R/data download/carpenter_2017.r

In chase-lab/BioTIMEx: Aggregating long-term ecological communities data

## carpenter_2017

# Package ID: knb-lter-ntl.353.4 Cataloging System:https://pasta.edirepository.org.
# Data set title: Cascade Project at North Temperate Lakes LTER Core Data Phytoplankton 1984 - 2015.
# Data set creator:  Stephen Carpenter - University of Wisconsin
# Data set creator:  Jim Kitchell - University of Wisconsin
# Data set creator:  Jon Cole - Cary Institute of Ecosystem Studies
# Data set creator:  Mike Pace - University of Virginia
# Contact:  Stephen Carpenter -  University of Wisconsin  - steve.carpenter@wisc.edu
# Contact:  Mike Pace -  University of Virginia  - pacem@virginia.edu
# Contact:  NTL Information Manager -  University of Wisconsin  - ntl.infomgr@gmail.com
# Stylesheet v2.10 for metadata conversion into program: John H. Porter, Univ. Virginia, jporter@virginia.edu


infile1 <- 'data/raw data/carpenter_2017/cascade_phytoplankton_v0.1.csv_upload.csv'
if(!dir.exists('data/raw data/carpenter_2017/') || !file.exists(infile1))   {
   dir.create('data/raw data/carpenter_2017/', showWarnings = FALSE)
   inUrl1  <- "https://pasta.lternet.edu/package/data/eml/knb-lter-ntl/353/4/c36bcc062259fe68fb719996eb470ce6"
   download.file(inUrl1, infile1, method="auto")
}



dt1 <-read.csv(infile1,header=F
               ,skip=1
               ,sep=","
               ,quot='"'
               , col.names=c(
                  "lakename",
                  "lakeid",
                  "year4",
                  "daynum",
                  "sampledate",
                  "division",
                  "genus",
                  "species",
                  "description",
                  "concentration",
                  "gal_dimension",
                  "mean_individ_vol",
                  "mean_individ_biovol",
                  "total_vol",
                  "total_biovol"    ), check.names=TRUE)


# Fix any interval or ratio columns mistakenly read in as nominal and nominal columns read as numeric or dates read as strings

if (class(dt1$lakename)!="factor") dt1$lakename<- as.factor(dt1$lakename)
if (class(dt1$lakeid)!="factor") dt1$lakeid<- as.factor(dt1$lakeid)
if (class(dt1$year4)=="factor") dt1$year4 <-as.numeric(levels(dt1$year4))[as.integer(dt1$year4) ]
if (class(dt1$year4)=="character") dt1$year4 <-as.numeric(dt1$year4)
if (class(dt1$daynum)=="factor") dt1$daynum <-as.numeric(levels(dt1$daynum))[as.integer(dt1$daynum) ]
if (class(dt1$daynum)=="character") dt1$daynum <-as.numeric(dt1$daynum)
# attempting to convert dt1$sampledate dateTime string to R date structure (date or POSIXct)

dt1$sampledate[is.na(dt1$sampledate)] <- as.character(as.Date(dt1$daynum[is.na(dt1$sampledate)], origin = paste0(dt1$year4[is.na(dt1$sampledate)], '-01-01')))   # added
tmpDateFormat <- "%Y-%m-%d"
tmp1sampledate <- as.Date(dt1$sampledate, format = tmpDateFormat)
# Keep the new dates only if they all converted correctly
if(length(tmp1sampledate) == length(tmp1sampledate[!is.na(tmp1sampledate)])){dt1$sampledate <- tmp1sampledate } else {print("Date conversion failed for dt1$sampledate. Please inspect the data and do the date conversion yourself.")}
rm(tmpDateFormat, tmp1sampledate)
if (class(dt1$division)!="factor") dt1$division<- as.factor(dt1$division)
if (class(dt1$genus)!="factor") dt1$genus<- as.factor(dt1$genus)
if (class(dt1$species)!="factor") dt1$species<- as.factor(dt1$species)
if (class(dt1$description)!="factor") dt1$description<- as.factor(dt1$description)
if (class(dt1$concentration)=="factor") dt1$concentration <-as.numeric(levels(dt1$concentration))[as.integer(dt1$concentration) ]
if (class(dt1$concentration)=="character") dt1$concentration <-as.numeric(dt1$concentration)
if (class(dt1$gal_dimension)=="factor") dt1$gal_dimension <-as.numeric(levels(dt1$gal_dimension))[as.integer(dt1$gal_dimension) ]
if (class(dt1$gal_dimension)=="character") dt1$gal_dimension <-as.numeric(dt1$gal_dimension)
if (class(dt1$mean_individ_vol)=="factor") dt1$mean_individ_vol <-as.numeric(levels(dt1$mean_individ_vol))[as.integer(dt1$mean_individ_vol) ]
if (class(dt1$mean_individ_vol)=="character") dt1$mean_individ_vol <-as.numeric(dt1$mean_individ_vol)
if (class(dt1$mean_individ_biovol)=="factor") dt1$mean_individ_biovol <-as.numeric(levels(dt1$mean_individ_biovol))[as.integer(dt1$mean_individ_biovol) ]
if (class(dt1$mean_individ_biovol)=="character") dt1$mean_individ_biovol <-as.numeric(dt1$mean_individ_biovol)
if (class(dt1$total_vol)=="factor") dt1$total_vol <-as.numeric(levels(dt1$total_vol))[as.integer(dt1$total_vol) ]
if (class(dt1$total_vol)=="character") dt1$total_vol <-as.numeric(dt1$total_vol)
if (class(dt1$total_biovol)=="factor") dt1$total_biovol <-as.numeric(levels(dt1$total_biovol))[as.integer(dt1$total_biovol) ]
if (class(dt1$total_biovol)=="character") dt1$total_biovol <-as.numeric(dt1$total_biovol)

# Convert Missing Values to NA for non-dates

dt1$year4 <- ifelse((trimws(as.character(dt1$year4))==trimws("NA")),NA,dt1$year4)
dt1$daynum <- ifelse((trimws(as.character(dt1$daynum))==trimws("NA")),NA,dt1$daynum)
dt1$concentration <- ifelse((trimws(as.character(dt1$concentration))==trimws("NA")),NA,dt1$concentration)
dt1$gal_dimension <- ifelse((trimws(as.character(dt1$gal_dimension))==trimws("NA")),NA,dt1$gal_dimension)
dt1$mean_individ_vol <- ifelse((trimws(as.character(dt1$mean_individ_vol))==trimws("NA")),NA,dt1$mean_individ_vol)
dt1$mean_individ_biovol <- ifelse((trimws(as.character(dt1$mean_individ_biovol))==trimws("NA")),NA,dt1$mean_individ_biovol)
dt1$total_vol <- ifelse((trimws(as.character(dt1$total_vol))==trimws("NA")),NA,dt1$total_vol)
dt1$total_biovol <- ifelse((trimws(as.character(dt1$total_biovol))==trimws("NA")),NA,dt1$total_biovol)

ddata <- dt1
save(ddata, file='data/raw data/carpenter_2017/ddata')












if(FALSE) {

      # Here is the structure of the input data frame:
      str(dt1)
      attach(dt1)
      # The analyses below are basic descriptions of the variables. After testing, they should be replaced.

      summary(lakename)
      summary(lakeid)
      summary(year4)
      summary(daynum)
      summary(sampledate)
      summary(division)
      summary(genus)
      summary(species)
      summary(description)
      summary(concentration)
      summary(gal_dimension)
      summary(mean_individ_vol)
      summary(mean_individ_biovol)
      summary(total_vol)
      summary(total_biovol)
      detach(dt1)

}