Add functionality to pull sample type #129
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Function that can be used if sample types have been used and multiple records are returned for the same trawl_id. This function would be up to the user to apply but a message has been added to the pull_catch function that prints if trawl_ids are not uniuqe.
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@kellijohnson-NOAA I wanted to check in to make sure you received an email for review. This pull request handles pulling all sample-type data that is particularly specific to Pacific hake. Let me know if you have questions or do not have time for review. |
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Sorry for the delay @chantelwetzel-noaa. I made some rough comments and would like to review it again after you respond. Two major things, I think that there should be more test written and that there should not be changes made to the deprecated function.
Removed the set.seed that was used throughout this function when these tests were created.
1. Remove partition samples that should not be used for index creation. 2. Add code to save the combined tows data 3. Add spaces for code style 4. Revise function documentation
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@kellijohnson-NOAA I think I have addressed all the items that you identified in your initial review. I also added code to the |
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Great, thank you so much @chantelwetzel-noaa for being so speedy. I will start this tonight but I probably won't have time to finish. But, tomorrow I have time. |
R/combine_tows.R
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| find <- grep("trawl_id", colnames(data), ignore.case = TRUE) | ||
| n_id <- table(data[, find]) | ||
| if (sum(n_id == 2) == 0) { |
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Would there ever be an instance where there are three or more? I think that a more robust test would be
if (all(n_id == 1)) {
R/pull_catch.R
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| @@ -262,17 +259,25 @@ pull_catch <- function(common_name = NULL, | |||
| catch$cpue_kg_km2 <- catch$cpue_kg_per_ha_der * 100 | |||
| colnames(catch)[which(colnames(catch) == "area_swept_ha_der")] <- "area_swept_ha" | |||
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| if(sum(c("Life Stage", "Size") %in% sample_types) == 2) { | |||
| n_id <- table(catch$trawl_id) | |||
| if(sum(n_id == 2) > 0){ | |||
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Same comment as above regarding a more robust test
if (any(n_id > 1)) {
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That is a great suggestion. Thank you!
These changes do the following: