <- c("Source", "keyword", "value")
 
 data_merge <- merge(data_reshape, keyword_map, by= "keyword")
 
-sum_by_group <- aggregate(value ~ keyword+keyword_id+group+Science_Center, data = data_merge, sum)
+sum_by_group <- aggregate(value ~ keyword+keyword_id+group+Source, data = data_merge, sum)
 sum_by_group <- sum_by_group[order(sum_by_group$keyword_id),]
 group <- unique(sum_by_group$group)
-figure <- vector(mode="list", length=length(group))
 
-for (i in 1:length(group)){
-  figure[[i]] <- ggplot(data = sum_by_group[sum_by_group$group==group[i], ], aes(x=keyword_id, y=value, fill=Science_Center)) +
-    geom_bar(position='dodge', stat='identity') +
-    labs(
-      x = group[i],
-      y = "Frequency"
-    )+
-    theme_bw()
-}
+jpeg(filename = here::here("TextAnalysis", "top10_barplot_sum.jpg"), width=200, height=150, units="mm", res=1200)
+ggplot(sum_by_group, aes(fill=Source, y=value, x=keyword_id)) + 
+  geom_bar(position="dodge", stat="identity") +
+  facet_wrap(~group, scales = "free_x") +
+  labs(
+    x = "Term ID",
+    y = "Frequency"
+  ) +
+  scale_fill_viridis(discrete = TRUE) +
+  theme_bw()
+dev.off()
+
+mean_by_group <- aggregate(value ~ keyword+keyword_id+group+Source, data = data_merge, mean)
+mean_by_group <- mean_by_group[order(mean_by_group$keyword_id),]
+group <- unique(mean_by_group$group)
 
-jpeg(filename = here::here("TextAnalysis", "top10_barplot.jpg"), width=300, height=270, units="mm", res=1200)
-(figure[[1]] + figure[[2]] + figure[[3]] + figure[[4]] + figure[[5]])/
-  (figure[[6]] + figure[[7]] + figure[[8]] + figure[[9]] + figure[[10]])
+jpeg(filename = here::here("TextAnalysis", "top10_barplot_mean.jpg"), width=200, height=150, units="mm", res=1200)
+ggplot(mean_by_group, aes(fill=Source, y=value*100, x=keyword_id)) + 
+  geom_bar(position="dodge", stat="identity") +
+  facet_wrap(~group, scales = "free_x") +
+  labs(
+    x = "Term ID",
+    y = "Presence (%)"
+  ) +
+  scale_fill_viridis(discrete = TRUE) +
+  theme_bw()
 dev.off()
diff --git a/TextAnalysis/top10_analysis.xlsx b/TextAnalysis/top10_analysis.xlsx
deleted file mode 100644
index af9264a..0000000
Binary files a/TextAnalysis/top10_analysis.xlsx and /dev/null differ
diff --git a/TextAnalysis/top10_barplot.jpg b/TextAnalysis/top10_barplot.jpg
deleted file mode 100644
index aba27f7..0000000
Binary files a/TextAnalysis/top10_barplot.jpg and /dev/null differ
diff --git a/TextAnalysis/top10_barplot_mean.jpg b/TextAnalysis/top10_barplot_mean.jpg
new file mode 100644
index 0000000..4f1208a
Binary files /dev/null and b/TextAnalysis/top10_barplot_mean.jpg differ
diff --git a/TextAnalysis/top10_barplot_sum.jpg b/TextAnalysis/top10_barplot_sum.jpg
new file mode 100644
index 0000000..9b46845
Binary files /dev/null and b/TextAnalysis/top10_barplot_sum.jpg differ
diff --git a/TextAnalysis/top10_frequency.csv b/TextAnalysis/top10_frequency.csv
new file mode 100644
index 0000000..2048c70
--- /dev/null
+++ b/TextAnalysis/top10_frequency.csv
@@ -0,0 +1,105 @@
+"ID","Source","File_Path","catch","total mortality","harvest","catch per unit effort|cpue","catch rate","index of abundance","catch per effort","fishing success","landings","retained catch","natural log of unfished recruitment|lnr0","logr0","logr_0","log(r0)","r0","projection","forecast","prediction","sex","gender","spawning biomass|sb","spawning stock biomass|ssb","spawning output","spawning stock output|sso","weight","mass"
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+"47","NOAA-NEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NEFSC/2021_summer_flounder_MTA_report.pdf",20,0,1,0,0,0,0,0,14,0,0,0,0,0,0,5,0,0,1,0,29,40,0,0,0,0
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diff --git a/TextAnalysis/top10_presence.csv b/TextAnalysis/top10_presence.csv
new file mode 100644
index 0000000..ab86ac9
--- /dev/null
+++ b/TextAnalysis/top10_presence.csv
@@ -0,0 +1,105 @@
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diff --git a/TextAnalysis/top10_proportion.csv b/TextAnalysis/top10_proportion.csv
new file mode 100644
index 0000000..49ef241
--- /dev/null
+++ b/TextAnalysis/top10_proportion.csv
@@ -0,0 +1,105 @@
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+"64","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/hake-assessment-post-srg-final_20210303.pdf",0.08,0,0.02,0,0,0,0,0,0.01,0,0,0,0,0,0.01,0,0.01,0,0,0,0.05,0,0,0,0.01,0
+"65","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/Longnose skate 2019_FINAL.pdf",0.08,0,0,0,0,0,0,0,0.07,0,0.01,0,0,0,0,0,0,0,0,0,0.03,0,0.01,0,0.01,0
+"66","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/PacificOceanPerch2017_Assessment_Final.pdf",0.04,0,0.01,0.01,0,0.01,0,0,0.03,0,0,0,0,0,0,0,0,0,0.01,0,0,0,0.04,0,0.02,0
+"67","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/sablefish_20191022.pdf",0.05,0,0.01,0,0,0,0,0,0.02,0,0,0,0,0,0,0,0,0,0,0,0.02,0,0,0,0.01,0
+"68","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/WidowAssessment2015.pdf",0.02,0,0,0,0,0,0,0,0.05,0,0,0,0,0,0,0,0,0,0,0,0.02,0,0,0,0.01,0
+"69","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/Yelloweye rockfish 2017.pdf",0.07,0,0,0.01,0,0,0,0,0.02,0,0,0,0,0,0,0,0,0,0,0,0,0,0.03,0,0,0
+"70","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/Yellowtail rockfish 2017.pdf",0.05,0,0.01,0.01,0,0,0,0,0.02,0,0,0,0,0,0,0,0,0,0,0,0,0,0.02,0,0.01,0
+"71","NOAA-PIFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-PIFSC/NMFS-PIFSC-60.pdf",0.21,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.01,0
+"72","NOAA-PIFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-PIFSC/noaa_17252_DS1.pdf",0.13,0,0.03,0.08,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.01,0
+"73","NOAA-PIFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-PIFSC/noaa_20062_DS1.pdf",0.18,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+"74","NOAA-PIFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-PIFSC/noaa_21164_DS1.pdf",0.13,0,0.08,0.07,0,0,0,0,0,0,0,0,0,0,0,0.01,0,0,0,0,0,0,0,0,0,0
+"75","NOAA-PIFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-PIFSC/SA-WP-06-[SP-alb-assessment] Rev 1.pdf",0.05,0,0,0.04,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.07,0,0,0,0.01,0
+"76","NOAA-PIFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-PIFSC/SC14-SA-WP-08 Silky shark stock assessment (1).pdf",0.1,0,0,0.1,0.02,0,0,0,0,0,0,0,0,0,0,0,0,0,0.01,0,0.01,0,0,0,0,0
+"77","NOAA-PIFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-PIFSC/SC15-SA-WP-05 SKJ-Assessment REV2 (1).pdf",0.03,0,0,0.04,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.09,0,0,0,0.01,0
+"78","NOAA-PIFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-PIFSC/SC15-SA-WP-06 Oceanic whitetip shark_assessment.pdf",0.12,0,0,0.03,0,0,0,0,0,0,0,0,0,0,0,0,0,0.01,0,0,0.06,0,0,0,0,0
+"79","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/05.-Traditional-Interim-assessment-report-RS-002-1.pdf",0.13,0,0.02,0,0,0.01,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.08,0
+"80","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/08b.-SEDAR61_2021IA_Final.pdf",0.12,0,0.04,0,0,0.05,0,0,0.03,0,0,0,0,0,0,0.01,0,0,0,0,0,0,0,0,0.06,0
+"81","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/2019_WHM_SA_ENG.pdf",0.06,0,0,0.04,0,0,0,0,0.01,0,0,0,0,0,0,0.01,0,0,0.01,0,0,0.01,0,0,0,0
+"82","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/2020_ALB_ENG.pdf",0.05,0,0,0.09,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.02,0
+"83","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/2021_WBFT_SA_ENG.pdf",0.03,0,0,0.01,0,0,0,0,0,0,0,0,0,0,0.01,0.01,0,0,0,0,0.03,0.03,0,0,0,0
+"84","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/Atl_Blacknose_SAR.pdf",0.06,0,0,0.04,0,0,0,0,0.02,0,0,0,0,0,0,0.01,0,0,0,0,0,0,0,0,0.01,0
+"85","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/B-8a-Gray_triggerfish_interim_9102020.pdf",0.14,0,0.03,0,0,0.02,0,0,0.03,0,0,0,0,0,0,0.01,0,0,0,0,0,0,0,0,0.06,0
+"86","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/Dusky_update_report_2016.pdf",0.03,0,0,0.01,0,0,0,0,0.01,0,0,0,0,0,0.01,0.01,0,0,0,0,0,0,0,0,0.01,0
+"87","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/KGM_GOM_SA_08282020_final-revision_3.pdf",0.03,0,0.01,0.01,0,0.01,0,0,0.09,0.02,0,0,0,0,0.01,0,0,0,0.01,0,0.04,0.08,0.01,0,0,0
+"88","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/S23_SAR_complete_and_final.pdf",0.03,0,0.02,0,0,0,0,0,0.05,0,0,0,0,0,0,0.01,0,0,0,0,0.02,0.03,0,0,0.01,0
+"89","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/S28UpdateSAR_V2.pdf",0.01,0,0.01,0.02,0,0,0,0,0.06,0,0,0,0,0,0,0,0,0,0,0,0.03,0.05,0,0,0.01,0
+"90","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/S34_ATSH_SAR.pdf",0.04,0,0.01,0.01,0,0,0,0,0.01,0,0,0,0,0,0.01,0.03,0,0,0,0,0,0,0,0,0.01,0
+"91","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/S51_FINAL_SAR_0.pdf",0.02,0,0,0.01,0,0,0,0,0.06,0,0,0,0,0,0,0,0,0,0,0,0.01,0.01,0,0,0.01,0
+"92","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/S52_Final_SAR_v2.pdf",0.01,0,0,0.01,0,0,0,0,0.01,0,0,0,0,0,0,0,0,0,0,0,0.01,0.01,0,0,0,0
+"93","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/S57_Final_SAR.pdf",0.02,0,0.01,0.01,0,0,0,0,0.07,0,0,0,0,0,0.02,0,0,0,0,0,0.01,0,0.01,0,0.01,0
+"94","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/S64_SAR_FINAL.pdf",0.02,0,0.01,0.01,0,0,0,0,0.05,0,0,0,0,0,0,0,0,0,0,0,0.01,0.02,0,0,0.01,0
+"95","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/S67_Final_SAR.pdf",0.03,0,0.01,0.03,0,0,0,0,0.04,0,0,0,0,0,0,0,0.01,0,0,0,0.03,0.04,0,0,0.01,0
+"96","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/S72_SAR_FINAL.pdf",0.01,0,0.01,0.02,0,0,0,0,0.04,0,0,0,0,0,0,0,0,0,0,0,0.06,0.06,0,0,0.03,0
+"97","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/SA BSB 2018.pdf",0.01,0,0.01,0,0,0,0,0,0.05,0,0,0,0,0,0,0.01,0,0,0,0,0.03,0.02,0,0,0.02,0
+"98","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/SEDAR_60_SA_Red_Porgy_SAR_4.9.2020.pdf",0.01,0,0.01,0,0,0,0,0,0.06,0,0,0,0,0,0,0.01,0,0,0,0,0.04,0.03,0,0,0.02,0
+"99","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/SEDAR65_FullSAR_12.8.2020_V3.pdf",0.04,0,0,0.01,0,0,0,0,0.02,0,0,0,0,0,0,0.02,0,0,0.01,0,0,0,0,0,0.01,0
+"100","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/SMA_ASS_ENG.pdf",0.12,0,0.01,0.06,0,0,0,0,0.01,0,0,0,0,0,0,0,0,0,0,0,0.01,0,0,0,0.01,0
+"101","NOAA-SWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SWFSC/agenda-item-d-3.pdf",0.02,0,0.01,0,0,0,0,0,0.02,0,0,0,0,0,0,0,0.01,0,0.01,0,0.02,0.02,0,0,0.01,0
+"102","NOAA-SWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SWFSC/SAC-11-07-MTG_Yellowfin tuna benchmark assessment 2019.pdf",0.05,0,0,0.01,0,0.02,0,0,0,0.01,0,0,0,0,0,0,0,0,0,0,0.03,0,0,0,0.01,0
+"103","NOAA-SWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SWFSC/SC14-SA-WP-11 ISC18 Shortfin Mako Stock Assessment.pdf",0.1,0,0,0.07,0,0,0,0,0,0,0,0.01,0,0.01,0.01,0,0.01,0,0.01,0,0,0,0,0,0.01,0
+"Sum",NA,NA,8.31,0.03,1.23,1.65,0.21,0.18,0,0,2.69,0.12,0.05,0.01,0,0.01,0.1,0.47,0.11,0.03,0.26,0.03,2.31,1.79,0.29,0,0.99,0.02
diff --git a/TextAnalysis/top20_analysis.R b/TextAnalysis/top20_analysis.R
index c722810..eb2a6c8 100644
--- a/TextAnalysis/top20_analysis.R
+++ b/TextAnalysis/top20_analysis.R
@@ -3,268 +3,298 @@ library(here)
 library(pdftools)
 library(tm)
 library(stringr)
-library(xlsx)
 library(wordcloud)
 library(RColorBrewer)
 
