MapTaxObs

[ashtonmj]

Error when running MapTaxObs function when loading the county boundary shapefile from GIT.

First ran the function with the directories that already existed in my wd. After the error I deleted the GIS and Maps directories and re-ran the function pulling the GIS data from GIT, but got the same error.

library(MBSStools)

Set Working Directory

wd <- getwd()

Create Example Data if Needed

Create Directories

myDir.create <- file.path(wd,"Data") ifelse(dir.exists(myDir.create)==FALSE,dir.create(myDir.create),"Directory already exists") [1] "Directory already exists" myDir.create <- file.path(wd,"GIS") ifelse(dir.exists(myDir.create)==FALSE,dir.create(myDir.create),"Directory already exists") [1] TRUE myDir.create <- file.path(wd,"Maps") ifelse(dir.exists(myDir.create)==FALSE,dir.create(myDir.create),"Directory already exists") [1] TRUE

Create Data

Taxa Data

myFiles <- c("AllFish_95to16.xls", "TaxaMapsCrossWalk20170731.xlsx") file.copy(file.path(path.package("MBSStools"),"extdata",myFiles),file.path(wd,"Data",myFiles)) [1] FALSE FALSE

GIS

unzip(file.path(path.package("MBSStools"),"extdata","MD_GIS.zip"),exdir=file.path(wd,"GIS"))

Inputs

Obs <- "AllFish_95to16.xls" XWalk <- "TaxaMapsCrossWalk20170731.xlsx" wd <- getwd()

Create maps

MapTaxaObs(Obs, XWalk, wd) C:/Users/mashton/Documents OGR data source with driver: ESRI Shapefile Source: "C:\Users\mashton\Documents\GIS", layer: "MD_State_Boundary" with 2 features It has 9 fields Integer64 fields read as strings: OBJECTID OGR data source with driver: ESRI Shapefile Source: "C:\Users\mashton\Documents\GIS", layer: "MD_Coast_Hydrology" with 1117 features It has 9 fields Integer64 fields read as strings: OBJECTID OGR data source with driver: ESRI Shapefile Source: "C:\Users\mashton\Documents\GIS", layer: "MD_Boundary_County_Detailed" with 24 features It has 7 fields Integer64 fields read as strings: OBJECTID DISTRICT COUNTY_FIP COUNTYNUM Error in as.double(y) : cannot coerce type 'S4' to vector of type 'double'

[leppott]

As time (workload) permits I'll investigate.

[ashtonmj]

Thanks! Seems like that specific error is a hot topic on GH after recent updates to R and package dependencies. Trying some package updates. Currently using 3.4.0 and wondering if an incompatible (3.4.1) devtools and its dependencies are the issue.

https://github.com/rmcelreath/rethinking/issues/22

[leppott]

Ran fine in testing on my machine.

session_info() Session info ----------------------------------------------------------------------------------------- setting value
version R version 3.4.3 (2017-11-30) system i386, mingw32
ui RStudio (1.1.383)
language (EN)
collate English_United States.1252
tz America/New_York
date 2018-05-11

Ran example from ?MapTaxaObs

Reloading installed MBSStools

Reload library

library(myLibrary,character.only = TRUE)

