formatData

Scripts to format various data.

How to create csv files

ssconvert is called to automatically convert xlsx files to csv. Some other files have already been saved as csv files:

Hasnain_S1.csv, Hasnain_S6.csv: Table S1 and S6 respectively from Hasnain, Sarah S., Brian J. Shuter, and Charles K. Minns. “Phylogeny Influences the Relationships Linking Key Ecological Thermal Metrics for North American Freshwater Fish Species.” Edited by Dylan Fraser. Canadian Journal of Fisheries and Aquatic Sciences 70, no. 7 (July 2013): 964–72. https://doi.org/10.1139/cjfas-2012-0217.

About txtFiles

For some files, data were retrieved from pdf files. In such case, it is very convenient to first turn the pdf into a txt files, then purge not relevant data and finally create a small piece of code to get data. regarding the first step pdftotext -layout.

Casselman2005_A1.txt: summary of findings from catch-and-release studies, appendix 1 of Casselman and Stephen (2005); available on line at https://www.ontario.ca/document/catch-and-release-fish-handling Casselman, Stephen J, Ontario, and Fish and Wildlife Branch. Catch-and-Release Angling: A Review with Guidelines for Proper Fish Handling Practices. Peterborough, Ont.: Fish & Wildlife Branch, 2005.

R

R packages required

magrittr
letiRmisc see https://github.com/inSileco/letiRmisc
taxize
rfishbase

Import data - examples

dfOntCur <- getOntCur(file = 'pathXX/csvFiles/Ontario-Main.csv')

Table S1

source('R/getHasnainS1.R')
df_hasnain <- getHasnainS1('csvFiles/Hasnain_S1.csv')
save(df_hasnain, file = 'df_hasnain.rda', compress = 'xz')
# saveRDS(df_hasnain, "df_hasnain.rds")

Table S6 includes Reproductive Guild

source('R/getHasnainS6.R')
df_hasnain_S6 <- getHasnainS6('csvFiles/Hasnain_S6.csv')
save(df_hasnain_S6, file = 'df_hasnain_S6.rda', compress = 'xz')
# saveRDS(df_hasnain_S6, "df_hasnain_S6.rds")

source('R/getCasselmanA1.R')
dfCasselmanA1 <- getCasselmanA1(file = "txtFiles/Casselman2005_A1.txt")
save(dfCasselmanA1, file = 'dfCasselmanA1.rda', compress = 'xz')

License

McCannLab/formatFishData

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