diff --git a/TextAnalysis/top10_analysis.R b/TextAnalysis/top10_analysis.R index 26aa218..5f97543 100644 --- a/TextAnalysis/top10_analysis.R +++ b/TextAnalysis/top10_analysis.R @@ -23,7 +23,7 @@ spawning_biomass <- data.frame( "spawning biomass|sb", "spawning stock biomass|ssb", "spawning output", - "spawning stock output|sso" + "spawning stock output|sso|spawners|effective spawning output" ), group = "spawning biomass" ) @@ -33,8 +33,7 @@ cpue <- data.frame( "catch per unit effort|cpue", "catch rate", "index of abundance", - "catch per effort", - "fishing success" + "catch per effort|fishing success" ), group = "catch per unit effort" ) @@ -43,7 +42,8 @@ catch <- data.frame( keyword = c( "catch", "total mortality", - "harvest" + "harvest", + "total removals" ), group = "catch" ) @@ -81,19 +81,19 @@ sex <- data.frame( # group = "spawner per recruit" # ) -weight <- data.frame( +mass <- data.frame( keyword = c( - "weight", - "mass" + "mass", + "weight" ), - group = "weight" + group = "mass" ) lnr0 <- data.frame( keyword = c( "natural log of unfished recruitment|lnr0", "logr0", - "logr_0", + # "logr_0", "log(r0)", "r0" ), @@ -101,7 +101,7 @@ lnr0 <- data.frame( ) keyword_map <- rbind(catch, cpue, landings, - lnr0, projection, sex, spawning_biomass, weight) + lnr0, projection, sex, spawning_biomass, mass) keyword_map$keyword_id <- as.factor(1:nrow(keyword_map)) keyword <- keyword_map$keyword @@ -112,7 +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", "Source", "File_Path", keyword) +col_name <- c("ID", "Region", "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) <- @@ -234,40 +234,48 @@ proportion_database<-read.csv(file=here::here("TextAnalysis", "top10_proportion. colnames(presence_database) <- col_name data_reshape <- reshape2::melt( presence_database[, c(2, 4:ncol(presence_database))], - id = c("Source") + id = c("Region") ) -colnames(data_reshape) <- c("Source", "keyword", "value") +colnames(data_reshape) <- c("Region", "keyword", "value") data_merge <- merge(data_reshape, keyword_map, by= "keyword") -sum_by_group <- aggregate(value ~ keyword+keyword_id+group+Source, data = data_merge, sum) +sum_by_group <- aggregate(value ~ keyword+keyword_id+group+Region, data = data_merge, sum) sum_by_group <- sum_by_group[order(sum_by_group$keyword_id),] group <- unique(sum_by_group$group) - -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)) + +sum_by_group$group <- factor(sum_by_group$group, levels = group) +# jpeg(filename = here::here("TextAnalysis", "top10_barplot_sum.jpg"), width=200, height=150, units="mm", res=1200) +ggplot(sum_by_group, aes(fill=Region, y=value, x=keyword_id)) + geom_bar(position="dodge", stat="identity") + - facet_wrap(~group, scales = "free_x") + + facet_wrap(~group, scales = "free_x", ncol = 2) + labs( x = "Term ID", y = "Frequency" ) + scale_fill_viridis(discrete = TRUE) + - theme_bw() -dev.off() + theme( + panel.background = NULL, + panel.grid.major.x = element_blank(), + panel.grid.major.y = element_blank()) +ggsave(here::here("TextAnalysis", "top10_barplot_sum.jpg")) +# dev.off() -mean_by_group <- aggregate(value ~ keyword+keyword_id+group+Source, data = data_merge, mean) +mean_by_group <- aggregate(value ~ keyword+keyword_id+group+Region, 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_mean.jpg"), width=200, height=150, units="mm", res=1200) -ggplot(mean_by_group, aes(fill=Source, y=value*100, x=keyword_id)) + +mean_by_group$group <- factor(sum_by_group$group, levels = group) +# jpeg(filename = here::here("TextAnalysis", "top10_barplot_mean.jpg"), width=200, height=150, units="mm", res=1200) +ggplot(mean_by_group, aes(fill=Region, y=value*100, x=keyword_id)) + geom_bar(position="dodge", stat="identity") + - facet_wrap(~group, scales = "free_x") + + facet_wrap(~group, scales = "free_x", ncol = 2) + labs( x = "Term ID", y = "Presence (%)" ) + scale_fill_viridis(discrete = TRUE) + + geom_vline(xintercept = c(0:5)+0.5) + + scale_y_continuous(expand=expand_scale(mult=c(0.0,0.0)))+ + scale_x_discrete(expand=expand_scale(mult=c(0.0,0.0))) + theme_bw() -dev.off() +ggsave(here::here("TextAnalysis", "top10_barplot_mean.jpg")) +# dev.off() diff --git a/TextAnalysis/top10_barplot_mean.jpg b/TextAnalysis/top10_barplot_mean.jpg index 4f1208a..9d60707 100644 Binary files a/TextAnalysis/top10_barplot_mean.jpg and b/TextAnalysis/top10_barplot_mean.jpg differ diff --git a/TextAnalysis/top10_barplot_sum.jpg b/TextAnalysis/top10_barplot_sum.jpg deleted file mode 100644 index 9b46845..0000000 Binary files a/TextAnalysis/top10_barplot_sum.jpg and /dev/null differ diff --git a/TextAnalysis/top10_frequency.csv b/TextAnalysis/top10_frequency.csv index 2048c70..018cec8 100644 --- a/TextAnalysis/top10_frequency.csv +++ b/TextAnalysis/top10_frequency.csv @@ -1,105 +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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-"100","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/SMA_ASS_ENG.pdf",136,0,9,69,0,1,0,0,11,0,0,0,0,0,4,1,1,3,5,0,6,3,1,0,12,0 -"101","NOAA-SWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SWFSC/agenda-item-d-3.pdf",52,0,32,6,0,10,0,0,53,0,8,0,0,0,0,1,27,1,14,2,44,47,0,3,15,0 -"102","NOAA-SWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SWFSC/SAC-11-07-MTG_Yellowfin tuna benchmark assessment 2019.pdf",81,0,5,18,3,34,0,0,0,10,6,0,0,0,4,2,0,1,4,0,46,0,0,1,8,1 -"103","NOAA-SWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SWFSC/SC14-SA-WP-11 ISC18 Shortfin Mako Stock Assessment.pdf",163,0,4,110,0,0,0,0,2,0,1,11,0,11,12,3,14,0,12,1,6,2,1,4,9,0 -"Sum",NA,NA,16718,236,2703,5221,576,417,6,3,10532,298,299,55,0,55,402,821,882,254,925,176,5130,3081,950,75,2672,94 +"ID","Region","File_Path","catch","total mortality","harvest","total removals","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","log(r0)","r0","projection","forecast","prediction","sex","gender","spawning biomass|sb","spawning stock biomass|ssb","spawning output","spawning stock output|sso|spawners|effective spawning output","mass","weight" +"1","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/blue-warehou-rebuilding-strategy-2022.pdf",83,0,14,0,14,0,12,0,2,0,0,0,0,0,0,0,0,2,0,6,0,0,4,0,2 +"2","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/frr276.pdf",435,18,1,0,1,6,6,0,0,0,0,0,0,0,0,0,0,38,0,4,7,0,18,0,12 +"3","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/frr294.pdf",337,1,53,0,39,28,7,0,12,2,0,0,0,2,15,0,0,26,0,5,0,0,8,0,12 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+"102","NOAA-SWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SWFSC/SAC-11-07-MTG_Yellowfin tuna benchmark assessment 2019.pdf",0.05,0,0,0,0.01,0,0.02,0,0,0.01,0,0,0,0,0,0,0,0,0,0.03,0,0,0.03,0,0.01 +"103","NOAA-SWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SWFSC/SC14-SA-WP-11 ISC18 Shortfin Mako Stock Assessment.pdf",0.1,0,0,0,0.07,0,0,0,0,0,0,0.01,0.01,0.01,0,0.01,0,0.01,0,0,0,0,0.01,0,0.01 +"Sum",NA,NA,8.31,0.03,1.23,0.03,1.65,0.21,0.18,0,2.69,0.12,0.05,0.01,0.01,0.1,0.47,0.11,0.03,0.26,0.03,2.31,1.79,0.29,0.95,0.02,0.99 diff --git a/TextAnalysis/top20_analysis.R b/TextAnalysis/top20_analysis.R index eb2a6c8..d3fbc25 100644 --- a/TextAnalysis/top20_analysis.R +++ b/TextAnalysis/top20_analysis.R @@ -5,6 +5,9 @@ library(tm) library(stringr) library(wordcloud) library(RColorBrewer) +library(jpeg) +library(grid) +library(gridExtra) # Download stock assessment reports from Google Drive ------------- @@ -80,24 +83,273 @@ if (authorize_GoogleDrive) { ) } + +# run_text_mining function ------------------------------------------------ + +run_text_mining <- function(keyword, xlabels, working_path, + subfolder_path_all, subfolder_name_all, + subfolder_info, scenario_name) { + wordcloud_data <- wordcloud_data_mean <-vector(mode="list", length=length(subfolder_info)) + 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", "Region", "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) + ) + + # 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) + ) + + 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], "_", scenario_name, ".csv")), row.names=FALSE) + write.csv(presence_database, file=here::here("TextAnalysis", paste0("top20_presence_", names(subfolder_info)[org], "_", scenario_name, ".csv")), row.names=FALSE) + write.csv(proportion_database, file=here::here("TextAnalysis", paste0("top20_proportion_", names(subfolder_info)[org], "_", scenario_name, ".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], "_", scenario_name, ".csv"))) + presence_database<-read.csv(file=here::here("TextAnalysis", paste0("top20_presence_", names(subfolder_info)[org], "_", scenario_name, ".csv"))) + proportion_database<-read.csv(file=here::here("TextAnalysis", paste0("top20_proportion_", names(subfolder_info)[org], "_", scenario_name, ".csv"))) + + word_frequency <- as.matrix(frequency_database[frequency_database$ID == "Sum", 4:ncol(frequency_database)]) + word_presence <- as.matrix(presence_database[presence_database$ID == "Sum", 4:ncol(presence_database)]) + word_presence_mean <- as.matrix(presence_database[presence_database$ID == "Sum", 4:ncol(presence_database)])/(nrow(presence_database)-1)*100 + word_proportion <- as.matrix(proportion_database[proportion_database$ID == "Sum", 4:ncol(proportion_database)]) + + # barplot + jpeg(filename = here::here("TextAnalysis", paste0("top20_barplot_", names(subfolder_info)[org], "_", scenario_name, ".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], "_", scenario_name, ".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 = "Presence (%)") + text(presence_barplot - 0.25, par("usr")[3] - 0.25, xlabels, xpd = TRUE, srt = 40, adj = 1, cex = 0.7) + dev.off() + + jpeg(filename = here::here("TextAnalysis", paste0("top20_presence_mean_", names(subfolder_info)[org], "_", scenario_name, ".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_mean, xaxt = "n", ylab = "Presence (%)") + 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], "_mean_presence_grays", "_", scenario_name, ".jpg")), width = 200, height = 200, units = "mm", res = 1200) + par(mar = c(0.1, 0.1, 0.1, 0.1), mfrow = c(1, 1)) + set.seed(123) + wordcloud( + words = xlabels, freq = word_presence_mean, rot.per = 0, + scale = c(1.5, 0.5), + min.freq = 1, + random.order = F, + colors = grDevices::gray.colors(10, rev = TRUE), + use.r.layout = T + ) + text(0.1, 0.8, scenario_name) + dev.off() + + jpeg(filename = here::here("TextAnalysis", paste0("top20_wordcloud_", names(subfolder_info)[org], "_mean_presence_black", "_", scenario_name, ".jpg")), width = 200, height = 200, units = "mm", res = 1200) + par(mar = c(0.1, 0.1, 0.1, 0.1), mfrow = c(1, 1)) + set.seed(123) + wordcloud( + words = xlabels, freq = word_presence_mean, rot.per = 0, + scale = c(1.5, 0.5), + min.freq = 1, + random.order = F, + use.r.layout = T + ) + text(0.1, 0.8, scenario_name) + dev.off() + } +} + # Define keyword --------------------------------------------------------------- +working_path <- here::here("StockAssessment") +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") + +keyword <- c( + "biomass|b", "abundance", + "spawning biomass|sb", "spawning stock biomass|ssb", "spawning output", "spawning stock output|sso", "mature biomass", "spawners", "effective spawning output", + "unfished", "virgin", "initial equilibrium", "unfished equilibrium", + "recruitment", + "recruits", "recruit", "age 0 fish", "age 1 fish", + "catch", "total mortality", "harvest", "total removals", + "catch per unit effort|cpue", "catch rate", "index of abundance", "catch per effort", "fishing success", + "landings", "retained catch", + "spawner per recruit|spr", "spawning potential ratio|spr", + "maximum sustainable yield|msy", + "instantaneous total mortality rate|z", + "fishing mortality|f", "instantaneous fishing mortality rate", "harvest rate", "exploitation rate", "finite fishing mortality", "apical f", + "fishing mortality at maximum sustainable yield|fmsy", + "mass", "weight", + "length composition", "length frequency", "length observation", "size frequency", "size composition", + "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" +) + +xlabels <- c( + "Biomass", "Abundance", + "Spawning biomass", "Spawning stock biomass", "Spawning output", "Spawning stock output", "Mature biomass", "Spawners", "Effective spawning output", + "Unfished", "Virgin", "Initial equilibrium", "Unfished equilibrium", + "Recruitment", + "Recruits", "Recruit", "Age 0 fish", "Age 1 fish", + "Catch", "Total mortality", "Harvest", "Total removals", + "Catch per unit effort", "Catch rate", "Index of abundance", "Catch per effort", "Fishing success", + "Landings", "Retained catch", + "Spawner per recruit", "Spawning potential ratio", + "Maximum sustainable yield", + "Instantaneous total mortality rate", + "Fishing mortality", "Instantaneous fishing mortality rate", "Harvest rate", "Exploitation rate", "Finite fishing mortality", "Apical f", + "Fishing mortality at maximum sustainable yield", + "Mass", "Weight", + "Length composition", "Length frequency", "Length observation", "Size frequency", "Size composition", + "Age composition", "Age frequency", "Age observation", + "Projection", "Forecast", "Prediction", + "Sex", "Gender", + "Natural log of unfished recruitment", "LogR0","LogR_0", "Log(R0)", "R0", + "Plus group" +) + +run_text_mining(keyword = keyword, xlabels = xlabels, working_path = working_path, + subfolder_path_all = subfolder_path_all, subfolder_name_all = subfolder_name_all, + subfolder_info = subfolder_info, scenario_name = "A") keyword <- c( "biomass|b|abundance", - "spawning biomass|sb|spawning stock biomass|ssb|spawning stock output|sso|mature biomass|spawners", - "unfished|virgin|initial|equilibrium|unfished equilibrium", + "spawning biomass|sb|spawning stock biomass|ssb|spawning output|spawning stock output|sso|mature biomass|spawners|effective spawning output", + "unfished|virgin|initial equilibrium|unfished equilibrium", "recruitment", - "recruits|recruit|age-0 fish|age-1 fish", - "catch|total mortality|harvest", + "recruits|recruit|age 0 fish|age 1 fish", + "catch|total mortality|harvest|total removals", "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", + "spawner 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|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", + "mass|weight", + "length composition|length frequency|length observation|size frequency|size composition", "age composition|age frequency|age observation", "projection|forecast|prediction", "sex|gender", @@ -105,196 +357,53 @@ keyword <- c( "plus group" ) -# Create keywords 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", + "Fishing mortality at maximum sustainable yield", + "Mass", + "Length composition", + "Age composition", + "Projection", + "Sex", + "Natural log of unfished recruitment", + "Plus group" +) -working_path <- here::here("StockAssessment") -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) +run_text_mining(keyword = keyword, xlabels = xlabels, working_path = working_path, + subfolder_path_all = subfolder_path_all, subfolder_name_all = subfolder_name_all, + subfolder_info = subfolder_info, scenario_name = "B") -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) - ) - - # 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]]$content)) * 100, digits = 2) - } - - if (subfolder_id == 1 & file_id == 1) { - frequency_database[1, ] <- c(NA, subfolder_name[subfolder_id], file_path[file_id], frequency) - - presence_database[1, ] <- c(NA, subfolder_name[subfolder_id], file_path[file_id], presence) - - proportion_database[1, ] <- c(NA, subfolder_name[subfolder_id], file_path[file_id], proportion) - } else { - frequency_database <- rbind( - frequency_database, - c(NA, subfolder_name[subfolder_id], file_path[file_id], frequency) - ) - - presence_database <- rbind( - presence_database, - c(NA, subfolder_name[subfolder_id], file_path[file_id], presence) - ) - - proportion_database <- rbind( - proportion_database, - c(NA, subfolder_name[subfolder_id], file_path[file_id], proportion) - ) - } - } - } - - frequency_database$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() - -} +jpeg(filename = here::here("TextAnalysis", "top20_wordcloud_All_mean_presence_grays_AB.jpg"), + width = 200, height = 120, units = "mm", res = 1200) +before_img <- rasterGrob(as.raster(jpeg::readJPEG(here::here("TextAnalysis", + "top20_wordcloud_All_mean_presence_grays_A.jpg"))), + interpolate = FALSE) +after_img <- rasterGrob(as.raster(jpeg::readJPEG(here::here("TextAnalysis", + "top20_wordcloud_All_mean_presence_grays_B.jpg"))), + interpolate = FALSE) +gridExtra::grid.arrange(before_img, after_img, ncol = 2) +dev.off() + +jpeg(filename = here::here("TextAnalysis", "top20_wordcloud_All_mean_presence_black_AB.jpg"), + width = 200, height = 120, units = "mm", res = 1200) +before_img <- rasterGrob(as.raster(jpeg::readJPEG(here::here("TextAnalysis", + "top20_wordcloud_All_mean_presence_black_A.jpg"))), + interpolate = FALSE) +after_img <- rasterGrob(as.raster(jpeg::readJPEG(here::here("TextAnalysis", + "top20_wordcloud_All_mean_presence_black_B.jpg"))), + interpolate = FALSE) +gridExtra::grid.arrange(before_img, after_img, ncol = 2) +dev.off() diff --git a/TextAnalysis/top20_barplot_All.jpg b/TextAnalysis/top20_barplot_All.jpg deleted file mode 100644 index f82ac0a..0000000 Binary files a/TextAnalysis/top20_barplot_All.jpg and /dev/null differ diff --git a/TextAnalysis/top20_barplot_Australia.jpg b/TextAnalysis/top20_barplot_Australia.jpg deleted file mode 100644 index 3dc410a..0000000 Binary files a/TextAnalysis/top20_barplot_Australia.jpg and /dev/null differ diff --git a/TextAnalysis/top20_barplot_ICES.jpg b/TextAnalysis/top20_barplot_ICES.jpg deleted file mode 100644 index 82766fd..0000000 Binary files a/TextAnalysis/top20_barplot_ICES.jpg and /dev/null differ diff --git a/TextAnalysis/top20_barplot_NOAA.jpg b/TextAnalysis/top20_barplot_NOAA.jpg deleted file mode 100644 index 84b5d6d..0000000 Binary files a/TextAnalysis/top20_barplot_NOAA.jpg and /dev/null differ diff --git a/TextAnalysis/top20_frequency_All_A.csv b/TextAnalysis/top20_frequency_All_A.csv new file mode 100644 index 0000000..778b273 --- /dev/null +++ b/TextAnalysis/top20_frequency_All_A.csv @@ -0,0 +1,105 @@ +"ID","Region","File_Path","biomass|b","abundance","spawning biomass|sb","spawning stock biomass|ssb","spawning output","spawning stock output|sso","mature biomass","spawners","effective spawning output","unfished","virgin","initial equilibrium","unfished equilibrium","recruitment","recruits","recruit","age 0 fish","age 1 fish","catch","total mortality","harvest","total removals","catch per unit effort|cpue","catch rate","index of abundance","catch per effort","fishing success","landings","retained catch","spawner per recruit|spr","spawning potential ratio|spr","maximum sustainable yield|msy","instantaneous total mortality rate|z","fishing mortality|f","instantaneous fishing mortality rate","harvest rate","exploitation rate","finite fishing mortality","apical f","fishing mortality at maximum sustainable yield|fmsy","mass","weight","length composition","length frequency","length observation","size frequency","size composition","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",18,23,6,0,0,0,0,0,0,5,0,0,0,4,0,1,0,0,83,0,14,0,14,0,12,0,0,2,0,1,2,3,0,409,0,0,0,0,0,0,0,2,0,0,0,0,0,1,0,0,0,0,0,2,0,0,0,0,0,0,0 +"2","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/frr276.pdf",137,14,4,7,0,0,0,0,0,8,0,0,0,95,0,12,0,0,435,18,1,0,1,6,6,0,0,0,0,87,100,0,62,1597,0,0,0,0,0,0,0,12,16,4,0,0,1,38,3,0,0,0,0,38,0,0,0,0,0,0,0 +"3","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/frr294.pdf",313,31,5,0,0,0,13,1,0,29,11,0,0,37,3,10,0,0,337,1,53,0,39,28,7,0,0,12,2,0,0,21,185,2089,0,0,6,0,0,0,0,12,0,0,0,0,44,7,0,0,15,0,0,26,0,0,0,0,0,2,0 