change wd back to package

setwd(paste0("./",myLibrary))

~~~~~~~~~~

library(MBSStools) ?MapTaxaObs

Set Working Directory

wd <- getwd()

Create Example Data if Needed

Create Directories

myDir.create <- file.path(wd,"Data") ifelse(dir.exists(myDir.create)==FALSE,dir.create(myDir.create),"Directory already exists") [1] "Directory already exists" myDir.create <- file.path(wd,"GIS") ifelse(dir.exists(myDir.create)==FALSE,dir.create(myDir.create),"Directory already exists") [1] TRUE myDir.create <- file.path(wd,"Maps") ifelse(dir.exists(myDir.create)==FALSE,dir.create(myDir.create),"Directory already exists") [1] TRUE

Create Data

Taxa Data

myFiles <- c("AllFish_95to16.xls", "TaxaMapsCrossWalk20170731.xlsx") file.copy(file.path(path.package("MBSStools"),"extdata",myFiles),file.path(wd,"Data",myFiles)) [1] TRUE TRUE

GIS

unzip(file.path(path.package("MBSStools"),"extdata","MD_GIS.zip"),exdir=file.path(wd,"GIS"))

Inputs

Obs <- "AllFish_95to16.xls" XWalk <- "TaxaMapsCrossWalk20170731.xlsx" wd <- getwd()

Create maps

MapTaxaObs(Obs, XWalk, wd) C:/Users/Erik.Leppo/OneDrive - Tetra Tech, Inc/MyDocs_OneDrive/GitHub/MBSStools OGR data source with driver: ESRI Shapefile Source: "C:/Users/Erik.Leppo/OneDrive - Tetra Tech, Inc/MyDocs_OneDrive/GitHub/MBSStools/GIS", layer: "MD_State_Boundary" with 2 features It has 9 fields Integer64 fields read as strings: OBJECTID OGR data source with driver: ESRI Shapefile Source: "C:/Users/Erik.Leppo/OneDrive - Tetra Tech, Inc/MyDocs_OneDrive/GitHub/MBSStools/GIS", layer: "MD_Coast_Hydrology" with 1117 features It has 9 fields Integer64 fields read as strings: OBJECTID OGR data source with driver: ESRI Shapefile Source: "C:/Users/Erik.Leppo/OneDrive - Tetra Tech, Inc/MyDocs_OneDrive/GitHub/MBSStools/GIS", layer: "MD_Boundary_County_Detailed" with 24 features It has 7 fields Integer64 fields read as strings: OBJECTID DISTRICT COUNTY_FIP COUNTYNUM Saving map 1 of 77; alewife. Saving map 2 of 77; american eel. Saving map 3 of 77; american shad. SNIP Saving map 75 of 77; white sucker. Saving map 76 of 77; yellow bullhead. Saving map 77 of 77; yellow perch. There are 54 non-matching taxa names. The non-matches are saved in a table with the maps.

[leppott]

Another user having issues with MapTaxaObs function.

.. I think I've run into an error. ,,, It seems like it has something to do with formatting in one of the "MD_Boundary_County_Detailed" files. I tried running both my own data and the code from the vignette in the helpfile and have gotten the same error (see end of output below). Any information would be greatly appreciated!

MapTaxaObs(Obs, XWalk, wd) X:/JWatson/ForJAy OGR data source with driver: ESRI Shapefile Source: "X:/JWatson/ForJAy/GIS", layer: "MD_State_Boundary" with 2 features It has 9 fields Integer64 fields read as strings: OBJECTID OGR data source with driver: ESRI Shapefile Source: "X:/JWatson/ForJAy/GIS", layer: "MD_Coast_Hydrology" with 1117 features It has 9 fields Integer64 fields read as strings: OBJECTID OGR data source with driver: ESRI Shapefile Source: "X:/JWatson/ForJAy/GIS", layer: "MD_Boundary_County_Detailed" with 24 features It has 7 fields Integer64 fields read as strings: OBJECTID DISTRICT COUNTY_FIP COUNTYNUM Error in as.double(y) : cannot coerce type 'S4' to vector of type 'double'

[leppott]

Matt's fix was to upgrade to v3.4.0 and all dependent packages.

Should update DESCRIPTION to specify minimum version of R as 3.4.0.

[leppott]

Modified DESCRIPTION for minimum version of R and moved rgdal and dplyr packages from Suggests to Imports to ensure they are loaded on user's computer when MBSStools is called.

[leppott]

Function example fails.

Relevant code that still has a hard coded directory and not the input parameter.

[leppott]

Updated function example variables to match the function inputs.

[leppott]

Works with edits but get errors.

If reload package rgdal then it works fine.

[leppott]

Still getting error even when reload rgdal.

[ashtonmj]

Erik, I have had major issues with anything related to rgdal around the transition from 3.5 to 3.6. After I went to 3.6.3 R and higher seems to have taken care of whatever bug. Lots of Stackoverflow and other gripping about errors from the package not being able to load, reinstall, etc.

Matt Ashton

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On Thu, Jun 17, 2021 at 12:51 PM Erik Leppo @.***> wrote:

Still getting error even when reload rgdal.

[image: image] https://user-images.githubusercontent.com/24276278/122440592-b3812380-cf6a-11eb-9c5e-349cad4cb8bc.png

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[leppott]

Switching to sf package instead of rdgal for loading and mapping of the three shapefiles in this function.

The "state.shp" was the one causing the issues. With sf package no errors.