In catrinanowakowski/ProcessIsodataOuts: What the Package Does (One Line, Title Case)

Started: 07-07-2021: Nowakowski

Updated: 08-09-2021: Nowakowski

Updated: 03-16-2022: Nowakowski

DO NOT CHANGE THE EXAMPLE_HOME.R FILE!!

PLEASE SAVE A NEW ONE WITH YOUR NAME OR PROJECT IN THE FILE NAME AND EDIT YOUR RUN SETTINGS FROM THERE

SAVE THIS TO THE HOME FILE - THIS IS WHERE ALL FILES THAT MAY BE CHANGED LIVE.

NEVER EDIT A FILE IN THE SOURCE FOLDER WITH OUT SAVING A COPY SEPERATLY FIRST

variables defined in this file are global and can be used by all functions

Current errors that run and code could be adjusted for

Note: Current case that does not work is if one sample has meth and the other two do not AND the standard also has Meth

still might need to add in an error for when isoreader goofs occasionally with the vendor data table when peak st and stop time are adjusted

REASONS WHY YOU MAY RUN AN ERROR

Is your AAstd name consistent with your file names?

Are your labstd names consistent with your file names?

Did you format the file name correctly? No extra "_", includes sample id, C or N, run with replicate number YYMMDD_HHMMSS_AA4_C_R1_xxxxxxxx OR YYMMDD_HHMMSS_Cal2003_C_R1_xxxxxxxx

Did you adjust the AAs in the standard run vector according to what your standards ran?

Did you delete all of your junk peaks?

Do you have any peaks in your sample that are not included in your AA standard runs? -- delete those

ASUMPTIONS

This is applied after you do your peak corrections in isodat

No need to remove extra columnsin the vendor table

dxf file name example format:

Standards:

YYMMDD_HHMMSS_AA4_C_R1_xxxxxxxx

YYMMDD_HHMMSS_AA4_C_R2_xxxxxxxx

Samples:

YYMMDD_HHMMSS_Cal2003_C_R1_xxxxxxxx

YYMMDD_HHMMSS_Cal2003_C_R2_xxxxxxxx

YYMMDD_HHMMSS_Cal2003_C_R3_xxxxxxxx

YYMMDD_HHMMSS_Cal2005_C_R1_xxxxxxxx

YYMMDD_HHMMSS_Cal2005_C_R2_xxxxxxxx

YYMMDD_HHMMSS_Cal2005_C_R3_xxxxxxxx

assumes the first five and last 3 peaks are always the one off runs and that there are no extra or "Junk" peaks

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(ProcessIsodataOuts)

###########################################################
# # # # #####
# ## EXAMPLE
#### rm(list = ls(all.names = TRUE)) ## USE THIS TO CELAR ENVIRONMENT IF NESSARY 
# ## Where are your dxf files saved?
# file_data <- c("C:/Thermo/Isodat NT/Global/User/Conflo IV Interface/Conflo IV Interface/Results/2021 Copepods/N_AA6_cyn6_Fish1_ty0710_cal979905")
# ## AA std id name for that run
# AAStd_name <-  "AA6"
# ## AA that were measured in your standard during the run  ## AA_list <- c("Ala", "Gly", "Thr", "Ser", "Val", "Leu", "Ile", "NLeu", "Pro", "Asp", "Met", "Glu", "Phe", "Lys", "Arg")
# # Note - if you did not measure a value in your standard, you need to deleate that peak from your isodate files also for each sample 
# AA_list <- c(  "Val", "Leu", "Ile", "NLeu", "Pro", "Asp", "Met", "Glu", "Phe", "Lys", "Arg")
# ## Nitrogen or carbon
# C_N <- "N"
# ## Name of the folder your files are in (or some way to identfy this spicific run when saving the std data in other folders)
# fl_nm <- "N_AA6_cyn6_Fish1_ty0710_cal979905"
# 
# ## the oder AA are plotted in (type is like source, trophic, essentia/non. Run is the order that the machine measures them in  )
# order_AAs <- "Type" # "Type" "Run"
# 
# ## the sample name of your lab standard (McMahon lab has been using cyano and a fish so that is why the name is cyano and not labstd for now)
# cyano <- "Cyn6"
# fish_muscle <- "Fish1"
# 

# 
file_data <- c("C:/Thermo/Isodat NT/Global/User/Conflo IV Interface/Conflo IV Interface/Results/2021 Copepods/N_AA7_cyn7_Fish2_ty969708_cal9608_TESTBUG")
AAStd_name <-  "AA7"
# AA_list <- c("Ala", "Gly", "Thr", "Ser", "Val", "Leu", "Ile", "NLeu", "Pro", "Asp", "Met", "Glu", "Phe", "Lys", "Arg")
AA_list <- c( "Val", "Leu", "Ile", "NLeu", "Pro", "Asp", "Met", "Glu", "Phe", "Lys", "Arg")
C_N <- "N"
fl_nm <- "test_run"
order_AAs <- "Type" # "type
cyano <- "cyn7"
fish_muscle <- "fish2"


# ## C_AA8_cyn8_f3_ty040616_cal040616
# file_data <- c("C:/Thermo/Isodat NT/Global/User/Conflo IV Interface/Conflo IV Interface/Results/2021 Copepods/C_AA8_cyn8_f3_ty040616_cal040616")
# AAStd_name <- "AA8"
# AA_list <- c("Ala", "Gly", "Thr", "Ser", "Val", "Leu", "Ile", "NLeu", "Pro", "Asp", "Met", "Glu", "Phe", "Lys", "Arg")
# C_N <- "C"
# fl_nm <- "C_AA8_cyn8_f3_ty040616_cal040616"
# order_AAs <- "Type" # "Type" "Run"
# cyano <- "cyn7"
# fish_muscle <- "fish2"



# # ## A separate place where you want your final sample data to be stored:
file_save <- "C:/Users/EcoGeoChemLab/Documents"
# 
# ## Where this file you are using now lives:
file_home <- "C:/Users/EcoGeoChemLab/isodat_processing"

## Carbon AA std files for your lab
file_save_AAstds_C <- "C:/Users/EcoGeoChemLab/Documents/AAStds_C"
## Carbon Labstd files for your lab
file_save_stds_C <- "C:/Users/EcoGeoChemLab/Documents/Stds_C"


## Nitrogen AA std files for your lab
file_save_AAstds_N <- "C:/Users/EcoGeoChemLab/Documents/AAStds_N"
## Nitrogen Labstd files for your lab
file_save_stds_N <- "C:/Users/EcoGeoChemLab/Documents/Stds_N"

##############################################################################
##############################################################################
## Code you shouldn't need to touch:

# file_sorc <- paste0(file_home, "/sorc") ## Where your source files are stored (These you should never have to touch, and should be the same if you are running normal data corrections or std test runs)

#######################
# source(paste0(file_sorc, "/process_CSIA_full_run.r"))     
outs <- process_CSIA_full_run()

all_fn_std_df <- outs$all_fn_std_df
all_fn_df <- outs$all_fn_df
rm(outs)

catrinanowakowski/ProcessIsodataOuts documentation built on Jan. 29, 2023, 5:09 p.m.