 # Download stock assessment reports from Google Drive -------------
 
-# googledrive set-up: https://github.com/nmfs-openscapes/GoogleDrive1
-download_assessments <- function(googledrive_url, folder_name, subfolder_name) {
+## If authorize_GoogleDrive <- TRUE:
+## Users need to authorize googledrive package to access your Google Drive
+## Please follow the instructions from https://googledrive.tidyverse.org/reference/drive_auth.html and https://github.com/nmfs-openscapes/GoogleDrive1 to
+## authorize googledrive
 
-  # Get the files in the folder
-  dir_files <- googledrive::drive_ls(path = googledrive_url)
-  file_name <- dir_files$name
+## If authorize_GoogleDrive <- FALSE:
+## Users need to manually download stock assessment reports from the
+## Assessment Docs Google Drive folder (https://drive.google.com/drive/folders/1uyLVjf7Xu2iMY6dhEjAAkB4l2vtSDMw9?usp=share_link) to fishdictionary/StockAssessment folder
+## The folder structure looks
 
-  # Create folders to save downloaded files
-  if (!dir.exists(here::here(folder_name))) dir.create(here::here(folder_name))
-  if (!dir.exists(here::here(folder_name, subfolder_name))) dir.create(here::here(folder_name, subfolder_name))
+authorize_GoogleDrive <- FALSE
+if (authorize_GoogleDrive) {
+  # googledrive set-up: https://github.com/nmfs-openscapes/GoogleDrive1
+  download_assessments <- function(googledrive_url, folder_name, subfolder_name) {
 
-  # Download files from Google Drive
-  for (i in 1:length(dir_files$id)) {
-    googledrive::drive_download(file = dir_files$id[i], overwrite = TRUE, path = here::here(folder_name, subfolder_name, file_name[i]))
-  }
-}
-
-# Download AFSC stock assessment reports
-download_assessments(
-  googledrive_url = "https://drive.google.com/drive/folders/1vbxiADIsjnCPGyOf-v4zTexOUSTidMTA",
-  folder_name = file.path("StockAssessment"),
-  subfolder_name = "AFSC"
-)
+    # Get the files in the folder
+    dir_files <- googledrive::drive_ls(path = googledrive_url)
+    file_name <- dir_files$name
 
-# Download NEFSC stock assessment reports
-download_assessments(
-  googledrive_url = "https://drive.google.com/drive/folders/1edP73M7Bd4SpGLsgXIS8-jlqclA1QTZ9",
-  folder_name = file.path("StockAssessment"),
-  subfolder_name = "NEFSC"
-)
-
-# Download NWFSC stock assessment reports
-download_assessments(
-  googledrive_url = "https://drive.google.com/drive/folders/1UHv3f7JDkz3T6OUFNGiurBZIWR_EzyQq",
-  folder_name = file.path("StockAssessment"),
-  subfolder_name = "NWFSC"
-)
+    # Create folders to save downloaded files
+    if (!dir.exists(here::here(folder_name))) dir.create(here::here(folder_name))
+    if (!dir.exists(here::here(folder_name, subfolder_name))) dir.create(here::here(folder_name, subfolder_name))
 
-# Download PIFSC stock assessment reports
-download_assessments(
-  googledrive_url = "https://drive.google.com/drive/folders/11I-3gwehVMEK_0aAkuytijNs7PXsu_e-",
-  folder_name = file.path("StockAssessment"),
-  subfolder_name = "PIFSC"
-)
-
-# Download SEFSC stock assessment reports
-download_assessments(
-  googledrive_url = "https://drive.google.com/drive/folders/12-09nqC7CvKfL2j1JX8ooi_bgMob2c1I",
-  folder_name = file.path("StockAssessment"),
-  subfolder_name = "SEFSC"
-)
+    # Download files from Google Drive
+    for (i in 1:length(dir_files$id)) {
+      googledrive::drive_download(file = dir_files$id[i], overwrite = TRUE, path = here::here(folder_name, subfolder_name, file_name[i]))
+    }
+  }
 
-# Download SWFSC stock assessment reports
-download_assessments(
-  googledrive_url = "https://drive.google.com/drive/folders/1IqbncWlwbSwmBKroIfo-C9ckI_uGe6NG",
-  folder_name = file.path("StockAssessment"),
-  subfolder_name = "SWFSC"
-)
+  # Download AFSC stock assessment reports
+  download_assessments(
+    googledrive_url = "https://drive.google.com/drive/folders/1vbxiADIsjnCPGyOf-v4zTexOUSTidMTA",
+    folder_name = file.path("StockAssessment"),
+    subfolder_name = "AFSC"
+  )
+
+  # Download NEFSC stock assessment reports
+  download_assessments(
+    googledrive_url = "https://drive.google.com/drive/folders/1edP73M7Bd4SpGLsgXIS8-jlqclA1QTZ9",
+    folder_name = file.path("StockAssessment"),
+    subfolder_name = "NEFSC"
+  )
+
+  # Download NWFSC stock assessment reports
+  download_assessments(
+    googledrive_url = "https://drive.google.com/drive/folders/1UHv3f7JDkz3T6OUFNGiurBZIWR_EzyQq",
+    folder_name = file.path("StockAssessment"),
+    subfolder_name = "NWFSC"
+  )
+
+  # Download PIFSC stock assessment reports
+  download_assessments(
+    googledrive_url = "https://drive.google.com/drive/folders/11I-3gwehVMEK_0aAkuytijNs7PXsu_e-",
+    folder_name = file.path("StockAssessment"),
+    subfolder_name = "PIFSC"
+  )
+
+  # Download SEFSC stock assessment reports
+  download_assessments(
+    googledrive_url = "https://drive.google.com/drive/folders/12-09nqC7CvKfL2j1JX8ooi_bgMob2c1I",
+    folder_name = file.path("StockAssessment"),
+    subfolder_name = "SEFSC"
+  )
+
+  # Download SWFSC stock assessment reports
+  download_assessments(
+    googledrive_url = "https://drive.google.com/drive/folders/1IqbncWlwbSwmBKroIfo-C9ckI_uGe6NG",
+    folder_name = file.path("StockAssessment"),
+    subfolder_name = "SWFSC"
+  )
+}
 
 # Define keyword ---------------------------------------------------------------
 
 keyword <- c(
   "biomass|b|abundance",
-  "spawning biomass|sb|spawning stock biomass|ssb|spawning stock output|sso|spawning output",
+  "spawning biomass|sb|spawning stock biomass|ssb|spawning stock output|sso|mature biomass|spawners",
   "unfished|virgin|initial|equilibrium|unfished equilibrium",
-  "recruits|age-0 fish",
-  "catch|total mortality",
-  "landings|retained catch|wanted catch",
-  "catch per unit effort|cpue|catch rate|index of abundance|standardized fishery catch time series|catch per effort|fishing success|availability",
-  "maximum sustainable yield|msy|msyproxy",
-  "instantaneous mortality rate|z",
-  "instantaneous fishing mortality rate|f|harvest rate|exploitation rate|finite fishing mortality|apical f",
-  "fishing mortality at maximum sustainable yield|fproxy|f_msy|fmsy",
-  "spawning per recruit|spr|spr30%|30%spr",
-  "weight|kg|mass",
+  "recruitment",
+  "recruits|recruit|age-0 fish|age-1 fish",
+  "catch|total mortality|harvest",
+  "catch per unit effort|cpue|catch rate|index of abundance|catch per effort|fishing success",
+  "landings|retained catch",
+  "spawning per recruit|spawning potential ratio|spr",
+  "maximum sustainable yield|msy",
+  "instantaneous total mortality rate|z",
+  "fishing mortality rate|f|instantaneous fishing mortality rate|harvest rate|exploitation rate|finite fishing mortality|apical f",
+  "fishing mortality at maximum sustainable yield|fmsy",
+  "weight|mass",
   "length composition|length frequency|length observation",
   "age composition|age frequency|age observation",
   "projection|forecast|prediction",
   "sex|gender",
-  "natural log of unfished recruitment|logr0|lnr0|r0|log(r0)",
-  "plus group",
-  "cohort|recruit"
+  "natural log of unfished recruitment|lnr0|logr0|logr_0|log(r0)|r0",
+  "plus group"
 )
 
 # Create keywords database ----------------------------------------------------------------
 
 working_path <- here::here("StockAssessment")
-subfolder_path <- list.dirs(path = working_path, full.names = TRUE, recursive = FALSE)
-subfolder_name <- list.dirs(path = working_path, full.names = FALSE, recursive = FALSE)
-
-# Create keyword database
-col_name <- c("ID", "Science_Center", "File_Path", keyword)
-frequency_database <- presence_database <- proportion_database <-
-  data.frame(matrix(NA, ncol = length(col_name)))
-colnames(frequency_database) <- colnames(presence_database) <- colnames(proportion_database) <-
-  col_name
-
-for (subfolder_id in seq_along(subfolder_path)) {
-  file_path <- list.files(subfolder_path[subfolder_id], recursive = FALSE, full.names = TRUE)
-
-  for (file_id in seq_along(file_path)) {
-    file <- file_path[file_id]
-
-    # Create metadata of files
-    docs <- tm::Corpus(URISource(file),
-      readerControl = list(reader = readPDF)
-    )
-
-    # Convert symbols to space
-    toSpace <- tm::content_transformer(
-      function(x, pattern) gsub(pattern, " ", x)
-    )
-    docs <- tm::tm_map(docs, toSpace, "/")
-    docs <- tm::tm_map(docs, toSpace, "@")
-    docs <- tm::tm_map(docs, toSpace, "\\|")
-
-    # Convert text to lower case
-    docs <- tm::tm_map(
-      docs,
-      content_transformer(tolower)
-    )
-
-    # Remove punctuations
-    docs <- tm::tm_map(docs, removePunctuation)
-
-    # Eliminate extra white spaces
-    docs <- tm::tm_map(docs, stripWhitespace)
-
-    frequency <- presence <- proportion <- c()
-    for (keyword_id in seq_along(keyword)) {
-      # print(paste0("Folder: ", subfolder_id, "; File: ", file_id, "; Keyword: ", keyword_id))
-      frequency[keyword_id] <- sum(stringr::str_count(docs[[1]]$content, paste("\\b", keyword[keyword_id], "\\b", sep = ""))) # Match if the current position is a word boundary
-      presence[keyword_id] <- ifelse(frequency[keyword_id] > 0, 1, 0)
-      proportion[keyword_id] <- round(frequency[keyword_id] / sum(stringr::str_count(docs[[1]]$content)) * 100, digits = 2)
-    }
-
-    if (subfolder_id == 1 & file_id == 1) {
-      frequency_database[1, ] <- c(NA, subfolder_name[subfolder_id], file_path[file_id], frequency)
-
-      presence_database[1, ] <- c(NA, subfolder_name[subfolder_id], file_path[file_id], presence)
-
-      proportion_database[1, ] <- c(NA, subfolder_name[subfolder_id], file_path[file_id], proportion)
-    } else {
-      frequency_database <- rbind(
-        frequency_database,
-        c(NA, subfolder_name[subfolder_id], file_path[file_id], frequency)
+subfolder_path_all <- list.dirs(path = working_path, full.names = TRUE, recursive = FALSE)
+subfolder_name_all <- list.dirs(path = working_path, full.names = FALSE, recursive = FALSE)
+
+subfolder_info <- list(1, 2, 3:length(subfolder_path_all), 1:length(subfolder_path_all))
+names(subfolder_info) <- c("Australia", "ICES", "NOAA", "All")
+ 
+for (org in seq_along(subfolder_info)){
+  subfolder_path <- subfolder_path_all[subfolder_info[[org]]]
+  subfolder_name <- subfolder_name_all[subfolder_info[[org]]]
+  
+  # Create keyword database
+  col_name <- c("ID", "Source", "File_Path", keyword)
+  frequency_database <- 
+    presence_database <- 
+    proportion_database <-
+    data.frame(matrix(NA, ncol = length(col_name)))
+  
+  colnames(frequency_database) <- 
+    colnames(presence_database) <- 
+    colnames(proportion_database) <-
+    col_name
+  
+  for (subfolder_id in seq_along(subfolder_path)) {
+    
+    file_path <- list.files(subfolder_path[subfolder_id], recursive = FALSE, full.names = TRUE)
+    
+    for (file_id in seq_along(file_path)) {
+      
+      # cat("file:", file_path[file_id], "\n")
+      file <- file_path[file_id]
+      
+      # Create metadata of files
+      docs <- tm::Corpus(URISource(file),
+                         readerControl = list(reader = readPDF)
       )
-
-      presence_database <- rbind(
-        presence_database,
-        c(NA, subfolder_name[subfolder_id], file_path[file_id], presence)
+      
+      # Convert symbols to space
+      toSpace <- tm::content_transformer(
+        function(x, pattern) gsub(pattern, " ", x)
       )
-
-      proportion_database <- rbind(
-        proportion_database,
-        c(NA, subfolder_name[subfolder_id], file_path[file_id], proportion)
+      docs <- tm::tm_map(docs, toSpace, "/")
+      docs <- tm::tm_map(docs, toSpace, "@")
+      docs <- tm::tm_map(docs, toSpace, "\\|")
+      
+      # Convert text to lower case
+      docs <- tm::tm_map(
+        docs,
+        content_transformer(tolower)
       )
+      
+      # Remove punctuations
+      docs <- tm::tm_map(docs, removePunctuation)
+      
+      # Eliminate extra white spaces
+      docs <- tm::tm_map(docs, stripWhitespace)
+      
+      frequency <- presence <- proportion <- c()
+      for (keyword_id in seq_along(keyword)) {
+        # print(paste0("Folder: ", subfolder_id, "; File: ", file_id, "; Keyword: ", keyword_id))
+        frequency[keyword_id] <- sum(stringr::str_count(docs[[1]]$content, paste("\\b", keyword[keyword_id], "\\b", sep = ""))) # Match if the current position is a word boundary
+        presence[keyword_id] <- ifelse(frequency[keyword_id] > 0, 1, 0)
+        proportion[keyword_id] <- round(frequency[keyword_id] / sum(stringr::str_count(docs[[1]]$content)) * 100, digits = 2)
+      }
+      
+      if (subfolder_id == 1 & file_id == 1) {
+        frequency_database[1, ] <- c(NA, subfolder_name[subfolder_id], file_path[file_id], frequency)
+        
+        presence_database[1, ] <- c(NA, subfolder_name[subfolder_id], file_path[file_id], presence)
+        
+        proportion_database[1, ] <- c(NA, subfolder_name[subfolder_id], file_path[file_id], proportion)
+      } else {
+        frequency_database <- rbind(
+          frequency_database,
+          c(NA, subfolder_name[subfolder_id], file_path[file_id], frequency)
+        )
+        
+        presence_database <- rbind(
+          presence_database,
+          c(NA, subfolder_name[subfolder_id], file_path[file_id], presence)
+        )
+        
+        proportion_database <- rbind(
+          proportion_database,
+          c(NA, subfolder_name[subfolder_id], file_path[file_id], proportion)
+        )
+      }
     }
   }
+  
+  frequency_database$ID <- 1:nrow(frequency_database)
+  presence_database$ID <- 1:nrow(presence_database)
+  proportion_database$ID <- 1:nrow(proportion_database)
+  
+  frequency_database[, 4:ncol(frequency_database)] <- sapply(frequency_database[, 4:ncol(frequency_database)], as.numeric)
+  
+  frequency_database <- rbind(
+    frequency_database,
+    c(NA, NA, NA, apply(frequency_database[, 4:ncol(frequency_database)], 2, sum))
+  )
+  frequency_database[nrow(frequency_database), "ID"] <- "Sum"
+  
+  presence_database[, 4:ncol(presence_database)] <- sapply(presence_database[, 4:ncol(presence_database)], as.numeric)
+  presence_database <- rbind(
+    presence_database,
+    c(NA, NA, NA, apply(presence_database[, 4:ncol(presence_database)], 2, sum))
+  )
+  presence_database[nrow(presence_database), "ID"] <- "Sum"
+  
+  proportion_database[, 4:ncol(proportion_database)] <- sapply(proportion_database[, 4:ncol(proportion_database)], as.numeric)
+  proportion_database <- rbind(
+    proportion_database,
+    c(NA, NA, NA, apply(proportion_database[, 4:ncol(proportion_database)], 2, sum))
+  )
+  proportion_database[nrow(proportion_database), "ID"] <- "Sum"
+  
+  write.csv(frequency_database, file=here::here("TextAnalysis", paste0("top20_frequency_", names(subfolder_info)[org], ".csv")), row.names=FALSE)
+  write.csv(presence_database, file=here::here("TextAnalysis", paste0("top20_presence_", names(subfolder_info)[org], ".csv")), row.names=FALSE)
+  write.csv(proportion_database, file=here::here("TextAnalysis", paste0("top20_proportion_", names(subfolder_info)[org], ".csv")), row.names=FALSE)
+  # Upload xlsx to Google Drive
+  if (authorize_GoogleDrive) {
+    # Google Drive folder id
+    id_googledrive <- "1BUsYYd11lE2TECqHru5tX6LwkMniVnKv"
+    googledrive::drive_upload(media = xlsx_path, path = as_id(id_googledrive), overwrite = TRUE, type = "spreadsheet")
+  }
+  
+  # Plot results ------------------------------------------------------------
+  frequency_database <- read.csv(file=here::here("TextAnalysis", paste0("top20_frequency_", names(subfolder_info)[org], ".csv")))
+  presence_database<-read.csv(file=here::here("TextAnalysis", paste0("top20_presence_", names(subfolder_info)[org], ".csv")))
+  proportion_database<-read.csv(file=here::here("TextAnalysis", paste0("top20_proportion_", names(subfolder_info)[org], ".csv")))
+  
+  word_frequency <- as.matrix(frequency_database[frequency_database$ID == "Sum", 4:ncol(frequency_database)])
+  word_presence <- as.matrix(presence_database[presence_database$ID == "Sum", 4:ncol(presence_database)])
+  word_proportion <- as.matrix(proportion_database[proportion_database$ID == "Sum", 4:ncol(proportion_database)])
+  
+  xlabels <- c(
+    "biomass",
+    "spawning biomass",
+    "unfished",
+    "recruitment",
+    "recruit(s)",
+    "catch",
+    "catch per unit effort",
+    "landings",
+    "spawner per recruit",
+    "maximum sustainable yield",
+    "instantaneous total mortality rate",
+    "fishing mortality",
+    "FMSY",
+    "weight",
+    "length composition",
+    "age composition",
+    "projection",
+    "sex",
+    "natural log of unfished recruitment",
+    "plus group"
+  )
+  
+  # barplot
+  jpeg(filename = here::here("TextAnalysis", paste0("top20_barplot_", names(subfolder_info)[org], ".jpg")), width = 200, height = 120, units = "mm", res = 1200)
+  par(mar = c(6, 4, 1, 1), mfrow = c(3, 1))
+  frequency_barplot <- barplot(height = word_frequency, xaxt = "n", ylab = "Frequency")
+  text(frequency_barplot - 0.25, par("usr")[3] - 0.25, xlabels, xpd = TRUE, srt = 40, adj = 1, cex = 0.8)
+  
+  
+  presence_barplot <- barplot(height = word_presence, xaxt = "n", ylab = "Presence")
+  text(presence_barplot - 0.25, par("usr")[3] - 0.25, xlabels, xpd = TRUE, srt = 40, adj = 1, cex = 0.8)
+  
+  proportion_barplot <- barplot(height = word_proportion, xaxt = "n", ylab = "Proportion")
+  text(proportion_barplot - 0.25, par("usr")[3] - 0.25, xlabels, xpd = TRUE, srt = 40, adj = 1, cex = 0.8)
+  
+  dev.off()
+  
+  jpeg(filename = here::here("TextAnalysis", paste0("top20_presence_", names(subfolder_info)[org], ".jpg")), width = 200, height = 120, units = "mm", res = 1200)
+  par(mar = c(6, 4, 1, 1), mfrow = c(1, 1))
+  presence_barplot <- barplot(height = word_presence, xaxt = "n", ylab = "Frequency") # range: 26-83, median:68
+  text(presence_barplot - 0.25, par("usr")[3] - 0.25, xlabels, xpd = TRUE, srt = 40, adj = 1, cex = 0.7)
+  dev.off()
+  
+  # wordcloud figure
+  jpeg(filename = here::here("TextAnalysis", paste0("top20_wordcloud_", names(subfolder_info)[org], ".jpg")), width = 200, height = 200, units = "mm", res = 1200)
+  par(mar = c(1, 1, 1, 1), mfrow = c(1, 1))
+  wordcloud(
+    words = xlabels, freq = word_presence, rot.per = 0.35,
+    colors = brewer.pal(8, "Dark2")
+  )
+  dev.off()
+  
 }
 
-frequency_database$ID <- 1:nrow(frequency_database)
-presence_database$ID <- 1:nrow(presence_database)
-proportion_database$ID <- 1:nrow(proportion_database)
-
-frequency_database[, 4:ncol(frequency_database)] <- sapply(frequency_database[, 4:ncol(frequency_database)], as.numeric)
-
-frequency_database <- rbind(
-  frequency_database,
-  c(NA, NA, NA, apply(frequency_database[, 4:ncol(frequency_database)], 2, sum))
-)
-frequency_database[nrow(frequency_database), "ID"] <- "Sum"
-
-presence_database[, 4:ncol(presence_database)] <- sapply(presence_database[, 4:ncol(presence_database)], as.numeric)
-presence_database <- rbind(
-  presence_database,
-  c(NA, NA, NA, apply(presence_database[, 4:ncol(presence_database)], 2, sum))
-)
-presence_database[nrow(presence_database), "ID"] <- "Sum"
-
-proportion_database[, 4:ncol(proportion_database)] <- sapply(proportion_database[, 4:ncol(proportion_database)], as.numeric)
-proportion_database <- rbind(
-  proportion_database,
-  c(NA, NA, NA, apply(proportion_database[, 4:ncol(proportion_database)], 2, sum))
-)
-proportion_database[nrow(proportion_database), "ID"] <- "Sum"
-
-xlsx_path <- here::here("TextAnalysis", "top20_analysis.xlsx")
-xlsx::write.xlsx(frequency_database, file = xlsx_path, sheetName = "frequency", row.names = FALSE)
-xlsx::write.xlsx(presence_database, file = xlsx_path, sheetName = "presence", append = TRUE, row.names = FALSE)
-xlsx::write.xlsx(proportion_database, file = xlsx_path, sheetName = "proportion", append = TRUE, row.names = FALSE)
 