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b/TextAnalysis/top20_frequency_All_B.csv @@ -1,105 +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 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-"100","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 -"101","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 -"102","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 -"103","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,282167,10742,4153,6506,8895,27574,8006,10900,2011,6418,1664,490620,2519,15161,2606,1608,3842,2081,780,208 +"ID","Region","File_Path","biomass|b|abundance","spawning biomass|sb|spawning stock biomass|ssb|spawning output|spawning stock output|sso|mature biomass|spawners|effective spawning output","unfished|virgin|initial equilibrium|unfished equilibrium","recruitment","recruits|recruit|age 0 fish|age 1 fish","catch|total mortality|harvest|total removals","catch per unit effort|cpue|catch rate|index of abundance|catch per effort|fishing success","landings|retained catch","spawner per recruit|spawning potential ratio|spr","maximum sustainable yield|msy","instantaneous total mortality rate|z","fishing mortality|f|instantaneous fishing mortality rate|harvest rate|exploitation rate|finite fishing mortality|apical f","fishing mortality at maximum sustainable yield|fmsy","mass|weight","length composition|length frequency|length observation|size frequency|size composition","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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+"91","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/S51_FINAL_SAR_0.pdf",4085,192,22,75,120,141,67,309,27,34,53,11298,14,67,91,7,61,25,18,0 +"92","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/S52_Final_SAR_v2.pdf",3443,190,32,154,247,132,83,108,48,37,108,11099,8,21,41,142,111,2,2,2 +"93","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/S57_Final_SAR.pdf",3514,128,72,40,75,105,28,194,17,45,58,4507,20,38,110,0,22,25,55,1 +"94","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/S64_SAR_FINAL.pdf",5816,328,62,136,204,203,109,340,96,47,81,11390,23,87,143,23,45,38,26,3 +"95","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/S67_Final_SAR.pdf",3248,229,31,114,186,175,107,145,47,65,29,6897,31,39,50,72,89,10,10,1 +"96","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/S72_SAR_FINAL.pdf",3539,430,36,83,124,152,68,178,6,42,93,8354,20,101,204,59,42,21,15,4 +"97","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/SA BSB 2018.pdf",3137,176,10,49,109,82,25,145,12,230,5,3782,103,65,32,38,95,6,7,1 +"98","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/SEDAR_60_SA_Red_Porgy_SAR_4.9.2020.pdf",2825,259,15,57,147,106,26,193,19,257,13,4900,118,57,43,40,111,7,18,1 +"99","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/SEDAR65_FullSAR_12.8.2020_V3.pdf",8869,91,52,154,243,518,107,125,4,318,53,11823,263,90,201,1,289,80,21,0 +"100","NOAA-SEFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SEFSC/SMA_ASS_ENG.pdf",1498,22,5,10,26,200,75,11,0,249,12,2043,49,14,21,0,19,16,4,0 +"101","NOAA-SWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SWFSC/agenda-item-d-3.pdf",2168,100,8,76,112,156,16,54,12,11,32,3675,3,17,8,46,40,22,8,0 +"102","NOAA-SWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SWFSC/SAC-11-07-MTG_Yellowfin tuna benchmark assessment 2019.pdf",1665,121,20,47,65,170,59,10,0,52,4,3325,18,10,33,1,3,6,10,0 +"103","NOAA-SWFSC","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/NOAA-SWFSC/SC14-SA-WP-11 ISC18 Shortfin Mako Stock Assessment.pdf",1461,17,55,79,110,241,123,3,33,99,15,3421,4,10,37,0,38,34,24,4 +"Sum",NA,NA,282167,11706,1730,6506,8926,28055,8006,10900,2008,6418,1664,490620,2519,3160,3089,1608,3842,2081,780,208 diff --git a/TextAnalysis/top20_frequency_Australia.csv b/TextAnalysis/top20_frequency_Australia.csv deleted file mode 100644 index dda8087..0000000 --- a/TextAnalysis/top20_frequency_Australia.csv +++ /dev/null @@ -1,16 +0,0 @@ -"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_Australia_A.csv b/TextAnalysis/top20_frequency_Australia_A.csv new file mode 100644 index 0000000..d8b7603 --- /dev/null +++ b/TextAnalysis/top20_frequency_Australia_A.csv @@ -0,0 +1,16 @@ +"ID","Region","File_Path","biomass|b","abundance","spawning biomass|sb","spawning stock biomass|ssb","spawning output","spawning stock output|sso","mature biomass","spawners","effective spawning output","unfished","virgin","initial equilibrium","unfished equilibrium","recruitment","recruits","recruit","age 0 fish","age 1 fish","catch","total mortality","harvest","total removals","catch per unit effort|cpue","catch rate","index of abundance","catch per effort","fishing success","landings","retained catch","spawner per recruit|spr","spawning potential ratio|spr","maximum sustainable yield|msy","instantaneous total mortality rate|z","fishing mortality|f","instantaneous fishing mortality rate","harvest rate","exploitation rate","finite fishing mortality","apical