fix vignette links for external excel files

vignettes/MassWateR.Rmd

@@ -208,7 +208,7 @@ If you are submitting your data to Mass DEP, you must follow all of their instru
 
 ## Uploading data to WQX
 
-If desired, all rows from the WQX output file (created with `tabMWRwqx()`) can be copied and pasted into the [WQX upload template](https://massbays-tech.github.io/MassWateR/WQX_Phys-Chem_Template_for_MassWateR.xlsx) (also available on the [Resources](https://massbays-tech.github.io/MassWateR/RESOURCES.html) tab), which offers an enhanced spreadsheet layout with more interactive functionality (e.g., drop-down lists, prompts) and additional tabs with supporting information (e.g., instructions, field definitions). This template is especially useful if manual edits to the data are needed prior to WQX upload.
+If desired, all rows from the WQX output file (created with `tabMWRwqx()`) can be copied and pasted into the [WQX upload template](https://github.com/massbays-tech/MassWateR/raw/refs/heads/main/inst/extdata/WQX_Phys-Chem_Template_for_MassWateR.xlsx) (also available on the [Resources](https://massbays-tech.github.io/MassWateR/RESOURCES.html) tab), which offers an enhanced spreadsheet layout with more interactive functionality (e.g., drop-down lists, prompts) and additional tabs with supporting information (e.g., instructions, field definitions). This template is especially useful if manual edits to the data are needed prior to WQX upload.
 
 To upload data to WQX, you will need to create or sign into [your WQX account](https://www.epa.gov/waterdata/wqx-web-account-registration){target="_blank"}. From there, you can upload your Projects, Locations, and Results spreadsheets individually. Note that Projects and Locations need only be uploaded once for your organization, unless the data change. For each spreadsheet upload, use the appropriate MassWateR custom import configuration, check that your Organization ID is assigned, browse to your upload file, and select Import Data (image below). The next screen will notify you of upload status and prompt you to correct any errors or warnings that arise. More information on error resolution can be found in the [WQX User Guide](https://www.epa.gov/sites/default/files/2020-03/documents/wqx_web_user_guide_v3.0.pdf){target="_blank"}.
 

vignettes/outofstate.Rmd

@@ -9,7 +9,7 @@ vignette: >
 
 MassWateR can be used anywhere with a few caveats. MassWateR was developed specifically for organizations in Massachusetts to support the data submission process to Massachusetts Department of Environmental Protection (Mass DEP). However, the structure, logic, and approach to analyzing data are universal and could be used by any organization. Here is a list of the MassWateR elements that are specific to Massachusetts:
 
-1. __Parameter thresholds__ - [Standard thresholds](https://massbays-tech.github.io/MassWateR/ThresholdMapping.xlsx) have been included for some parameters so that a threshold line can be easily added to the analysis graphs. Some of these thresholds have been defined by Mass DEP or MassBays, while others are EPA standards. There are two ways to handle this if the thresholds are not relevant. You can simply turn the thresholds off in the graphing functions with the `thresh = "none"` argument, or you can manually add your own as described in the [modifying plots](https://massbays-tech.github.io/MassWateR/articles/modifying.html) vignette.
+1. __Parameter thresholds__ - [Standard thresholds](https://github.com/massbays-tech/MassWateR/raw/refs/heads/main/inst/extdata/ThresholdMapping.xlsx) have been included for some parameters so that a threshold line can be easily added to the analysis graphs. Some of these thresholds have been defined by Mass DEP or MassBays, while others are EPA standards. There are two ways to handle this if the thresholds are not relevant. You can simply turn the thresholds off in the graphing functions with the `thresh = "none"` argument, or you can manually add your own as described in the [modifying plots](https://massbays-tech.github.io/MassWateR/articles/modifying.html) vignette.
 1. __Mapping water bodies__ - In the mapping function `anlzMWRmap()`, there is an option to add a waterbody layer (`addwater = "high"/"medium"/"low"`). This waterbody layer only includes watersheds that have portions in Massachusetts. If you are outside of Massachusetts, you can still use the base maps available with the maptype argument or you can add your own waterbody layer following the instructions in the [modifying plots](https://massbays-tech.github.io/MassWateR/articles/modifying.html) vignette.
 1. __QC Report format__ - The QC Report Word document that is created with the `qcMWRreview()` function has been designed jointly with Mass DEP based on their requirements. Mass DEP has approved this format for data submissions from Massachusetts organizations. This document may not meet the requirements of other state organizations. However, the structure and logic of the document are theoretically universal. We believe that it should meet the QC needs of any state. Also, it can be easily customized since it is a Word document.
 1. __Time-zone__ - The WQX output file that is created with the `tabMWRwqx()` function is hard-coded to fill in the *WQX Activity Start Time Zone* field with `"EDT"`. If this is not the correct time zone for your organization, you can manually change the time zone in your WQX upload file prior to uploading to WQX.

vignettes/wqx.Rmd

@@ -72,7 +72,7 @@ If you are submitting your data to Mass DEP, you must follow all of their instru
 
 ## Uploading data to WQX
 
-If desired, all rows from the WQX output file (created with `tabMWRwqx()`) can be copied and pasted into the [WQX upload template](https://massbays-tech.github.io/MassWateR/WQX_Phys-Chem_Template_for_MassWateR.xlsx) (also available on the [Resources](https://massbays-tech.github.io/MassWateR/RESOURCES.html) tab), which offers an enhanced spreadsheet layout with more interactive functionality (e.g., drop-down lists, prompts) and additional tabs with supporting information (e.g., instructions, field definitions). This template is especially useful if manual edits to the data are needed prior to WQX upload.
+If desired, all rows from the WQX output file (created with `tabMWRwqx()`) can be copied and pasted into the [WQX upload template](https://github.com/massbays-tech/MassWateR/raw/refs/heads/main/inst/extdata/WQX_Phys-Chem_Template_for_MassWateR.xlsx) (also available on the [Resources](https://massbays-tech.github.io/MassWateR/RESOURCES.html) tab), which offers an enhanced spreadsheet layout with more interactive functionality (e.g., drop-down lists, prompts) and additional tabs with supporting information (e.g., instructions, field definitions). This template is especially useful if manual edits to the data are needed prior to WQX upload.
 
 To upload data to WQX, you will need to create or sign into [your WQX account](https://www.epa.gov/waterdata/wqx-web-account-registration){target="_blank"}. From there, you can upload your Projects, Locations, and Results spreadsheets individually. Note that Projects and Locations need only be uploaded once for your organization, unless the data change. For each spreadsheet upload, assign the appropriate MassWateR custom import configuration, check that your Organization ID is assigned, browse to your upload file, and select Import Data (image below). The next screen will notify you of upload status and prompt you to correct any errors or warnings that arise. More information on error resolution can be found in the [WQX User Guide](https://www.epa.gov/sites/default/files/2020-03/documents/wqx_web_user_guide_v3.0.pdf){target="_blank"}.