-# Upload xlsx to Google Drive
-# Google Drive folder id
-id_googledrive <- "1BUsYYd11lE2TECqHru5tX6LwkMniVnKv"
-googledrive::drive_upload(media = xlsx_path, path = as_id(id_googledrive), overwrite = TRUE, type = "spreadsheet")
-
-# Plot results ------------------------------------------------------------
-xlsx_path <- here::here("TextAnalysis", "top20_analysis.xlsx")
-frequency_database <- xlsx::read.xlsx(file = xlsx_path, sheetName = "frequency")
-presence_database <- xlsx::read.xlsx(file = xlsx_path, sheetName = "presence")
-proportion_database <- xlsx::read.xlsx(file = xlsx_path, sheetName = "proportion")
-
-word_frequency <- as.matrix(frequency_database[frequency_database$ID == "Sum", 4:ncol(frequency_database)])
-word_presence <- as.matrix(presence_database[presence_database$ID == "Sum", 4:ncol(presence_database)])
-word_proportion <- as.matrix(proportion_database[proportion_database$ID == "Sum", 4:ncol(proportion_database)])
-
-xlabels <- c(
-  "biomass",
-  "spawning biomass",
-  "unfished",
-  "recruitment",
-  "catch",
-  "landings",
-  "catch per unit effort",
-  "MSY",
-  "Z",
-  "F",
-  "FMSY",
-  "spawner per recruit",
-  "weight",
-  "length composition",
-  "age composition",
-  "projection",
-  "sex",
-  "natural log of unfished recruitment",
-  "plus group",
-  "cohort"
-)
-
-# barplot
-jpeg(filename = here::here("TextAnalysis", "top20_barplot.jpg"), width = 200, height = 120, units = "mm", res = 1200)
-par(mar = c(6, 4, 1, 1), mfrow = c(3, 1))
-frequency_barplot <- barplot(height = word_frequency, xaxt = "n", ylab = "Frequency")
-text(frequency_barplot - 0.25, par("usr")[3] - 0.25, xlabels, xpd = TRUE, srt = 40, adj = 1, cex = 0.8)
-
-
-presence_barplot <- barplot(height = word_presence, xaxt = "n", ylab = "Presence")
-text(presence_barplot - 0.25, par("usr")[3] - 0.25, xlabels, xpd = TRUE, srt = 40, adj = 1, cex = 0.8)
-
-proportion_barplot <- barplot(height = word_proportion, xaxt = "n", ylab = "Proportion")
-text(proportion_barplot - 0.25, par("usr")[3] - 0.25, xlabels, xpd = TRUE, srt = 40, adj = 1, cex = 0.8)
-
-dev.off()
-
-jpeg(filename = here::here("TextAnalysis", "top20_presence.jpg"), width = 200, height = 120, units = "mm", res = 1200)
-par(mar = c(6, 4, 1, 1), mfrow = c(1, 1))
-presence_barplot <- barplot(height = word_presence, xaxt = "n", ylab = "Frequency") # range: 26-84, median:67.5
-text(presence_barplot - 0.25, par("usr")[3] - 0.25, xlabels, xpd = TRUE, srt = 40, adj = 1, cex = 0.7)
-dev.off()
-
-# wordcloud figure
-jpeg(filename = here::here("TextAnalysis", "top20_wordcloud.jpg"), width = 200, height = 200, units = "mm", res = 1200)
-par(mar = c(1, 1, 1, 1), mfrow = c(1, 1))
-wordcloud(
-  words = xlabels, freq = word_presence, rot.per = 0.35,
-  colors = brewer.pal(8, "Dark2")
-)
-dev.off()
diff --git a/TextAnalysis/top20_analysis.xlsx b/TextAnalysis/top20_analysis.xlsx
deleted file mode 100644
index c7ec6c1..0000000
Binary files a/TextAnalysis/top20_analysis.xlsx and /dev/null differ
diff --git a/TextAnalysis/top20_barplot.jpg b/TextAnalysis/top20_barplot.jpg
deleted file mode 100644
index 5089d6a..0000000
Binary files a/TextAnalysis/top20_barplot.jpg and /dev/null differ
diff --git a/TextAnalysis/top20_barplot_All.jpg b/TextAnalysis/top20_barplot_All.jpg
new file mode 100644
index 0000000..f82ac0a
Binary files /dev/null and b/TextAnalysis/top20_barplot_All.jpg differ
diff --git a/TextAnalysis/top20_barplot_Australia.jpg b/TextAnalysis/top20_barplot_Australia.jpg
new file mode 100644
index 0000000..3dc410a
Binary files /dev/null and b/TextAnalysis/top20_barplot_Australia.jpg differ
diff --git a/TextAnalysis/top20_barplot_ICES.jpg b/TextAnalysis/top20_barplot_ICES.jpg
new file mode 100644
index 0000000..82766fd
Binary files /dev/null and b/TextAnalysis/top20_barplot_ICES.jpg differ
diff --git a/TextAnalysis/top20_barplot_NOAA.jpg b/TextAnalysis/top20_barplot_NOAA.jpg
new file mode 100644
index 0000000..84b5d6d
Binary files /dev/null and b/TextAnalysis/top20_barplot_NOAA.jpg differ
diff --git a/TextAnalysis/top20_frequency_All.csv b/TextAnalysis/top20_frequency_All.csv
new file mode 100644
index 0000000..2fbf09b
--- /dev/null
+++ b/TextAnalysis/top20_frequency_All.csv
@@ -0,0 +1,105 @@
+"ID","Source","File_Path","biomass|b|abundance","spawning biomass|sb|spawning stock biomass|ssb|spawning stock output|sso|mature biomass|spawners","unfished|virgin|initial|equilibrium|unfished equilibrium","recruitment","recruits|recruit|age-0 fish|age-1 fish","catch|total mortality|harvest","catch per unit effort|cpue|catch rate|index of abundance|catch per effort|fishing success","landings|retained catch","spawning per recruit|spawning potential ratio|spr","maximum sustainable yield|msy","instantaneous total mortality rate|z","fishing mortality rate|f|instantaneous fishing mortality rate|harvest rate|exploitation rate|finite fishing mortality|apical f","fishing mortality at maximum sustainable yield|fmsy","weight|mass","length composition|length frequency|length observation","age composition|age frequency|age observation","projection|forecast|prediction","sex|gender","natural log of unfished recruitment|lnr0|logr0|logr_0|log(r0)|r0","plus group"
+"1","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/blue-warehou-rebuilding-strategy-2022.pdf",711,10,5,4,6,129,31,2,2,3,0,1214,0,16,0,1,0,2,0,0
+"2","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/frr276.pdf",2720,37,15,95,143,542,65,0,100,0,62,4451,0,51,21,42,0,100,0,0
+"3","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/frr294.pdf",3139,30,63,37,57,569,135,14,0,21,185,6161,0,185,0,7,55,35,5,0
+"4","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Gummy-assessment-report-Dec2020.pdf",1207,12,9,4,5,97,126,5,0,3,0,1780,0,50,16,20,10,12,0,7
+"5","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/King threadfin stock assessment 2020.pdf",1666,105,53,35,52,354,121,6,5,12,3,3765,0,127,25,9,5,9,17,1
+"6","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Marine_Scalefish_Fishery_Assessment_Report_2020_-_FINAL_20200424.pdf",3471,53,4,67,74,1139,341,2,0,0,5,9234,0,72,1,2,0,11,0,0
+"7","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/puntae_x2006a.pdf",1279,87,11,40,52,266,21,4,2,6,3,2063,1,114,2,0,6,5,1,0
+"8","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/stock-status-summary-2021-22-gemfish.pdf",289,7,4,6,9,93,14,9,3,0,0,645,0,21,3,2,3,6,1,0
+"9","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Stock assessment of black jewfish with data to December 2021.pdf",1332,74,55,10,21,231,45,16,0,20,0,2475,8,131,10,4,4,0,12,0
+"10","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Stock assessment of Queensland east coast dusky flathead with data to December 2020.pdf",1071,85,46,23,27,245,57,19,0,18,1,2560,2,130,27,0,4,64,9,0
+"11","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Stock assessment of Queensland red emperor 2022.pdf",1575,161,100,21,24,372,95,34,0,22,0,4852,0,175,16,5,2,25,4,0
+"12","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Stock assessment of the Queensland ballots saucer scallop_2022ed..pdf",1101,52,36,30,35,249,109,1,0,5,3,1763,0,77,0,0,13,0,8,0
+"13","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Stock assessments for SESSF- 2019 - Part 2.pdf",5919,21,35,0,0,1638,1536,4,0,0,1,12834,0,43,0,0,1,0,0,0
+"14","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Stock Assessments for SESSF 2020–21 - Part 1.pdf",8327,512,235,768,846,992,378,48,17,6,3,15600,0,682,170,51,121,24,20,72
+"15","ICES","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/ICES/01_WGNSSK_Report_2019.pdf",18719,814,27,514,647,2179,153,1543,36,820,37,26921,428,919,54,54,593,57,1,21
+"16","ICES","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/ICES/ices2023_WKBCOD_report_2023.pdf",4945,277,10,176,221,453,13,402,0,136,14,7439,36,299,3,29,119,0,0,12
+"17","ICES","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/ICES/WKBALTCOD2_2019.pdf",6066,173,15,78,82,546,80,88,0,23,38,8095,15,212,52,14,42,18,11,1
+"18","ICES","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/ICES/WKBBALTPEL_2023_final_report.pdf",8102,298,55,120,169,529,16,126,58,409,45,10875,215,310,3,19,73,23,7,20
+"19","ICES","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/ICES/wkdem_2020.pdf",2111,85,9,37,44,310,6,80,0,48,10,3594,32,143,2,12,24,0,1,5
+"20","ICES","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/ICES/WKFlatNSCS_2020.pdf",12799,239,33,132,166,683,51,3373,1,388,6,19156,206,638,4,76,56,117,6,19
+"21","ICES","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/ICES/WKMSYSPiCT_2021.pdf",4958,34,77,13,14,580,266,254,0,311,37,7983,133,202,15,1,79,16,0,1
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diff --git a/TextAnalysis/top20_frequency_Australia.csv b/TextAnalysis/top20_frequency_Australia.csv
new file mode 100644
index 0000000..dda8087
--- /dev/null
+++ b/TextAnalysis/top20_frequency_Australia.csv
@@ -0,0 +1,16 @@
+"ID","Source","File_Path","biomass|b|abundance","spawning biomass|sb|spawning stock biomass|ssb|spawning stock output|sso|mature biomass|spawners","unfished|virgin|initial|equilibrium|unfished equilibrium","recruitment","recruits|recruit|age-0 fish|age-1 fish","catch|total mortality|harvest","catch per unit effort|cpue|catch rate|index of abundance|catch per effort|fishing success","landings|retained catch","spawning per recruit|spawning potential ratio|spr","maximum sustainable yield|msy","instantaneous total mortality rate|z","fishing mortality rate|f|instantaneous fishing mortality rate|harvest rate|exploitation rate|finite fishing mortality|apical f","fishing mortality at maximum sustainable yield|fmsy","weight|mass","length composition|length frequency|length observation","age composition|age frequency|age observation","projection|forecast|prediction","sex|gender","natural log of unfished recruitment|lnr0|logr0|logr_0|log(r0)|r0","plus group"
+"1","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/blue-warehou-rebuilding-strategy-2022.pdf",711,10,5,4,6,129,31,2,2,3,0,1214,0,16,0,1,0,2,0,0
+"2","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/frr276.pdf",2720,37,15,95,143,542,65,0,100,0,62,4451,0,51,21,42,0,100,0,0
+"3","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/frr294.pdf",3139,30,63,37,57,569,135,14,0,21,185,6161,0,185,0,7,55,35,5,0
+"4","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Gummy-assessment-report-Dec2020.pdf",1207,12,9,4,5,97,126,5,0,3,0,1780,0,50,16,20,10,12,0,7
+"5","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/King threadfin stock assessment 2020.pdf",1666,105,53,35,52,354,121,6,5,12,3,3765,0,127,25,9,5,9,17,1
+"6","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Marine_Scalefish_Fishery_Assessment_Report_2020_-_FINAL_20200424.pdf",3471,53,4,67,74,1139,341,2,0,0,5,9234,0,72,1,2,0,11,0,0
+"7","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/puntae_x2006a.pdf",1279,87,11,40,52,266,21,4,2,6,3,2063,1,114,2,0,6,5,1,0
+"8","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/stock-status-summary-2021-22-gemfish.pdf",289,7,4,6,9,93,14,9,3,0,0,645,0,21,3,2,3,6,1,0
+"9","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Stock assessment of black jewfish with data to December 2021.pdf",1332,74,55,10,21,231,45,16,0,20,0,2475,8,131,10,4,4,0,12,0
+"10","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Stock assessment of Queensland east coast dusky flathead with data to December 2020.pdf",1071,85,46,23,27,245,57,19,0,18,1,2560,2,130,27,0,4,64,9,0
+"11","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Stock assessment of Queensland red emperor 2022.pdf",1575,161,100,21,24,372,95,34,0,22,0,4852,0,175,16,5,2,25,4,0
+"12","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Stock assessment of the Queensland ballots saucer scallop_2022ed..pdf",1101,52,36,30,35,249,109,1,0,5,3,1763,0,77,0,0,13,0,8,0
+"13","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Stock assessments for SESSF- 2019 - Part 2.pdf",5919,21,35,0,0,1638,1536,4,0,0,1,12834,0,43,0,0,1,0,0,0
+"14","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Stock Assessments for SESSF 2020–21 - Part 1.pdf",8327,512,235,768,846,992,378,48,17,6,3,15600,0,682,170,51,121,24,20,72
+"Sum",NA,NA,33807,1246,671,1140,1351,6916,3074,164,129,116,266,69397,11,1874,291,143,224,293,77,80
diff --git a/TextAnalysis/top20_frequency_ICES.csv b/TextAnalysis/top20_frequency_ICES.csv
new file mode 100644
index 0000000..e355d27
--- /dev/null
+++ b/TextAnalysis/top20_frequency_ICES.csv
@@ -0,0 +1,10 @@
+"ID","Source","File_Path","biomass|b|abundance","spawning biomass|sb|spawning stock biomass|ssb|spawning stock output|sso|mature biomass|spawners","unfished|virgin|initial|equilibrium|unfished equilibrium","recruitment","recruits|recruit|age-0 fish|age-1 fish","catch|total mortality|harvest","catch per unit effort|cpue|catch rate|index of abundance|catch per effort|fishing success","landings|retained catch","spawning per recruit|spawning potential ratio|spr","maximum sustainable yield|msy","instantaneous total mortality rate|z","fishing mortality rate|f|instantaneous fishing mortality rate|harvest rate|exploitation rate|finite fishing mortality|apical f","fishing mortality at maximum sustainable yield|fmsy","weight|mass","length composition|length frequency|length observation","age composition|age frequency|age observation","projection|forecast|prediction","sex|gender","natural log of unfished recruitment|lnr0|logr0|logr_0|log(r0)|r0","plus group"
+"1","ICES","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/ICES/01_WGNSSK_Report_2019.pdf",18719,814,27,514,647,2179,153,1543,36,820,37,26921,428,919,54,54,593,57,1,21
+"2","ICES","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/ICES/ices2023_WKBCOD_report_2023.pdf",4945,277,10,176,221,453,13,402,0,136,14,7439,36,299,3,29,119,0,0,12
+"3","ICES","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/ICES/WKBALTCOD2_2019.pdf",6066,173,15,78,82,546,80,88,0,23,38,8095,15,212,52,14,42,18,11,1
+"4","ICES","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/ICES/WKBBALTPEL_2023_final_report.pdf",8102,298,55,120,169,529,16,126,58,409,45,10875,215,310,3,19,73,23,7,20
+"5","ICES","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/ICES/wkdem_2020.pdf",2111,85,9,37,44,310,6,80,0,48,10,3594,32,143,2,12,24,0,1,5
+"6","ICES","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/ICES/WKFlatNSCS_2020.pdf",12799,239,33,132,166,683,51,3373,1,388,6,19156,206,638,4,76,56,117,6,19
+"7","ICES","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/ICES/WKMSYSPiCT_2021.pdf",4958,34,77,13,14,580,266,254,0,311,37,7983,133,202,15,1,79,16,0,1
+"8","ICES","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/ICES/WKSPRAT_2018_Report.pdf",1127,29,0,43,47,143,7,5,1,3,8,1712,1,39,1,2,29,0,0,1
+"Sum",NA,NA,58827,1949,226,1113,1390,5423,592,5871,96,2138,195,85775,1066,2762,134,207,1015,231,26,80
diff --git a/TextAnalysis/top20_frequency_NOAA.csv b/TextAnalysis/top20_frequency_NOAA.csv
new file mode 100644
index 0000000..b994d16
--- /dev/null
+++ b/TextAnalysis/top20_frequency_NOAA.csv
@@ -0,0 +1,83 @@
+"ID","Source","File_Path","biomass|b|abundance","spawning biomass|sb|spawning stock biomass|ssb|spawning stock output|sso|mature biomass|spawners","unfished|virgin|initial|equilibrium|unfished equilibrium","recruitment","recruits|recruit|age-0 fish|age-1 fish","catch|total mortality|harvest","catch per unit effort|cpue|catch rate|index of abundance|catch per effort|fishing success","landings|retained catch","spawning per recruit|spawning potential ratio|spr","maximum sustainable yield|msy","instantaneous total mortality rate|z","fishing mortality rate|f|instantaneous fishing mortality rate|harvest rate|exploitation rate|finite fishing mortality|apical f","fishing mortality at maximum sustainable yield|fmsy","weight|mass","length composition|length frequency|length observation","age composition|age frequency|age observation","projection|forecast|prediction","sex|gender","natural log of unfished recruitment|lnr0|logr0|logr_0|log(r0)|r0","plus group"
+"1","NOAA-AFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-AFSC/BSAIatf.pdf",249,5,0,0,0,40,1,0,0,0,1,414,0,18,0,2,11,0,0,0
+"2","NOAA-AFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-AFSC/BSAIatka.pdf",3107,98,11,58,77,294,46,8,1,7,27,4540,0,303,6,43,26,6,2,1
+"3","NOAA-AFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-AFSC/BSAIocto.pdf",1096,11,1,5,5,118,11,1,0,2,6,1615,0,47,0,0,1,3,0,0
+"4","NOAA-AFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-AFSC/BSAIoflat (8).pdf",532,6,0,6,6,42,1,0,0,0,0,850,0,66,1,0,0,0,0,0
+"5","NOAA-AFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-AFSC/BSAIorock (5).pdf",1104,21,1,5,5,95,4,0,0,0,8,1595,0,89,3,0,1,0,0,0
+"6","NOAA-AFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-AFSC/BSAIpop.pdf",128,4,0,0,0,22,0,0,0,0,0,168,0,14,0,1,9,0,0,0
+"7","NOAA-AFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-AFSC/BSAIrocksole.pdf",1488,36,10,95,119,119,6,0,0,24,4,2074,2,143,2,65,35,41,0,1
+"8","NOAA-AFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-AFSC/BSAIrougheye (2).pdf",2288,62,4,65,74,172,34,0,0,5,10,3047,0,245,32,27,12,0,1,1
+"9","NOAA-AFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-AFSC/BSAIskate.pdf",152,1,0,0,0,28,0,0,0,0,0,170,0,23,0,0,4,0,0,0
+"10","NOAA-AFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-AFSC/EBSpcod.pdf",10350,339,97,135,179,461,237,20,16,14,29,14839,2,551,3,61,33,2,0,0
+"11","NOAA-AFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-AFSC/EBSPollock.pdf",3362,111,17,89,135,307,35,11,7,23,24,4802,3,316,9,37,46,11,5,0
+"12","NOAA-AFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-AFSC/GOAdeepflat.pdf",1381,43,11,43,57,147,5,0,5,5,8,2710,0,124,25,12,9,17,3,0
+"13","NOAA-AFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-AFSC/GOAskate (9).pdf",1104,4,3,6,7,93,12,0,0,0,1,1830,0,86,16,0,0,0,0,0
+"14","NOAA-AFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-AFSC/PIRKC.pdf",1056,5,7,21,25,54,1,8,1,10,10,1245,0,71,12,0,1,24,1,0
+"15","NOAA-AFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-AFSC/sablefish.pdf",6892,296,33,257,309,460,156,18,1,9,27,10617,0,387,47,84,68,20,0,4
+"16","NOAA-AFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-AFSC/SAFE_snow.pdf",2413,32,11,32,48,122,4,30,0,14,5,2270,3,109,10,0,1,35,0,0
+"17","NOAA-NEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NEFSC/2020_FLD_GMGB_RPT.pdf",87,2,0,1,1,17,0,3,0,6,0,213,2,17,0,0,6,0,0,0
+"18","NOAA-NEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NEFSC/2020_FLW_GM_RPT_Update_report_08_26_095440 (1).pdf",77,2,0,1,2,15,0,5,0,1,0,269,0,21,0,0,6,0,0,0
+"19","NOAA-NEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NEFSC/2020_Herring_Unit_Report.pdf",95,14,0,12,16,18,0,0,0,1,0,227,0,8,0,0,19,0,0,0
+"20","NOAA-NEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NEFSC/2020_HKR_SNEMA_RPT.pdf",97,3,0,1,1,13,0,4,0,5,0,200,4,17,0,0,6,0,0,0
+"21","NOAA-NEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NEFSC/2020_HKS_GM_RPT.pdf",71,2,1,2,2,13,0,2,0,1,0,205,0,12,0,0,7,0,0,0
+"22","NOAA-NEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NEFSC/2020_scallop_unit_maindoc_rev.pdf",105,8,0,5,11,2,0,3,0,12,0,149,6,15,1,0,1,0,0,0
+"23","NOAA-NEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NEFSC/2021_COD_GB_REPORT_ver3.pdf",116,5,0,1,1,19,0,0,0,1,0,151,0,14,0,0,6,0,0,0
+"24","NOAA-NEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NEFSC/2021_scup_MTA_report.pdf",215,51,1,17,23,36,4,15,0,24,0,390,8,27,0,0,13,0,0,0
+"25","NOAA-NEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NEFSC/2021_summer_flounder_MTA_report.pdf",220,60,2,21,31,27,0,14,0,24,0,400,7,26,0,1,15,3,0,0
+"26","NOAA-NEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NEFSC/4d_SkateAssessmentUpdate_July_2020.pdf",234,0,0,0,0,14,1,1,0,9,0,416,1,33,0,0,0,0,0,0
+"27","NOAA-NEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NEFSC/Bluefish_2021_Assesssment_Update_v4.pdf",157,40,1,17,19,22,0,12,0,16,0,291,6,14,0,0,8,0,0,0
+"28","NOAA-NEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NEFSC/crd0609a.pdf",4033,138,20,76,227,198,38,336,0,49,45,6593,18,314,14,6,19,12,0,1
+"29","NOAA-NEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NEFSC/Georges_Bank_Winter_Flounder_Update_2020_09_18_111359.pdf",155,32,0,4,8,18,0,4,0,4,0,357,2,21,2,2,14,0,0,0
+"30","NOAA-NEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NEFSC/Golden_Tile_Assessment_MT2021_2.pdf",181,53,1,14,17,13,20,27,0,28,0,413,13,18,3,0,5,0,0,0
+"31","NOAA-NEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NEFSC/noaa_24818_DS1.pdf",597,24,0,4,19,112,1,39,0,0,2,1101,0,86,0,3,7,0,0,0
+"32","NOAA-NEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NEFSC/TSR_EGB_Haddock_2021_meeting_draft.pdf",399,7,1,5,8,73,0,20,0,0,9,633,0,73,5,2,0,0,0,0
+"33","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/2011Dick3.pdf",2641,177,77,51,65,315,37,133,61,80,15,6248,8,100,122,20,45,40,24,0
+"34","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/agenda-item-h-5-attachment-9-2.pdf",3625,111,111,65,90,287,26,99,46,41,22,6107,4,232,32,15,17,15,32,1
+"35","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/Blue-Deacon_Assessment_2017_Final.pdf",8666,190,137,139,174,662,198,253,52,56,35,14756,9,204,77,51,56,77,63,0
+"36","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/c-6-attachment-1-full-assessment-electronic-only-status-of-lingcod-ophiodon-elongatus-along-the-northern-u-s-west-coast-in-2021.pdf",2978,100,92,40,56,241,61,152,24,23,11,6353,1,118,26,26,18,432,6,1
+"37","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/Cabezon-2019_FINAL.pdf",6248,337,154,248,318,475,103,108,159,79,16,10513,16,430,115,34,73,46,60,0
+"38","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/California Scorpionfish.pdf",2467,62,47,69,88,301,61,66,24,3,16,5764,0,128,61,11,37,48,10,1
+"39","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/dover_sole_december_2021_final.pdf",2667,141,85,54,66,163,22,80,37,13,3,4979,0,242,43,19,25,109,6,2
+"40","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/g-5-attachment-3-draft-full-assessment-of-status-of-the-pacific-spiny-dogfish-shark-resource-off-the-continental-u-s-pacific-coast-in-2021-electronic-only.pdf",2119,67,63,38,80,302,9,113,46,22,2,4935,0,76,59,11,10,29,14,0
+"41","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/Gopher_BlackandYellow_Assessment_2019-1.pdf",2703,35,44,90,111,330,38,109,22,2,11,5330,0,78,76,14,20,9,17,1
+"42","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/hake-assessment-post-srg-final_20210303.pdf",4432,296,74,189,250,569,26,30,81,51,10,7230,3,532,2,45,90,10,30,0
+"43","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/Longnose skate 2019_FINAL.pdf",2660,154,64,43,75,318,26,176,56,26,3,4696,0,195,61,20,8,16,20,0
+"44","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/PacificOceanPerch2017_Assessment_Final.pdf",1948,25,46,64,85,154,42,62,21,9,1,4307,0,134,16,20,15,18,6,0
+"45","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/sablefish_20191022.pdf",5976,185,73,407,524,372,49,109,43,16,60,10656,2,298,23,24,56,26,23,11
+"46","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/WidowAssessment2015.pdf",2449,124,62,101,125,259,9,227,28,23,13,5768,4,211,58,41,46,29,19,0
+"47","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/Yelloweye rockfish 2017.pdf",2243,82,58,68,124,294,40,60,43,22,1,5459,0,94,76,40,11,19,18,0
+"48","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/Yellowtail rockfish 2017.pdf",2741,42,42,44,80,220,44,62,23,3,0,5953,0,147,22,13,29,19,12,0
+"49","NOAA-PIFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-PIFSC/NMFS-PIFSC-60.pdf",2013,27,26,7,11,411,0,2,173,2,16,3107,0,74,2,0,0,1,0,0
+"50","NOAA-PIFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-PIFSC/noaa_17252_DS1.pdf",3076,15,60,0,0,523,484,0,0,186,3,5303,7,221,1,0,33,3,0,0
+"51","NOAA-PIFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-PIFSC/noaa_20062_DS1.pdf",1568,31,8,11,17,243,0,4,139,2,14,2389,0,85,1,0,0,3,0,0
+"52","NOAA-PIFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-PIFSC/noaa_21164_DS1.pdf",3752,15,66,2,2,628,178,6,0,519,4,6004,0,326,1,0,39,0,0,0
+"53","NOAA-PIFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-PIFSC/SA-WP-06-[SP-alb-assessment] Rev 1.pdf",1221,93,30,63,70,88,50,0,0,45,6,2723,8,87,14,3,1,5,0,1
+"54","NOAA-PIFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-PIFSC/SC14-SA-WP-08 Silky shark stock assessment (1).pdf",2319,229,32,35,37,302,320,0,0,18,15,4382,6,41,34,0,0,25,2,0
+"55","NOAA-PIFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-PIFSC/SC15-SA-WP-05 SKJ-Assessment REV2 (1).pdf",1601,222,24,55,68,125,73,0,0,74,5,3976,28,113,53,0,18,5,0,1