f","fishing mortality at maximum sustainable yield|fmsy","mass","weight","length composition","length frequency","length observation","size frequency","size composition","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",18,23,6,0,0,0,0,0,0,5,0,0,0,4,0,1,0,0,83,0,14,0,14,0,12,0,0,2,0,1,2,3,0,409,0,0,0,0,0,0,0,2,0,0,0,0,0,1,0,0,0,0,0,2,0,0,0,0,0,0,0 +"2","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/frr276.pdf",137,14,4,7,0,0,0,0,0,8,0,0,0,95,0,12,0,0,435,18,1,0,1,6,6,0,0,0,0,87,100,0,62,1597,0,0,0,0,0,0,0,12,16,4,0,0,1,38,3,0,0,0,0,38,0,0,0,0,0,0,0 +"3","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/frr294.pdf",313,31,5,0,0,0,13,1,0,29,11,0,0,37,3,10,0,0,337,1,53,0,39,28,7,0,0,12,2,0,0,21,185,2089,0,0,6,0,0,0,0,12,0,0,0,0,44,7,0,0,15,0,0,26,0,0,0,0,0,2,0 +"4","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Gummy-assessment-report-Dec2020.pdf",48,15,2,0,0,0,7,0,0,4,0,0,0,4,0,0,0,0,34,0,2,0,122,0,4,0,0,5,0,0,0,3,0,391,0,0,0,0,0,0,0,10,1,15,0,0,0,13,1,1,0,0,0,11,0,0,0,0,0,0,7 +"5","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/King threadfin stock assessment 2020.pdf",132,30,40,0,14,0,0,0,0,33,1,0,0,35,15,1,0,0,148,0,138,0,7,59,0,0,0,5,1,5,5,12,3,1066,1,0,0,0,0,0,0,18,4,0,0,0,0,9,0,0,1,1,0,5,0,6,0,0,0,11,1 +"6","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Marine_Scalefish_Fishery_Assessment_Report_2020_-_FINAL_20200424.pdf",412,16,8,0,0,0,0,2,0,0,0,0,0,67,1,1,0,0,861,0,30,0,216,46,0,0,0,2,0,0,0,0,5,2845,0,0,3,0,0,0,0,11,0,1,0,1,1,2,0,0,0,0,0,4,0,0,0,0,0,0,0 +"7","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/puntae_x2006a.pdf",151,26,72,10,0,0,0,0,0,5,2,0,0,40,0,0,0,0,82,0,0,0,12,2,3,0,0,3,1,0,2,6,3,602,0,0,8,0,0,1,9,7,0,2,0,0,0,0,0,0,1,0,1,2,0,0,0,0,0,1,0 +"8","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/stock-status-summary-2021-22-gemfish.pdf",24,5,6,1,0,0,0,0,0,4,0,0,0,6,0,0,0,0,50,0,7,1,6,2,0,0,0,7,2,1,3,0,0,185,0,0,0,0,0,0,0,2,1,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,1,0 +"9","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Stock assessment of black jewfish with data to December 2021.pdf",100,12,36,13,6,0,0,0,0,30,0,0,0,10,5,0,0,0,202,0,10,0,0,6,1,0,0,1,15,0,0,20,0,571,0,0,0,0,0,8,0,25,2,0,0,0,0,3,0,0,1,0,0,0,0,10,0,0,0,2,0 +"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",122,10,47,2,5,0,0,0,0,32,1,0,1,23,0,0,0,0,120,0,120,0,0,15,0,0,0,0,19,0,0,18,1,672,0,0,0,0,0,2,4,11,8,6,0,0,0,0,0,0,0,1,2,20,42,9,0,0,0,0,0 +"11","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Stock assessment of Queensland red emperor 2022.pdf",179,22,96,8,5,0,0,0,0,36,4,0,0,21,2,0,0,0,196,1,169,0,0,35,4,0,0,0,34,0,0,22,0,1474,0,0,0,0,0,0,1,25,3,1,0,1,0,4,0,0,0,1,0,11,0,4,0,0,0,0,0 +"12","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Stock assessment of the Queensland ballots saucer scallop_2022ed..pdf",91,15,35,1,0,0,0,0,0,16,11,0,0,30,2,0,0,0,160,0,73,0,11,46,2,0,0,1,0,0,0,5,3,552,0,2,0,0,0,0,0,13,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,7,0 +"13","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Stock assessments for SESSF- 2019 - Part 2.pdf",171,45,6,0,0,0,0,0,0,8,0,0,0,0,0,0,0,0,1044,0,36,9,1103,117,1,0,0,4,0,0,0,0,1,4421,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0 +"14","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Stock Assessments for SESSF 2020–21 - Part 1.pdf",671,103,283,124,0,0,0,0,0,77,21,1,5,768,9,2,0,0,522,2,93,8,281,53,2,0,0,34,14,12,17,6,3,4334,0,0,0,0,0,0,21,34,114,24,0,0,1,38,0,5,8,8,0,13,1,10,0,0,0,9,72 +"Sum",NA,NA,2569,367,646,166,30,0,20,3,0,287,51,1,6,1140,37,27,0,0,4274,22,746,18,1812,415,42,0,0,76,88,106,129,116,266,21208,1,2,17,0,0,11,36,182,149,53,0,2,47,115,4,6,29,11,3,132,43,39,0,0,0,33,80 diff --git a/TextAnalysis/top20_frequency_Australia_B.csv b/TextAnalysis/top20_frequency_Australia_B.csv new file mode 100644 index 0000000..9a03d00 --- /dev/null +++ b/TextAnalysis/top20_frequency_Australia_B.csv @@ -0,0 +1,16 @@ +"ID","Region","File_Path","biomass|b|abundance","spawning biomass|sb|spawning stock biomass|ssb|spawning output|spawning stock output|sso|mature biomass|spawners|effective spawning output","unfished|virgin|initial equilibrium|unfished equilibrium","recruitment","recruits|recruit|age 0 fish|age 1 fish","catch|total mortality|harvest|total removals","catch per unit effort|cpue|catch rate|index of abundance|catch per effort|fishing success","landings|retained catch","spawner per recruit|spawning potential ratio|spr","maximum sustainable yield|msy","instantaneous total mortality rate|z","fishing mortality|f|instantaneous fishing mortality rate|harvest rate|exploitation rate|finite fishing mortality|apical f","fishing mortality at maximum sustainable yield|fmsy","mass|weight","length composition|length frequency|length observation|size frequency|size composition","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",711,10,5,4,6,133,31,2,2,3,0,1214,0,2,0,1,0,2,0,0 +"2","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/frr276.pdf",2720,37,8,95,143,543,65,0,100,0,62,4451,0,12,22,42,0,100,0,0 +"3","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/frr294.pdf",3139,30,40,37,57,573,135,14,0,21,185,6161,0,12,44,7,55,35,5,0 +"4","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Gummy-assessment-report-Dec2020.pdf",1207,12,4,4,5,98,126,5,0,3,0,1780,0,10,18,20,10,12,0,7 +"5","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/King threadfin stock assessment 2020.pdf",1666,119,34,35,52,380,121,6,5,12,3,3765,0,18,25,9,5,9,17,1 +"6","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Marine_Scalefish_Fishery_Assessment_Report_2020_-_FINAL_20200424.pdf",3471,53,0,67,74,1167,341,2,0,0,5,9234,0,11,3,2,0,11,0,0 +"7","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/puntae_x2006a.pdf",1279,87,7,40,52,267,21,4,2,6,3,2063,1,17,2,0,6,5,1,0 +"8","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/stock-status-summary-2021-22-gemfish.pdf",289,7,4,6,9,95,14,9,3,0,0,645,0,3,3,2,3,6,1,0 +"9","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Stock assessment of black jewfish with data to December 2021.pdf",1332,80,31,10,21,231,45,16,0,20,0,2475,8,25,10,4,4,0,12,0 +"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",1071,90,33,23,27,284,57,19,0,18,1,2560,2,16,27,0,4,64,9,0 +"11","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Stock assessment of Queensland red emperor 2022.pdf",1575,166,40,21,24,385,95,34,0,22,0,4852,0,27,17,5,2,25,4,0 +"12","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Stock assessment of the Queensland ballots saucer scallop_2022ed..pdf",1101,52,27,30,35,255,109,1,0,5,3,1763,0,15,0,0,13,0,8,0 +"13","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Stock assessments for SESSF- 2019 - Part 2.pdf",5919,21,8,0,0,1648,1536,4,0,0,1,12834,0,1,0,0,1,0,0,0 +"14","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Stock Assessments for SESSF 2020–21 - Part 1.pdf",8327,512,99,768,846,1001,378,48,17,6,3,15600,0,82,171,51,121,24,20,72 +"Sum",NA,NA,33807,1276,340,1140,1351,7060,3074,164,129,116,266,69397,11,251,342,143,224,293,77,80 diff --git a/TextAnalysis/top20_frequency_ICES.csv b/TextAnalysis/top20_frequency_ICES.csv deleted file mode 100644 index e355d27..0000000 --- a/TextAnalysis/top20_frequency_ICES.csv +++ /dev/null @@ -1,10 +0,0 @@ -"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 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-"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_ICES_A.csv b/TextAnalysis/top20_frequency_ICES_A.csv new file mode 100644 index 0000000..c062293 --- /dev/null +++ b/TextAnalysis/top20_frequency_ICES_A.csv @@ -0,0 +1,10 @@ +"ID","Region","File_Path","biomass|b","abundance","spawning biomass|sb","spawning stock biomass|ssb","spawning output","spawning stock output|sso","mature biomass","spawners","effective spawning output","unfished","virgin","initial equilibrium","unfished equilibrium","recruitment","recruits","recruit","age 0 fish","age 1 fish","catch","total mortality","harvest","total removals","catch per unit effort|cpue","catch rate","index of abundance","catch per effort","fishing success","landings","retained catch","spawner per recruit|spr","spawning potential ratio|spr","maximum sustainable yield|msy","instantaneous total mortality rate|z","fishing mortality|f","instantaneous fishing mortality rate","harvest rate","exploitation rate","finite fishing mortality","apical f","fishing mortality at 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b/TextAnalysis/top20_frequency_ICES_B.csv new file mode 100644 index 0000000..42aa5d9 --- /dev/null +++ b/TextAnalysis/top20_frequency_ICES_B.csv @@ -0,0 +1,10 @@ +"ID","Region","File_Path","biomass|b|abundance","spawning biomass|sb|spawning stock biomass|ssb|spawning output|spawning stock output|sso|mature biomass|spawners|effective spawning output","unfished|virgin|initial equilibrium|unfished equilibrium","recruitment","recruits|recruit|age 0 fish|age 1 fish","catch|total mortality|harvest|total removals","catch per unit effort|cpue|catch rate|index of abundance|catch per effort|fishing success","landings|retained catch","spawner per recruit|spawning potential ratio|spr","maximum sustainable yield|msy","instantaneous total mortality rate|z","fishing mortality|f|instantaneous fishing mortality rate|harvest rate|exploitation rate|finite fishing mortality|apical f","fishing mortality at maximum sustainable yield|fmsy","mass|weight","length composition|length frequency|length observation|size frequency|size composition","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",18719,814,3,514,649,2190,153,1543,38,820,37,26921,428,257,59,54,593,57,1,21 +"2","ICES","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/ICES/ices2023_WKBCOD_report_2023.pdf",4945,277,0,176,221,453,13,402,0,136,14,7439,36,73,4,29,119,0,0,12 +"3","ICES","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/ICES/WKBALTCOD2_2019.pdf",6066,173,0,78,82,550,80,88,0,23,38,8095,15,97,54,14,42,18,11,1 +"4","ICES","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/ICES/WKBBALTPEL_2023_final_report.pdf",8102,298,2,120,169,529,16,126,59,409,45,10875,215,99,3,19,73,23,7,20 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b/TextAnalysis/top20_frequency_NOAA_B.csv @@ -1,83 +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 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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" +"ID","Region","File_Path","biomass|b|abundance","spawning biomass|sb|spawning stock biomass|ssb|spawning output|spawning stock output|sso|mature biomass|spawners|effective spawning output","unfished|virgin|initial equilibrium|unfished equilibrium","recruitment","recruits|recruit|age 0 fish|age 1 fish","catch|total mortality|harvest|total removals","catch per unit effort|cpue|catch rate|index of abundance|catch per effort|fishing success","landings|retained catch","spawner per recruit|spawning potential ratio|spr","maximum sustainable yield|msy","instantaneous total mortality rate|z","fishing mortality|f|instantaneous fishing mortality rate|harvest rate|exploitation rate|finite fishing mortality|apical f","fishing mortality at maximum sustainable yield|fmsy","mass|weight","length composition|length frequency|length observation|size frequency|size composition","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 +"3","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/frr294.pdf",1,1,1,1,1,1,1,1,0,1,1,1,0,1,1,1,1,1,1,0 "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 +"6","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Marine_Scalefish_Fishery_Assessment_Report_2020_-_FINAL_20200424.pdf",1,1,0,1,1,1,1,1,0,0,1,1,0,1,1,1,0,1,0,0 "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 @@ -14,26 +14,26 @@ 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b/TextAnalysis/top20_presence_Australia_B.csv @@ -1,10 +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" +"ID","Region","File_Path","biomass|b|abundance","spawning biomass|sb|spawning stock biomass|ssb|spawning output|spawning stock output|sso|mature biomass|spawners|effective spawning output","unfished|virgin|initial equilibrium|unfished equilibrium","recruitment","recruits|recruit|age 0 fish|age 1 fish","catch|total mortality|harvest|total removals","catch per unit effort|cpue|catch rate|index of abundance|catch per effort|fishing success","landings|retained catch","spawner per recruit|spawning potential ratio|spr","maximum sustainable yield|msy","instantaneous total mortality rate|z","fishing mortality|f|instantaneous fishing mortality rate|harvest rate|exploitation rate|finite fishing mortality|apical f","fishing mortality at maximum sustainable yield|fmsy","mass|weight","length composition|length frequency|length observation|size frequency|size composition","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 +"3","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/frr294.pdf",1,1,1,1,1,1,1,1,0,1,1,1,0,1,1,1,1,1,1,0 "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 +"6","Australia","C:/Users/bai.li/Documents/GitHub/fishdictionary/StockAssessment/Australia/Marine_Scalefish_Fishery_Assessment_Report_2020_-_FINAL_20200424.pdf",1,1,0,1,1,1,1,1,0,0,1,1,0,1,1,1,0,1,0,0 "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 @@ -13,4 +13,4 @@ "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 +"Sum",NA,NA,14,14,13,13,13,14,14,13,6,10,9,14,3,14,11,10,11,11,9,3 diff --git a/TextAnalysis/top20_presence_ICES.csv b/TextAnalysis/top20_presence_ICES.csv deleted file mode 100644 index 7b0bca3..0000000 --- a/TextAnalysis/top20_presence_ICES.csv +++ /dev/null @@ -1,10 +0,0 @@ -"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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-"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 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+"ID","Region","File_Path","biomass|b|abundance","spawning biomass|sb|spawning stock biomass|ssb|spawning output|spawning stock output|sso|mature biomass|spawners|effective spawning output","unfished|virgin|initial equilibrium|unfished equilibrium","recruitment","recruits|recruit|age 0 fish|age 1 fish","catch|total mortality|harvest|total removals","catch per unit effort|cpue|catch rate|index of abundance|catch per effort|fishing success","landings|retained catch","spawner per recruit|spawning potential ratio|spr","maximum sustainable yield|msy","instantaneous total mortality rate|z","fishing mortality|f|instantaneous fishing mortality rate|harvest rate|exploitation rate|finite fishing mortality|apical f","fishing mortality at maximum sustainable yield|fmsy","mass|weight","length composition|length frequency|length observation|size frequency|size composition","age composition|age frequency|age observation","projection|forecast|prediction","sex|gender","natural log of unfished 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