+"56","NOAA-PIFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-PIFSC/SC15-SA-WP-06 Oceanic whitetip shark_assessment.pdf",2044,296,60,27,41,310,90,0,0,81,1,2742,27,78,3,0,15,11,4,0
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+"65","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/KGM_GOM_SA_08282020_final-revision_3.pdf",791,101,35,35,45,36,17,95,0,5,0,1655,2,62,20,4,11,10,10,0
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+"75","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/SA BSB 2018.pdf",3137,176,73,49,109,80,25,145,12,230,5,3782,103,148,31,38,95,6,7,1
+"76","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/SEDAR_60_SA_Red_Porgy_SAR_4.9.2020.pdf",2825,259,67,57,147,94,26,193,19,257,13,4900,118,165,42,40,111,7,18,1
+"77","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/SEDAR65_FullSAR_12.8.2020_V3.pdf",8869,91,163,154,243,500,107,125,4,318,53,11823,263,158,194,1,289,80,21,0
+"78","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/SMA_ASS_ENG.pdf",1498,21,15,10,26,197,75,11,0,249,12,2043,49,80,21,0,19,16,4,0
+"79","NOAA-SWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SWFSC/agenda-item-d-3.pdf",2168,100,45,76,108,153,16,54,12,11,32,3675,3,225,8,46,40,22,8,0
+"80","NOAA-SWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SWFSC/SAC-11-07-MTG_Yellowfin tuna benchmark assessment 2019.pdf",1665,121,38,47,65,170,59,10,0,52,4,3325,18,88,26,1,3,6,10,0
+"81","NOAA-SWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SWFSC/SC14-SA-WP-11 ISC18 Shortfin Mako Stock Assessment.pdf",1461,16,118,79,110,241,123,3,33,99,15,3421,4,37,24,0,38,34,24,4
+"Sum",NA,NA,189533,7547,3256,4253,6154,15235,4340,4865,1786,4164,1203,335448,1442,10525,2181,1258,2603,1557,677,48
diff --git a/TextAnalysis/top20_presence_All.csv b/TextAnalysis/top20_presence_All.csv
new file mode 100644
index 0000000..73dfe86
--- /dev/null
+++ b/TextAnalysis/top20_presence_All.csv
@@ -0,0 +1,105 @@
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+"58","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/c-6-attachment-1-full-assessment-electronic-only-status-of-lingcod-ophiodon-elongatus-along-the-northern-u-s-west-coast-in-2021.pdf",1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
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+"60","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/California Scorpionfish.pdf",1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1
+"61","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/dover_sole_december_2021_final.pdf",1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1
+"62","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/g-5-attachment-3-draft-full-assessment-of-status-of-the-pacific-spiny-dogfish-shark-resource-off-the-continental-u-s-pacific-coast-in-2021-electronic-only.pdf",1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,0
+"63","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/Gopher_BlackandYellow_Assessment_2019-1.pdf",1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1
+"64","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/hake-assessment-post-srg-final_20210303.pdf",1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0
+"65","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/Longnose skate 2019_FINAL.pdf",1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,0
+"66","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/PacificOceanPerch2017_Assessment_Final.pdf",1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,0
+"67","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/sablefish_20191022.pdf",1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
+"68","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/WidowAssessment2015.pdf",1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0
+"69","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/Yelloweye rockfish 2017.pdf",1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,0
+"70","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/Yellowtail rockfish 2017.pdf",1,1,1,1,1,1,1,1,1,1,0,1,0,1,1,1,1,1,1,0
+"71","NOAA-PIFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-PIFSC/NMFS-PIFSC-60.pdf",1,1,1,1,1,1,0,1,1,1,1,1,0,1,1,0,0,1,0,0
+"72","NOAA-PIFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-PIFSC/noaa_17252_DS1.pdf",1,1,1,0,0,1,1,0,0,1,1,1,1,1,1,0,1,1,0,0
+"73","NOAA-PIFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-PIFSC/noaa_20062_DS1.pdf",1,1,1,1,1,1,0,1,1,1,1,1,0,1,1,0,0,1,0,0
+"74","NOAA-PIFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-PIFSC/noaa_21164_DS1.pdf",1,1,1,1,1,1,1,1,0,1,1,1,0,1,1,0,1,0,0,0
+"75","NOAA-PIFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-PIFSC/SA-WP-06-[SP-alb-assessment] Rev 1.pdf",1,1,1,1,1,1,1,0,0,1,1,1,1,1,1,1,1,1,0,1
+"76","NOAA-PIFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-PIFSC/SC14-SA-WP-08 Silky shark stock assessment (1).pdf",1,1,1,1,1,1,1,0,0,1,1,1,1,1,1,0,0,1,1,0
+"77","NOAA-PIFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-PIFSC/SC15-SA-WP-05 SKJ-Assessment REV2 (1).pdf",1,1,1,1,1,1,1,0,0,1,1,1,1,1,1,0,1,1,0,1
+"78","NOAA-PIFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-PIFSC/SC15-SA-WP-06 Oceanic whitetip shark_assessment.pdf",1,1,1,1,1,1,1,0,0,1,1,1,1,1,1,0,1,1,1,0
+"79","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/05.-Traditional-Interim-assessment-report-RS-002-1.pdf",1,0,0,0,0,1,1,1,0,0,1,1,0,1,0,0,1,0,0,0
+"80","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/08b.-SEDAR61_2021IA_Final.pdf",1,0,0,1,1,1,1,1,0,0,0,1,0,1,0,0,1,0,0,0
+"81","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/2019_WHM_SA_ENG.pdf",1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,0,1,1,1,0
+"82","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/2020_ALB_ENG.pdf",1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1,1,0,0
+"83","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/2021_WBFT_SA_ENG.pdf",1,1,1,1,1,1,1,0,0,0,1,1,0,1,1,1,1,0,1,0
+"84","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/Atl_Blacknose_SAR.pdf",1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
+"85","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/B-8a-Gray_triggerfish_interim_9102020.pdf",1,1,1,0,0,1,1,1,0,0,0,1,0,1,0,0,1,0,0,0
+"86","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/Dusky_update_report_2016.pdf",1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
+"87","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/KGM_GOM_SA_08282020_final-revision_3.pdf",1,1,1,1,1,1,1,1,0,1,0,1,1,1,1,1,1,1,1,0
+"88","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/S23_SAR_complete_and_final.pdf",1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0,0
+"89","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/S28UpdateSAR_V2.pdf",1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1,1
+"90","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/S34_ATSH_SAR.pdf",1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0
+"91","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/S51_FINAL_SAR_0.pdf",1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0
+"92","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/S52_Final_SAR_v2.pdf",1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
+"93","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/S57_Final_SAR.pdf",1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1
+"94","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/S64_SAR_FINAL.pdf",1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
+"95","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/S67_Final_SAR.pdf",1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
+"96","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/S72_SAR_FINAL.pdf",1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
+"97","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/SA BSB 2018.pdf",1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
+"98","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/SEDAR_60_SA_Red_Porgy_SAR_4.9.2020.pdf",1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
+"99","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/SEDAR65_FullSAR_12.8.2020_V3.pdf",1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0
+"100","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/SMA_ASS_ENG.pdf",1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,0,1,1,1,0
+"101","NOAA-SWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SWFSC/agenda-item-d-3.pdf",1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0
+"102","NOAA-SWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SWFSC/SAC-11-07-MTG_Yellowfin tuna benchmark assessment 2019.pdf",1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1,1,1,0
+"103","NOAA-SWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SWFSC/SC14-SA-WP-11 ISC18 Shortfin Mako Stock Assessment.pdf",1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1
+"Sum",NA,NA,103,100,87,95,95,103,88,85,50,87,77,103,59,103,81,67,93,71,57,35
diff --git a/TextAnalysis/top20_presence_All.jpg b/TextAnalysis/top20_presence_All.jpg
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diff --git a/TextAnalysis/top20_presence_Australia.csv b/TextAnalysis/top20_presence_Australia.csv
new file mode 100644
index 0000000..7bbfb7f
--- /dev/null
+++ b/TextAnalysis/top20_presence_Australia.csv
@@ -0,0 +1,16 @@
+"ID","Source","File_Path","biomass|b|abundance","spawning biomass|sb|spawning stock biomass|ssb|spawning stock output|sso|mature biomass|spawners","unfished|virgin|initial|equilibrium|unfished equilibrium","recruitment","recruits|recruit|age-0 fish|age-1 fish","catch|total mortality|harvest","catch per unit effort|cpue|catch rate|index of abundance|catch per effort|fishing success","landings|retained catch","spawning per recruit|spawning potential ratio|spr","maximum sustainable yield|msy","instantaneous total mortality rate|z","fishing mortality rate|f|instantaneous fishing mortality rate|harvest rate|exploitation rate|finite fishing mortality|apical f","fishing mortality at maximum sustainable yield|fmsy","weight|mass","length composition|length frequency|length observation","age composition|age frequency|age observation","projection|forecast|prediction","sex|gender","natural log of unfished recruitment|lnr0|logr0|logr_0|log(r0)|r0","plus group"
+"1","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/blue-warehou-rebuilding-strategy-2022.pdf",1,1,1,1,1,1,1,1,1,1,0,1,0,1,0,1,0,1,0,0
+"2","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/frr276.pdf",1,1,1,1,1,1,1,0,1,0,1,1,0,1,1,1,0,1,0,0
+"3","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/frr294.pdf",1,1,1,1,1,1,1,1,0,1,1,1,0,1,0,1,1,1,1,0
+"4","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Gummy-assessment-report-Dec2020.pdf",1,1,1,1,1,1,1,1,0,1,0,1,0,1,1,1,1,1,0,1
+"5","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/King threadfin stock assessment 2020.pdf",1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1
+"6","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Marine_Scalefish_Fishery_Assessment_Report_2020_-_FINAL_20200424.pdf",1,1,1,1,1,1,1,1,0,0,1,1,0,1,1,1,0,1,0,0
+"7","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/puntae_x2006a.pdf",1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,0
+"8","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/stock-status-summary-2021-22-gemfish.pdf",1,1,1,1,1,1,1,1,1,0,0,1,0,1,1,1,1,1,1,0
+"9","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Stock assessment of black jewfish with data to December 2021.pdf",1,1,1,1,1,1,1,1,0,1,0,1,1,1,1,1,1,0,1,0
+"10","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Stock assessment of Queensland east coast dusky flathead with data to December 2020.pdf",1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,0,1,1,1,0
+"11","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Stock assessment of Queensland red emperor 2022.pdf",1,1,1,1,1,1,1,1,0,1,0,1,0,1,1,1,1,1,1,0
+"12","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Stock assessment of the Queensland ballots saucer scallop_2022ed..pdf",1,1,1,1,1,1,1,1,0,1,1,1,0,1,0,0,1,0,1,0
+"13","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Stock assessments for SESSF- 2019 - Part 2.pdf",1,1,1,0,0,1,1,1,0,0,1,1,0,1,0,0,1,0,0,0
+"14","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Stock Assessments for SESSF 2020–21 - Part 1.pdf",1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1
+"Sum",NA,NA,14,14,14,13,13,14,14,13,6,10,9,14,3,14,10,10,11,11,9,3
diff --git a/TextAnalysis/top20_presence_Australia.jpg b/TextAnalysis/top20_presence_Australia.jpg
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index 0000000..4565a5b
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diff --git a/TextAnalysis/top20_presence_ICES.csv b/TextAnalysis/top20_presence_ICES.csv
new file mode 100644
index 0000000..7b0bca3
--- /dev/null
+++ b/TextAnalysis/top20_presence_ICES.csv
@@ -0,0 +1,10 @@
+"ID","Source","File_Path","biomass|b|abundance","spawning biomass|sb|spawning stock biomass|ssb|spawning stock output|sso|mature biomass|spawners","unfished|virgin|initial|equilibrium|unfished equilibrium","recruitment","recruits|recruit|age-0 fish|age-1 fish","catch|total mortality|harvest","catch per unit effort|cpue|catch rate|index of abundance|catch per effort|fishing success","landings|retained catch","spawning per recruit|spawning potential ratio|spr","maximum sustainable yield|msy","instantaneous total mortality rate|z","fishing mortality rate|f|instantaneous fishing mortality rate|harvest rate|exploitation rate|finite fishing mortality|apical f","fishing mortality at maximum sustainable yield|fmsy","weight|mass","length composition|length frequency|length observation","age composition|age frequency|age observation","projection|forecast|prediction","sex|gender","natural log of unfished recruitment|lnr0|logr0|logr_0|log(r0)|r0","plus group"
+"1","ICES","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/ICES/01_WGNSSK_Report_2019.pdf",1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
+"2","ICES","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/ICES/ices2023_WKBCOD_report_2023.pdf",1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1,0,0,1
+"3","ICES","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/ICES/WKBALTCOD2_2019.pdf",1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1,1,1,1
+"4","ICES","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/ICES/WKBBALTPEL_2023_final_report.pdf",1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
+"5","ICES","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/ICES/wkdem_2020.pdf",1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1,0,1,1
+"6","ICES","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/ICES/WKFlatNSCS_2020.pdf",1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
+"7","ICES","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/ICES/WKMSYSPiCT_2021.pdf",1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1,1,0,1
+"8","ICES","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/ICES/WKSPRAT_2018_Report.pdf",1,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0,0,1
+"Sum",NA,NA,8,8,7,8,8,8,8,8,4,8,8,8,8,8,8,8,8,5,5,8
diff --git a/TextAnalysis/top20_presence_ICES.jpg b/TextAnalysis/top20_presence_ICES.jpg
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index 0000000..48cbeab
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diff --git a/TextAnalysis/top20_presence_NOAA.csv b/TextAnalysis/top20_presence_NOAA.csv
new file mode 100644
index 0000000..18b0fda
--- /dev/null
+++ b/TextAnalysis/top20_presence_NOAA.csv
@@ -0,0 +1,83 @@
+"ID","Source","File_Path","biomass|b|abundance","spawning biomass|sb|spawning stock biomass|ssb|spawning stock output|sso|mature biomass|spawners","unfished|virgin|initial|equilibrium|unfished equilibrium","recruitment","recruits|recruit|age-0 fish|age-1 fish","catch|total mortality|harvest","catch per unit effort|cpue|catch rate|index of abundance|catch per effort|fishing success","landings|retained catch","spawning per recruit|spawning potential ratio|spr","maximum sustainable yield|msy","instantaneous total mortality rate|z","fishing mortality rate|f|instantaneous fishing mortality rate|harvest rate|exploitation rate|finite fishing mortality|apical f","fishing mortality at maximum sustainable yield|fmsy","weight|mass","length composition|length frequency|length observation","age composition|age frequency|age observation","projection|forecast|prediction","sex|gender","natural log of unfished recruitment|lnr0|logr0|logr_0|log(r0)|r0","plus group"
+"1","NOAA-AFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-AFSC/BSAIatf.pdf",1,1,0,0,0,1,1,0,0,0,1,1,0,1,0,1,1,0,0,0
+"2","NOAA-AFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-AFSC/BSAIatka.pdf",1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1
+"3","NOAA-AFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-AFSC/BSAIocto.pdf",1,1,1,1,1,1,1,1,0,1,1,1,0,1,0,0,1,1,0,0
+"4","NOAA-AFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-AFSC/BSAIoflat (8).pdf",1,1,0,1,1,1,1,0,0,0,0,1,0,1,1,0,0,0,0,0
+"5","NOAA-AFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-AFSC/BSAIorock (5).pdf",1,1,1,1,1,1,1,0,0,0,1,1,0,1,1,0,1,0,0,0
+"6","NOAA-AFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-AFSC/BSAIpop.pdf",1,1,0,0,0,1,0,0,0,0,0,1,0,1,0,1,1,0,0,0
+"7","NOAA-AFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-AFSC/BSAIrocksole.pdf",1,1,1,1,1,1,1,0,0,1,1,1,1,1,1,1,1,1,0,1
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+"36","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/c-6-attachment-1-full-assessment-electronic-only-status-of-lingcod-ophiodon-elongatus-along-the-northern-u-s-west-coast-in-2021.pdf",1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
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+"38","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/California Scorpionfish.pdf",1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1
+"39","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/dover_sole_december_2021_final.pdf",1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1
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+"42","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/hake-assessment-post-srg-final_20210303.pdf",1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0
+"43","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/Longnose skate 2019_FINAL.pdf",1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,0
+"44","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/PacificOceanPerch2017_Assessment_Final.pdf",1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,0
+"45","NOAA-NWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-NWFSC/sablefish_20191022.pdf",1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
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+"49","NOAA-PIFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-PIFSC/NMFS-PIFSC-60.pdf",1,1,1,1,1,1,0,1,1,1,1,1,0,1,1,0,0,1,0,0
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+"75","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/SA BSB 2018.pdf",1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
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+"77","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/SEDAR65_FullSAR_12.8.2020_V3.pdf",1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0
+"78","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/SMA_ASS_ENG.pdf",1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,0,1,1,1,0
+"79","NOAA-SWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SWFSC/agenda-item-d-3.pdf",1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0
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+"81","NOAA-SWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SWFSC/SC14-SA-WP-11 ISC18 Shortfin Mako Stock Assessment.pdf",1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1
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diff --git a/TextAnalysis/top20_presence.jpg b/TextAnalysis/top20_presence_NOAA.jpg
similarity index 58%
rename from TextAnalysis/top20_presence.jpg
rename to TextAnalysis/top20_presence_NOAA.jpg
index dd781fd..d9d49c2 100644
Binary files a/TextAnalysis/top20_presence.jpg and b/TextAnalysis/top20_presence_NOAA.jpg differ
diff --git a/TextAnalysis/top20_proportion_All.csv b/TextAnalysis/top20_proportion_All.csv
new file mode 100644
index 0000000..ac7ebc7
--- /dev/null
+++ b/TextAnalysis/top20_proportion_All.csv
@@ -0,0 +1,105 @@
+"ID","Source","File_Path","biomass|b|abundance","spawning biomass|sb|spawning stock biomass|ssb|spawning stock output|sso|mature biomass|spawners","unfished|virgin|initial|equilibrium|unfished equilibrium","recruitment","recruits|recruit|age-0 fish|age-1 fish","catch|total mortality|harvest","catch per unit effort|cpue|catch rate|index of abundance|catch per effort|fishing success","landings|retained catch","spawning per recruit|spawning potential ratio|spr","maximum sustainable yield|msy","instantaneous total mortality rate|z","fishing mortality rate|f|instantaneous fishing mortality rate|harvest rate|exploitation rate|finite fishing mortality|apical f","fishing mortality at maximum sustainable yield|fmsy","weight|mass","length composition|length frequency|length observation","age composition|age frequency|age observation","projection|forecast|prediction","sex|gender","natural log of unfished recruitment|lnr0|logr0|logr_0|log(r0)|r0","plus group"
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+"74","NOAA-PIFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-PIFSC/noaa_21164_DS1.pdf",1.4,0.01,0.02,0,0,0.23,0.07,0,0,0.19,0,2.23,0,0.12,0,0,0.01,0,0,0
+"75","NOAA-PIFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-PIFSC/SA-WP-06-[SP-alb-assessment] Rev 1.pdf",1.08,0.08,0.03,0.06,0.06,0.08,0.04,0,0,0.04,0.01,2.4,0.01,0.08,0.01,0,0,0,0,0
+"76","NOAA-PIFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-PIFSC/SC14-SA-WP-08 Silky shark stock assessment (1).pdf",1.05,0.1,0.01,0.02,0.02,0.14,0.14,0,0,0.01,0.01,1.98,0,0.02,0.02,0,0,0.01,0,0
+"77","NOAA-PIFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-PIFSC/SC15-SA-WP-05 SKJ-Assessment REV2 (1).pdf",0.92,0.13,0.01,0.03,0.04,0.07,0.04,0,0,0.04,0,2.29,0.02,0.07,0.03,0,0.01,0,0,0
+"78","NOAA-PIFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-PIFSC/SC15-SA-WP-06 Oceanic whitetip shark_assessment.pdf",1.23,0.18,0.04,0.02,0.02,0.19,0.05,0,0,0.05,0,1.65,0.02,0.05,0,0,0.01,0.01,0,0
+"79","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/05.-Traditional-Interim-assessment-report-RS-002-1.pdf",1,0,0,0,0,0.16,0.03,0,0,0,0.01,1.89,0,0.08,0,0,0.01,0,0,0
+"80","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/08b.-SEDAR61_2021IA_Final.pdf",1,0,0,0,0,0.18,0.05,0.04,0,0,0,2.03,0,0.07,0,0,0.06,0,0,0
+"81","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/2019_WHM_SA_ENG.pdf",1.09,0.02,0.02,0.01,0.01,0.1,0.06,0.01,0,0.09,0.01,1.65,0.04,0.04,0,0,0.03,0.01,0,0
+"82","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/2020_ALB_ENG.pdf",1.58,0.01,0.01,0,0,0.08,0.11,0,0,0.07,0.03,1.54,0.03,0.07,0,0,0.02,0.01,0,0
+"83","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/2021_WBFT_SA_ENG.pdf",1.17,0.06,0.04,0.07,0.08,0.05,0.01,0,0,0,0.02,1.57,0,0.04,0.01,0,0.02,0,0.01,0
+"84","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/Atl_Blacknose_SAR.pdf",1.25,0.02,0.01,0,0.01,0.09,0.05,0.02,0,0.04,0,1.9,0.03,0.03,0,0,0.02,0,0,0
+"85","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/B-8a-Gray_triggerfish_interim_9102020.pdf",1.25,0.01,0.01,0,0,0.17,0.02,0.03,0,0,0,1.96,0,0.07,0,0,0.05,0,0,0
+"86","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/Dusky_update_report_2016.pdf",1.1,0.02,0.06,0.03,0.04,0.06,0.01,0.01,0,0.07,0,2.05,0.04,0.04,0.01,0,0.03,0,0.01,0
+"87","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/KGM_GOM_SA_08282020_final-revision_3.pdf",0.93,0.12,0.04,0.04,0.05,0.04,0.02,0.11,0,0.01,0,1.95,0,0.07,0.02,0,0.01,0.01,0.01,0
+"88","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/S23_SAR_complete_and_final.pdf",1,0.05,0.01,0.01,0.01,0.07,0,0.05,0.07,0.01,0.01,2.06,0.01,0.03,0,0,0.02,0,0,0
+"89","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/S28UpdateSAR_V2.pdf",1.07,0.09,0.03,0.04,0.07,0.03,0.02,0.06,0.01,0,0,2.14,0,0.07,0.03,0.02,0.03,0,0.01,0
+"90","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/S34_ATSH_SAR.pdf",0.92,0.01,0.02,0.01,0.01,0.08,0.02,0.01,0,0.07,0,1.82,0.05,0.03,0,0,0.05,0,0.01,0
+"91","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/S51_FINAL_SAR_0.pdf",0.78,0.04,0.01,0.01,0.02,0.03,0.01,0.06,0.01,0.01,0.01,2.15,0,0.03,0.01,0,0.01,0,0,0
+"92","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/S52_Final_SAR_v2.pdf",0.52,0.03,0.01,0.02,0.04,0.02,0.01,0.02,0.01,0.01,0.02,1.69,0,0.02,0.01,0.02,0.02,0,0,0
+"93","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/S57_Final_SAR.pdf",1.31,0.04,0.06,0.01,0.03,0.04,0.01,0.07,0.01,0.02,0.02,1.68,0.01,0.04,0.04,0,0.01,0.01,0.02,0
+"94","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/S64_SAR_FINAL.pdf",0.83,0.05,0.02,0.02,0.03,0.03,0.02,0.05,0.01,0.01,0.01,1.63,0,0.04,0.02,0,0.01,0.01,0,0
+"95","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/S67_Final_SAR.pdf",0.91,0.06,0.02,0.03,0.05,0.05,0.03,0.04,0.01,0.02,0.01,1.94,0.01,0.03,0.01,0.02,0.03,0,0,0
+"96","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/S72_SAR_FINAL.pdf",0.94,0.11,0.03,0.02,0.03,0.04,0.02,0.05,0,0.01,0.02,2.21,0.01,0.08,0.05,0.02,0.01,0.01,0,0
+"97","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/SA BSB 2018.pdf",1.15,0.06,0.03,0.02,0.04,0.03,0.01,0.05,0,0.08,0,1.39,0.04,0.05,0.01,0.01,0.03,0,0,0
+"98","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/SEDAR_60_SA_Red_Porgy_SAR_4.9.2020.pdf",0.94,0.09,0.02,0.02,0.05,0.03,0.01,0.06,0.01,0.09,0,1.63,0.04,0.05,0.01,0.01,0.04,0,0.01,0
+"99","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/SEDAR65_FullSAR_12.8.2020_V3.pdf",1.26,0.01,0.02,0.02,0.03,0.07,0.02,0.02,0,0.05,0.01,1.68,0.04,0.02,0.03,0,0.04,0.01,0,0
+"100","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/SMA_ASS_ENG.pdf",1.32,0.02,0.01,0.01,0.02,0.17,0.07,0.01,0,0.22,0.01,1.8,0.04,0.07,0.02,0,0.02,0.01,0,0
+"101","NOAA-SWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SWFSC/agenda-item-d-3.pdf",0.96,0.04,0.02,0.03,0.05,0.07,0.01,0.02,0.01,0,0.01,1.63,0,0.1,0,0.02,0.02,0.01,0,0
+"102","NOAA-SWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SWFSC/SAC-11-07-MTG_Yellowfin tuna benchmark assessment 2019.pdf",1.1,0.08,0.03,0.03,0.04,0.11,0.04,0.01,0,0.03,0,2.2,0.01,0.06,0.02,0,0,0,0.01,0
+"103","NOAA-SWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SWFSC/SC14-SA-WP-11 ISC18 Shortfin Mako Stock Assessment.pdf",0.94,0.01,0.08,0.05,0.07,0.16,0.08,0,0.02,0.06,0.01,2.2,0,0.02,0.02,0,0.02,0.02,0.02,0
+"Sum",NA,NA,113.05,5.21,1.55,2.63,3.66,13.04,2.86,2.91,0.68,2.73,0.55,199.35,0.92,8.08,0.92,0.51,2.16,0.72,0.24,0.02
diff --git a/TextAnalysis/top20_proportion_Australia.csv b/TextAnalysis/top20_proportion_Australia.csv
new file mode 100644
index 0000000..4634532
--- /dev/null
+++ b/TextAnalysis/top20_proportion_Australia.csv
@@ -0,0 +1,16 @@
+"ID","Source","File_Path","biomass|b|abundance","spawning biomass|sb|spawning stock biomass|ssb|spawning stock output|sso|mature biomass|spawners","unfished|virgin|initial|equilibrium|unfished equilibrium","recruitment","recruits|recruit|age-0 fish|age-1 fish","catch|total mortality|harvest","catch per unit effort|cpue|catch rate|index of abundance|catch per effort|fishing success","landings|retained catch","spawning per recruit|spawning potential ratio|spr","maximum sustainable yield|msy","instantaneous total mortality rate|z","fishing mortality rate|f|instantaneous fishing mortality rate|harvest rate|exploitation rate|finite fishing mortality|apical f","fishing mortality at maximum sustainable yield|fmsy","weight|mass","length composition|length frequency|length observation","age composition|age frequency|age observation","projection|forecast|prediction","sex|gender","natural log of unfished recruitment|lnr0|logr0|logr_0|log(r0)|r0","plus group"
+"1","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/blue-warehou-rebuilding-strategy-2022.pdf",1.25,0.02,0.01,0.01,0.01,0.23,0.05,0,0,0.01,0,2.14,0,0.03,0,0,0,0,0,0
+"2","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/frr276.pdf",1.27,0.02,0.01,0.04,0.07,0.25,0.03,0,0.05,0,0.03,2.07,0,0.02,0.01,0.02,0,0.05,0,0
+"3","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/frr294.pdf",1.17,0.01,0.02,0.01,0.02,0.21,0.05,0.01,0,0.01,0.07,2.29,0,0.07,0,0,0.02,0.01,0,0
+"4","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Gummy-assessment-report-Dec2020.pdf",0.98,0.01,0.01,0,0,0.08,0.1,0,0,0,0,1.44,0,0.04,0.01,0.02,0.01,0.01,0,0.01
+"5","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/King threadfin stock assessment 2020.pdf",1.05,0.07,0.03,0.02,0.03,0.22,0.08,0,0,0.01,0,2.37,0,0.08,0.02,0.01,0,0.01,0.01,0
+"6","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Marine_Scalefish_Fishery_Assessment_Report_2020_-_FINAL_20200424.pdf",0.92,0.01,0,0.02,0.02,0.3,0.09,0,0,0,0,2.44,0,0.02,0,0,0,0,0,0
+"7","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/puntae_x2006a.pdf",1.22,0.08,0.01,0.04,0.05,0.25,0.02,0,0,0.01,0,1.96,0,0.11,0,0,0.01,0,0,0
+"8","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/stock-status-summary-2021-22-gemfish.pdf",1,0.02,0.01,0.02,0.03,0.32,0.05,0.03,0.01,0,0,2.22,0,0.07,0.01,0.01,0.01,0.02,0,0
+"9","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Stock assessment of black jewfish with data to December 2021.pdf",1.16,0.06,0.05,0.01,0.02,0.2,0.04,0.01,0,0.02,0,2.16,0.01,0.11,0.01,0,0,0,0.01,0
+"10","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Stock assessment of Queensland east coast dusky flathead with data to December 2020.pdf",0.81,0.06,0.03,0.02,0.02,0.19,0.04,0.01,0,0.01,0,1.94,0,0.1,0.02,0,0,0.05,0.01,0
+"11","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Stock assessment of Queensland red emperor 2022.pdf",0.69,0.07,0.04,0.01,0.01,0.16,0.04,0.01,0,0.01,0,2.13,0,0.08,0.01,0,0,0.01,0,0
+"12","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Stock assessment of the Queensland ballots saucer scallop_2022ed..pdf",1.2,0.06,0.04,0.03,0.04,0.27,0.12,0,0,0.01,0,1.91,0,0.08,0,0,0.01,0,0.01,0
+"13","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Stock assessments for SESSF- 2019 - Part 2.pdf",0.86,0,0.01,0,0,0.24,0.22,0,0,0,0,1.86,0,0.01,0,0,0,0,0,0
+"14","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Stock Assessments for SESSF 2020–21 - Part 1.pdf",1.05,0.06,0.03,0.1,0.11,0.12,0.05,0.01,0,0,0,1.96,0,0.09,0.02,0.01,0.02,0,0,0.01
+"Sum",NA,NA,14.63,0.55,0.3,0.33,0.43,3.04,0.98,0.08,0.06,0.09,0.1,28.89,0.01,0.91,0.11,0.07,0.08,0.16,0.04,0.02
diff --git a/TextAnalysis/top20_proportion_ICES.csv b/TextAnalysis/top20_proportion_ICES.csv
new file mode 100644
index 0000000..30dc6d2
--- /dev/null
+++ b/TextAnalysis/top20_proportion_ICES.csv
@@ -0,0 +1,10 @@
+"ID","Source","File_Path","biomass|b|abundance","spawning biomass|sb|spawning stock biomass|ssb|spawning stock output|sso|mature biomass|spawners","unfished|virgin|initial|equilibrium|unfished equilibrium","recruitment","recruits|recruit|age-0 fish|age-1 fish","catch|total mortality|harvest","catch per unit effort|cpue|catch rate|index of abundance|catch per effort|fishing success","landings|retained catch","spawning per recruit|spawning potential ratio|spr","maximum sustainable yield|msy","instantaneous total mortality rate|z","fishing mortality rate|f|instantaneous fishing mortality rate|harvest rate|exploitation rate|finite fishing mortality|apical f","fishing mortality at maximum sustainable yield|fmsy","weight|mass","length composition|length frequency|length observation","age composition|age frequency|age observation","projection|forecast|prediction","sex|gender","natural log of unfished recruitment|lnr0|logr0|logr_0|log(r0)|r0","plus group"
+"1","ICES","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/ICES/01_WGNSSK_Report_2019.pdf",0.96,0.04,0,0.03,0.03,0.11,0.01,0.08,0,0.04,0,1.39,0.02,0.05,0,0,0.03,0,0,0
+"2","ICES","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/ICES/ices2023_WKBCOD_report_2023.pdf",1.18,0.07,0,0.04,0.05,0.11,0,0.1,0,0.03,0,1.78,0.01,0.07,0,0.01,0.03,0,0,0
+"3","ICES","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/ICES/WKBALTCOD2_2019.pdf",1.24,0.04,0,0.02,0.02,0.11,0.02,0.02,0,0,0.01,1.66,0,0.04,0.01,0,0.01,0,0,0
+"4","ICES","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/ICES/WKBBALTPEL_2023_final_report.pdf",1.43,0.05,0.01,0.02,0.03,0.09,0,0.02,0.01,0.07,0.01,1.92,0.04,0.05,0,0,0.01,0,0,0
+"5","ICES","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/ICES/wkdem_2020.pdf",1,0.04,0,0.02,0.02,0.15,0,0.04,0,0.02,0,1.7,0.02,0.07,0,0.01,0.01,0,0,0
+"6","ICES","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/ICES/WKFlatNSCS_2020.pdf",1.38,0.03,0,0.01,0.02,0.07,0.01,0.36,0,0.04,0,2.06,0.02,0.07,0,0.01,0.01,0.01,0,0
+"7","ICES","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/ICES/WKMSYSPiCT_2021.pdf",1.18,0.01,0.02,0,0,0.14,0.06,0.06,0,0.07,0.01,1.91,0.03,0.05,0,0,0.02,0,0,0
+"8","ICES","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/ICES/WKSPRAT_2018_Report.pdf",1.15,0.03,0,0.04,0.05,0.15,0.01,0.01,0,0,0.01,1.75,0,0.04,0,0,0.03,0,0,0
+"Sum",NA,NA,9.52,0.31,0.03,0.18,0.22,0.93,0.11,0.69,0.01,0.27,0.04,14.17,0.14,0.44,0.01,0.03,0.15,0.01,0,0
diff --git a/TextAnalysis/top20_proportion_NOAA.csv b/TextAnalysis/top20_proportion_NOAA.csv
new file mode 100644
index 0000000..3c2eff7
--- /dev/null
+++ b/TextAnalysis/top20_proportion_NOAA.csv
@@ -0,0 +1,83 @@
+"ID","Source","File_Path","biomass|b|abundance","spawning biomass|sb|spawning stock biomass|ssb|spawning stock output|sso|mature biomass|spawners","unfished|virgin|initial|equilibrium|unfished equilibrium","recruitment","recruits|recruit|age-0 fish|age-1 fish","catch|total mortality|harvest","catch per unit effort|cpue|catch rate|index of abundance|catch per effort|fishing success","landings|retained catch","spawning per recruit|spawning potential ratio|spr","maximum sustainable yield|msy","instantaneous total mortality rate|z","fishing mortality rate|f|instantaneous fishing mortality rate|harvest rate|exploitation rate|finite fishing mortality|apical f","fishing mortality at maximum sustainable yield|fmsy","weight|mass","length composition|length frequency|length observation","age composition|age frequency|age observation","projection|forecast|prediction","sex|gender","natural log of unfished recruitment|lnr0|logr0|logr_0|log(r0)|r0","plus group"
+"1","NOAA-AFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-AFSC/BSAIatf.pdf",1.38,0.03,0,0,0,0.22,0.01,0,0,0,0.01,2.29,0,0.1,0,0.01,0.06,0,0,0
+"2","NOAA-AFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-AFSC/BSAIatka.pdf",1.2,0.04,0,0.02,0.03,0.11,0.02,0,0,0,0.01,1.75,0,0.12,0,0.02,0.01,0,0,0
+"3","NOAA-AFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-AFSC/BSAIocto.pdf",1.4,0.01,0,0.01,0.01,0.15,0.01,0,0,0,0.01,2.07,0,0.06,0,0,0,0,0,0
+"4","NOAA-AFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-AFSC/BSAIoflat (8).pdf",1.37,0.02,0,0.02,0.02,0.11,0,0,0,0,0,2.19,0,0.17,0,0,0,0,0,0
+"5","NOAA-AFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-AFSC/BSAIorock (5).pdf",1.51,0.03,0,0.01,0.01,0.13,0.01,0,0,0,0.01,2.18,0,0.12,0,0,0,0,0,0
+"6","NOAA-AFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-AFSC/BSAIpop.pdf",1.56,0.05,0,0,0,0.27,0,0,0,0,0,2.05,0,0.17,0,0.01,0.11,0,0,0
+"7","NOAA-AFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-AFSC/BSAIrocksole.pdf",1.32,0.03,0.01,0.08,0.11,0.11,0.01,0,0,0.02,0,1.84,0,0.13,0,0.06,0.03,0.04,0,0
+"8","NOAA-AFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-AFSC/BSAIrougheye (2).pdf",1.31,0.04,0,0.04,0.04,0.1,0.02,0,0,0,0.01,1.74,0,0.14,0.02,0.02,0.01,0,0,0
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+"78","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/SMA_ASS_ENG.pdf",1.32,0.02,0.01,0.01,0.02,0.17,0.07,0.01,0,0.22,0.01,1.8,0.04,0.07,0.02,0,0.02,0.01,0,0
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diff --git a/TextAnalysis/top20_wordcloud.jpg b/TextAnalysis/top20_wordcloud.jpg
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diff --git a/TextAnalysis/top20_wordcloud_ICES.jpg b/TextAnalysis/top20_wordcloud_ICES.jpg
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diff --git a/TextAnalysis/top20_wordcloud_NOAA.jpg b/TextAnalysis/top20_wordcloud_NOAA.jpg
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diff --git a/TextAnalysis/tree.txt b/TextAnalysis/tree.txt
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diff --git a/_pkgdown.yml b/_pkgdown.yml
index 4eb3102..8516f37 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -32,6 +32,8 @@ reference:
   - add_object
   - read_in
   - shiny_dd
+  - validate_Rd
+  
 
 navbar:
   structure:
diff --git a/stockassessmentdictionary.Rproj b/fishdictionary.Rproj
similarity index 100%
rename from stockassessmentdictionary.Rproj
rename to fishdictionary.Rproj